WO2020048607A1 - Srsf2 as rna epigenetic factor - Google Patents

Srsf2 as rna epigenetic factor Download PDF

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WO2020048607A1
WO2020048607A1 PCT/EP2018/074097 EP2018074097W WO2020048607A1 WO 2020048607 A1 WO2020048607 A1 WO 2020048607A1 EP 2018074097 W EP2018074097 W EP 2018074097W WO 2020048607 A1 WO2020048607 A1 WO 2020048607A1
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srsf2
polypeptide
rna
agent
mr5c
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PCT/EP2018/074097
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French (fr)
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François FUKS
Christelle SOARES DA COSTA
Eric J DE BONY
Bouchra HASSABI
Emilie CALONNE
Pascale PUTMANS
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Université Libre de Bruxelles
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Priority to PCT/EP2018/074097 priority Critical patent/WO2020048607A1/en
Publication of WO2020048607A1 publication Critical patent/WO2020048607A1/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6875—Nucleoproteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/02—Screening involving studying the effect of compounds C on the interaction between interacting molecules A and B (e.g. A = enzyme and B = substrate for A, or A = receptor and B = ligand for the receptor)

Definitions

  • the invention relates to biomarkers and targets for diseases and conditions in subjects, in particular for neoplastic diseases, and to related methods, uses, kits and therapeutic agents.
  • RNA modifications more than 100 kinds of which have been reported in different RNA species, are involved in diverse biological and physiological processes.
  • Post-transcriptional RNA modifications or“RNA epigenetics” are becoming increasingly recognised as the third pillar of epigenetics, in addition to histone modifications and DNA modifications.
  • Enzymes involved in methylation of adenosine in RNA have been shown to be elevated in tumours and to be associated with increased cancer risk, including breast cancers.
  • N6-Methyadenosine (m6A) the most abundant modification on higher eukaryote mRNAs, is recognized by YTHDF2 (YTH domain family 2), a specific m6A reader implicated in mRNA degradation.
  • YTHDF2 YTH domain family 2
  • HCC hepatocellular carcinoma
  • RNA epigenetic events are dynamic and reversible, providing attractive targets for the development of new anti-cancer therapies.
  • agents capable of modulating disease-associated RNA epigenetic factors such as RNA readers, could be employed as therapeutic agents in the presence of mutated or otherwise transformed RNA epigenetic factors or altered epitranscriptomic landscape.
  • MDS myelodysplastic syndrome
  • AML acute myeloid leukaemia
  • Somatic mutations in genes encoding components of the spliceosome have been identified in about 60% of patients with MDS.
  • the incidence of MDS approximates 3 to 4 cases per 100,000 population per year, with 30 cases per 100,000 population per year in patients more than 70 years old. It is estimated that approximately 10,000 to 15,000 new cases are diagnosed annually in the United States. Data analysis on MDS from 2001 through 2008 suggested that the observed 3-year survival rate was of 42% and the 5-year survival rate of 29%.
  • SRSF2 Serine and arginine rich splicing factor 2
  • CMML chronic myelomonocytic leukaemia
  • anti-tumour drugs which manipulate the altered splicing machinery, such as TG003 (( 1 Z)- 1 -(3-Ethyl-5-mcthoxy-2(3//)- benzothiazolylidene)-2-propanone), mainly act by inhibiting kinase-mediated phosphorylation of the target splicing factors.
  • kinase inhibitors tend to have pleiotropic actions which detracts from the drugs’ specificity and increases the risk of unwanted side effects.
  • SRSF2 serine and arginine rich splicing factor 2
  • mr5C 5-methylcytosine
  • the present inventors identified SRSF2 as an RNA epigenetic factor, a reader, capable of recognising the mr5C modification.
  • This realisation opens new avenues for exploiting the interaction of SRSF2 with mr5C on RNA inter alia for SRSF2 detection, mr5C- containing RNA detection, phenotypic characterisation of SRSF2 mutations, drug discovery, and diagnosis or treatment of diseases, such as neoplastic diseases.
  • screening of SRSF2 mutations for their ability to alter SRSF2’s mr5C reader ability and splicing factor function can reveal mutations which cause or contribute to diseases, such as neoplastic diseases, and can be employed to identify diseased subjects carrying such mutations.
  • SRSF2’s mr5C reader function and splicing events dependent thereon can provide novel therapeutic avenues in diseases, such as neoplastic diseases.
  • certain subjects may be heterozygous for mutated SRSF2 which binds with altered (such as increased) specificity or strength to RNA sequence elements in mRNAs with dysregulated splicing lnterfering with such binding of the mutated SRSF2 may restore normal SRSF2 function owing to SRSF2 encoded by the wild-type allele and/or owing to the activity of other SR family members with redundant functions.
  • oligonucleotide therapy with mr5C-enriched oligonucleotides designed to hybridise to SRSF2 targets could be used to direct SRSF2 binding to mRNAs with altered mr5C landscape, thereby also avoiding pathologic splicing events.
  • an aspect of the invention relates to an in vitro method for identifying a serine and arginine rich splicing factor 2 (SRSF2)-modulating agent, said method comprising:
  • RNA ribonucleic acid
  • mr5C 5-methylcytosines
  • test agent determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
  • test agent identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
  • a further aspect relates to an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
  • Another aspect relates to an in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
  • a further aspect relates to an in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
  • Another aspect relates to a method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
  • Fig. 1 schematically illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay used to identify novel mr5C-binding proteins.
  • Fig. 2 illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay, followed by mass spectrometry (MS) to identify novel mr5C-binding proteins.
  • Fig. 3 illustrates a control RNA affinity approach involving biotinylated-RNA pull-down assay for known mr6A-readers of YTH family proteins.
  • Fig. 4 illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay, followed by Western blotting (WB) to validate novel mr5C-binding proteins.
  • Fig. 5 illustrates an RNA affinity approach involving biotinylated-labelled-RNA pull-down assay, followed by WB to validate SRSF2 as a specific and direct mr5C-reader.
  • Fig. 6 schematically illustrates the operation of the NanoBRETTM platform for detecting protein- protein interactions (PPI).
  • the illustration depicts energy transfer from a NanoLuc®-Protein A fusion (energy donor) to a fluorescently labelled HaloTag®-Protein B fusion (energy acceptor) upon interaction of Protein A and Protein B.
  • Fig. 7 schematically illustrates the operation of the modified NanoBRETTM platform for detecting protein-RNA interactions.
  • Fig. 8 illustrates validation of SRSF2 as a specific and direct mr5C-reader using the modified NanoBRETTM platform for detecting protein-RNA interactions in cellulo.
  • Fig. 9 illustrates the frequency of non-synonymous single nucleotide variations (nsSNV) in SRSF2 in various types of cancer.
  • Fig. 10 illustrates the frequency of nsSNV in SRSF2 across all cancers by SRSF2 amino acid position.
  • “one or more” or“at least one”, such as one or more members or at least one member of a group of members, is clear per se, by means of further exemplification, the term encompasses inter alia a reference to any one of said members, or to any two or more of said members, such as, e.g., any >3, >4, >5, >6 or >7 etc. of said members, and up to all said members.
  • “one or more” or“at least one” may refer to 1, 2, 3, 4, 5, 6, 7 or more.
  • SRSF2 serine and arginine rich splicing factor 2
  • mr5C 5-methylcytosine
  • an aspect provides an in vitro method for identifying SRSF2-modulating agent, said method comprising:
  • RNA ribonucleic acid
  • mr5C 5-methylcytosines
  • test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule; identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
  • SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof may also be referred to throughout this specification as“SRSF2 component”, and the RNA molecule comprising one or more mr5C and capable of being bound by SRSF2 may also be referred to throughout this specification as “RNA component”.
  • SRSF2 component RNA molecule comprising one or more mr5C and capable of being bound by SRSF2
  • in vitro generally denotes outside, or external to, a body, e.g., an animal or human body.
  • the term also encompasses“ex vivo”.
  • SRSF2 arginine rich splicing factor 2
  • SRSF2 is also known as protein PR264, splicing component 35 kDa, splicing factor SC35, SC-35, and splicing factor arginine/serine-rich 2.
  • the terms denote SRSF2 nucleic acids, as well as SRSF2 peptides, polypeptides and proteins, as apparent from the context.
  • SRSF2 polypeptide as used herein is synonymous with “SRSF2 protein”.
  • human SRSF2 mRNA is annotated under NCBI Genbank (http://www.ncbi.nlm.nih.gov/) accession numbers NM 003016.4 (“transcript variant 1”), NM 001195427.1 (“transcript variant 2”), or XM 017024942.1 (“predicted transcript variant XI”) Nucleotides 252 (start codon) to 917 (stop codon) of NM 003016.4 and NM 001195427.1, and nucleotides 272 to 937 of XM 017024942.1 constitute the SRSF2 coding sequence.
  • nucleotides 252 to 917 of NM 003016.4 are reproduced below (SEQ ID NO: 6)
  • human SRSF2 protein sequence is annotated under NCBI Genbank accession numbers NP 003007.2, NP 001182356.1, and XP 016880431.1, and Uniprot (www.uniprot.org) accession number Q01130-1, and is further reproduced below (SEQ ID NO: 7):
  • amino acid sequence of said SRSF2 polypeptide is as set forth in GenBank accession no. NP 001182356.1.
  • human SRSF2 gene is annotated under NCBI Genbank Gene ID 6427.
  • sequences represented in sequence databases or in the present specification may be of precursors of markers, peptides, polypeptides, proteins, or nucleic acids and may include parts which are processed away from mature molecules.
  • the term“marker” is widespread in the art and commonly broadly denotes a biological molecule, more particularly an endogenous biological molecule, and/or a detectable portion thereof, whose qualitative and/or quantitative evaluation in a tested object (e.g., in or on a cell, cell population, tissue, organ, or organism, e.g., in a biological sample of a subject) is predictive or informative with respect to one or more aspects of the tested object’s phenotype and/or genotype.
  • the terms “marker” and“biomarker” may be used interchangeably throughout this specification.
  • markers as intended herein may be peptide-, polypeptide- and/or protein-based, or may be nucleic acid-based.
  • a marker may be comprised of peptide(s), polypeptide(s) and/or protein(s) encoded by a given gene, or of detectable portions thereof.
  • the term“nucleic acid” generally encompasses DNA, RNA and DNA/RNA hybrid molecules, in the context of markers the term may typically refer to heterogeneous nuclear RNA (hnRNA), pre- mRNA, messenger RNA (mRNA), or copy DNA (cDNA), or detectable portions thereof.
  • hnRNA heterogeneous nuclear RNA
  • mRNA messenger RNA
  • cDNA copy DNA
  • Such nucleic acid species are particularly useful as markers, since they contain qualitative and/or quantitative information about the expression of the gene.
  • a nucleic acid- based marker may encompass mRNA of a given gene, or cDNA made of the mRNA, or detectable portions thereof.
  • protein as used throughout this specification generally encompasses macromolecules comprising one or more polypeptide chains, i.e., polymeric chains of amino acid residues linked by peptide bonds.
  • the term may encompass naturally, recombinantly, semi-synthetically or synthetically produced proteins.
  • the term also encompasses proteins that carry one or more co- or post-expression-type modifications of the polypeptide chain(s), such as, without limitation, glycosylation, acetylation, phosphorylation, sulfonation, methylation, ubiquitination, signal peptide removal, N-terminal Met removal, conversion of pro-enzymes or pre-hormones into active forms, etc.
  • the term further also includes protein variants or mutants which carry amino acid sequence variations vis-a-vis a corresponding native proteins, such as, e.g., amino acid deletions, additions and/or substitutions.
  • the term contemplates both full-length proteins and protein parts or fragments, e.g., naturally- occurring protein parts that ensue from processing of such full-length proteins.
  • polypeptide as used throughout this specification generally encompasses polymeric chains of amino acid residues linked by peptide bonds. Hence, especially when a protein is only composed of a single polypeptide chain, the terms“protein” and“polypeptide” may be used interchangeably herein to denote such a protein. The term is not limited to any minimum length of the polypeptide chain. The term may encompass naturally, recombinantly, semi-synthetically or synthetically produced polypeptides.
  • polypeptides that carry one or more co- or post-expression-type modifications of the polypeptide chain, such as, without limitation, glycosylation, acetylation, phosphorylation, sulfonation, methylation, ubiquitination, signal peptide removal, N-terminal Met removal, conversion of pro-enzymes or pre-hormones into active forms, etc.
  • the term further also includes polypeptide variants or mutants which carry amino acid sequence variations vis-a-vis a corresponding native polypeptide, such as, e.g., amino acid deletions, additions and/or substitutions.
  • the term contemplates both full-length polypeptides and polypeptide parts or fragments, e.g., naturally- occurring polypeptide parts that ensue from processing of such full-length polypeptides.
  • peptide as used throughout this specification preferably refers to a polypeptide as used herein consisting essentially of 50 amino acids or less, e.g., 45 amino acids or less, preferably 40 amino acids or less, e.g., 35 amino acids or less, more preferably 30 amino acids or less, e.g., 25 or less, 20 or less, 15 or less, 10 or less or 5 or less amino acids.
  • protein, polypeptides or peptides can be produced recombinantly by a suitable host or host cell expression system and isolated therefrom (e.g., a suitable bacterial, yeast, fungal, plant or animal host or host cell expression system), or produced recombinantly by cell-free transcription and/or translation, or non-biological protein, polypeptide or peptide synthesis.
  • a suitable host or host cell expression system and isolated therefrom e.g., a suitable bacterial, yeast, fungal, plant or animal host or host cell expression system
  • cell-free transcription and/or translation e.g., cell-free transcription and/or translation, or non-biological protein, polypeptide or peptide synthesis.
  • nucleic acid typically refers to a polymer (preferably a linear polymer) of any length composed essentially of nucleoside units.
  • a nucleoside unit commonly includes a heterocyclic base and a sugar group.
  • Heterocyclic bases may include inter alia purine and pyrimidine bases such as adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) which are widespread in naturally- occurring nucleic acids, other naturally- occurring bases (e.g., xanthine, inosine, hypoxanthine) as well as chemically or biochemically modified (e.g., methylated), non-natural or derivatised bases.
  • A adenine
  • G guanine
  • C cytosine
  • T thymine
  • U uracil
  • modified nucleobases include without limitation 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine.
  • 5- methylcytosine substitutions have been shown to increase nucleic acid duplex stability and may be preferred base substitutions in for example antisense agents, even more particularly when combined with 2'-0-methoxyethyl sugar modifications.
  • Sugar groups may include inter alia pentose (pentofuranose) groups such as preferably ribose and/or 2-deoxyribose common in naturally- occurring nucleic acids, or arabinose, 2-deoxyarabinose, threose or hexose sugar groups, as well as modified or substituted sugar groups (such as without limitation 2'-0-alkylated, e.g., 2'-0- methylated or 2'-0-ethylated sugars such as ribose; 2'-0-alkyloxyalkylated, e.g., 2’-0- methoxyethylated sugars such as ribose; or 2'-0,4'-C-alkylene-linked, e.g., 2'-0,4'-C-methylene- linked or 2'-0,4'-C-ethylene-linked sugars such as ribose; 2’-fluoro-arabinose, etc.).
  • pentose
  • Nucleic acid molecules comprising at least one ribonucleoside unit may be typically referred to as ribonucleic acids or RNA.
  • Such ribonucleoside unit(s) comprise a 2'-OH moiety, wherein -H may be substituted as known in the art for ribonucleosides (e.g., by a methyl, ethyl, alkyl, or alkyloxyalkyl).
  • ribonucleic acids or RNA may be composed primarily of ribonucleoside units, for example, > 80%, > 85%, > 90%, > 95%, > 96%, > 97%, > 98%, > 99% or even 100% (by number) of nucleoside units constituting the nucleic acid molecule may be ribonucleoside units.
  • Nucleic acid molecules comprising at least one deoxyribonucleoside unit may be typically referred to as deoxyribonucleic acids or DNA.
  • deoxyribonucleoside unit(s) comprise 2'-H.
  • deoxyribonucleic acids or DNA may be composed primarily of deoxyribonucleoside units, for example, > 80%, > 85%, > 90%, > 95%, > 96%, > 97%, > 98%, > 99% or even 100% (by number) of nucleoside units constituting the nucleic acid molecule may be deoxyribonucleoside units.
  • Nucleoside units may be linked to one another by any one of numerous known inter-nucleoside linkages, including inter alia phosphodiester linkages common in naturally-occurring nucleic acids, and further modified phosphate- or phosphonate-based linkages such as phosphorothioate, alkyl phosphorothioate such as methyl phosphorothioate, phosphorodithioate, alkylphosphonate such as methylphosphonate, alkylphosphonothioate, phosphotriester such as alkylphosphotriester, phosphoramidate, phosphoropiperazidate, phosphoromorpholidate, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate; and further siloxane, carbonate, sulfamate, carboalkoxy, acetamidate, carbamate such as 3’-N-carbamate, morpholino, borano, thioether, 3’-thi
  • inter-nucleoside linkages may be phosphate-based linkages including modified phosphate-based linkages, such as more preferably phosphodiester, phosphorothioate or phosphorodithioate linkages or combinations thereof.
  • nucleic acid also encompasses any other nucleobase containing polymers such as nucleic acid mimetics, including, without limitation, peptide nucleic acids (PNA), peptide nucleic acids with phosphate groups (PHONA), locked nucleic acids (LNA), morpholino phosphorodiamidate-backbone nucleic acids (PMO), cyclohexene nucleic acids (CeNA), tricyclo- DNA (tcDNA), and nucleic acids having backbone sections with alkyl linkers or amino linkers (see, e.g., Kurreck 2003 (Eur J Biochem 270: 1628-1644)).“Alkyl” as used herein particularly encompasses lower hydrocarbon moieties, e
  • Nucleic acids as intended herein may include naturally occurring nucleosides, modified nucleosides or mixtures thereof.
  • a modified nucleoside may include a modified heterocyclic base, a modified sugar moiety, a modified inter-nucleoside linkage or a combination thereof.
  • nucleic acid further preferably encompasses DNA, RNA and DNA/RNA hybrid molecules, specifically including hnRNA, pre-mRNA, mRNA, cDNA, genomic DNA, amplification products, oligonucleotides, and synthetic (e.g., chemically synthesised) DNA, RNA or DNA/RNA hybrids.
  • RNA is inclusive of RNAi (inhibitory RNA), dsRNA (double stranded RNA), siRNA (small interfering RNA), mRNA (messenger RNA), mi RNA (micro-RNA), tRNA (transfer RNA, whether charged or discharged with a corresponding acylated amino acid), and cRNA (complementary RNA).
  • a nucleic acid can be naturally occurring, e.g., present in or isolated from nature, can be recombinant, i.e., produced by recombinant DNA technology, and/or can be, partly or entirely, chemically or biochemically synthesised.
  • nucleic acids can be produced recombinantly by a suitable host or host cell expression system and isolated therefrom (e.g., a suitable bacterial, yeast, fungal, plant or animal host or host cell expression system), or produced recombinantly by cell-free transcription, or non-biological nucleic acid synthesis.
  • a nucleic acid can be double-stranded, partly double stranded, or single-stranded. Where single- stranded, the nucleic acid can be the sense strand or the antisense strand ln addition, nucleic acid can be circular or linear.
  • any marker, peptide, polypeptide, protein, or nucleic acid corresponds to the marker, peptide, polypeptide, protein, or nucleic acid, commonly known under the respective designations in the art.
  • the terms encompass such markers peptides, polypeptides, proteins, or nucleic acids, of any organism where found, and particularly of animals, preferably warm-blooded animals, more preferably vertebrates, yet more preferably mammals, including humans and non human mammals, still more preferably of humans.
  • the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
  • the RNA molecule is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
  • the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant and the RNA molecule are of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
  • native sequences may differ between different species due to genetic divergence between such species.
  • native sequences may differ between or within different individuals of the same species due to normal genetic diversity (variation) within a given species.
  • native sequences may differ between or even within different individuals of the same species due to somatic mutations, or post-transcriptional or post-translational modifications.
  • markers, peptides, polypeptides, proteins, or nucleic acids are intended herein. Accordingly, all sequences of markers, peptides, polypeptides, proteins, or nucleic acids found in or derived from nature are considered“native”.
  • the terms encompass the markers, peptides, polypeptides, proteins, or nucleic acids when forming a part of a living organism, organ, tissue or cell, when forming a part of a biological sample, as well as when at least partly isolated from such sources.
  • the terms also encompass markers, peptides, polypeptides, proteins, or nucleic acids when produced by recombinant or synthetic means.
  • markers, peptides, polypeptides, proteins, or nucleic acids may be human, i.e., their primary sequence may be the same as a corresponding primary sequence of or present in a naturally occurring human markers, peptides, polypeptides, proteins, or nucleic acids.
  • the qualifier“human” in this connection relates to the primary sequence of the respective markers, peptides, polypeptides, proteins, or nucleic acids, rather than to their origin or source.
  • markers, peptides, polypeptides, proteins, or nucleic acids may be present in or isolated from samples of human subjects or may be obtained by other means (e.g., by recombinant expression, cell- free transcription or translation, or non-biological nucleic acid or peptide synthesis).
  • any marker, peptide, polypeptide, protein, or nucleic acid, or fragment thereof may generally also encompass modified forms of said marker, peptide, polypeptide, protein, or nucleic acid, or fragment thereof, such as bearing post expression modifications including, for example, phosphorylation, glycosylation, lipidation, methylation, cysteinylation, sulphonation, glutathionylation, acetylation, oxidation of methionine to methionine sulphoxide or methionine sulphone, and the like.
  • Fragments of any marker, peptide, polypeptide, protein, or nucleic acid, are also envisaged herein.
  • the reference herein to measuring (or measuring the quantity of) any one marker, peptide, polypeptide, protein, or nucleic acid may encompass measuring the marker, peptide, polypeptide, protein, or nucleic acid, and/or measuring one or more fragments thereof.
  • any marker, peptide, polypeptide, protein, or nucleic acid, and/or one or more fragments thereof may be measured collectively, such that the measured quantity corresponds to the sum amounts of the collectively measured species ln another example, any marker, peptide, polypeptide, protein, or nucleic acid, and/or one or more fragments thereof may be measured each individually.
  • fragment as used throughout this specification with reference to a peptide, polypeptide, or protein generally denotes a portion of the peptide, polypeptide, or protein, such as typically an N- and/or C-terminally truncated form of the peptide, polypeptide, or protein.
  • a fragment may comprise at least about 30%, e.g., at least about 50% or at least about 70%, preferably at least about 80%, e.g., at least about 85%, more preferably at least about 90%, and yet more preferably at least about 95% or even about 99% of the amino acid sequence length of said peptide, polypeptide, or protein.
  • a fragment may include a sequence of > 5 consecutive amino acids, or > 10 consecutive amino acids, or > 20 consecutive amino acids, or > 30 consecutive amino acids, e.g., >40 consecutive amino acids, such as for example > 50 consecutive amino acids, e.g., > 60, > 70, > 80, > 90, > 100, > 200, > 300, > 400, > 500 or > 600 consecutive amino acids of the corresponding full-length peptide, polypeptide, or protein.
  • a fragment of SRSF2 polypeptide may include a sequence of > 5 consecutive amino acids, or > 10 consecutive amino acids, or > 20 consecutive amino acids, or > 30 consecutive amino acids, e.g., >40 consecutive amino acids, such as for example > 50 consecutive amino acids, e.g., > 60, > 70, > 80, > 90, > 100, > 110, > 120, > 130, > 140, > 150, > 160, > 170, > 180, > 190, > 200, or > 210 consecutive amino acids of the corresponding full-length SRSF2 polypeptide.
  • fragment with reference to a nucleic acid (polynucleotide) generally denotes a 5’- and/or 3’-truncated form of a nucleic acid.
  • a fragment may comprise at least about 30%, e.g., at least about 50% or at least about 70%, preferably at least about 80%, e.g., at least about 85%, more preferably at least about 90%, and yet more preferably at least about 95% or even about 99% of the nucleic acid sequence length of said nucleic acid.
  • a fragment may include a sequence of > 5 consecutive nucleotides, or > 10 consecutive nucleotides, or > 20 consecutive nucleotides, or > 30 consecutive nucleotides, e.g., >40 consecutive nucleotides, such as for example > 50 consecutive nucleotides, e.g., > 60, > 70, > 80, > 90, > 100, > 200, > 300, > 400, > 500 or > 600 consecutive nucleotides of the corresponding full-length nucleic acid.
  • the terms encompass fragments arising by any mechanism, in vivo and/or in vitro, such as, without limitation, by alternative transcription or translation, exo- and/or endo-proteolysis, exo- and/or endo-nucleolysis, or degradation of the peptide, polypeptide, protein, or nucleic acid, such as, for example, by physical, chemical and/or enzymatic proteolysis or nucleolysis.
  • variant of a protein, polypeptide, peptide, or nucleic acid generally refers to proteins, polypeptides or peptides the amino acid sequence of which, or nucleic acids the nucleotide sequence of which, is substantially identical (i.e., largely but not wholly identical) to the sequence of the protein, polypeptide, peptide, or nucleic acid, e.g., at least about 80% identical or at least about 85% identical, e.g., preferably at least about 90% identical, e.g., at least 91% identical, 92% identical, more preferably at least about 93% identical, e.g., at least 94% identical, even more preferably at least about 95% identical, e.g., at least 96% identical, yet more preferably at least about 97% identical, e.g., at least 98% identical, and most preferably at least 99% identical to the sequence of the recited protein, polypeptide, peptide, or nucleic acid.
  • a variant may display such degrees of identity to a recited protein, polypeptide, peptide or nucleic acid when the whole sequence of the recited protein, polypeptide, peptide or nucleic acid is queried in the sequence alignment (i.e., overall sequence identity).
  • Sequence identity may be determined using suitable algorithms for performing sequence alignments and determination of sequence identity as know per se. Exemplary but non-limiting algorithms include those based on the Basic Local Alignment Search Tool (BLAST) originally described by Altschul et al.
  • BLAST Basic Local Alignment Search Tool
  • An example procedure to determine the percent identity between a particular amino acid sequence and the amino acid sequence of a query polypeptide will entail aligning the two amino acid sequences using the Blast 2 sequences (B12seq) algorithm, available as a web application or as a standalone executable programme (BLAST version 2.2.31+) at the NCBI web site (www.nchi.nlm.nih.gov), using suitable algorithm parameters.
  • the output will not present aligned sequences.
  • the number of matches will be determined by counting the number of positions where an identical amino acid residue is presented in both sequences.
  • the percent identity is determined by dividing the number of matches by the length of the query polypeptide, followed by multiplying the resulting value by 100.
  • the percent identity value may, but need not, be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 may be rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 may be rounded up to 78.2. It is further noted that the detailed view for each segment of alignment as outputted by B12seq already conveniently includes the percentage of identities.
  • a variant of a protein, polypeptide, peptide, or nucleic acid may be a homologue (e.g., orthologue or paralogue) of said protein, polypeptide, peptide, or nucleic acid.
  • homologue e.g., orthologue or paralogue
  • the term “homology” generally denotes structural similarity between two macromolecules from same or different taxons, wherein said similarity is due to shared ancestry.
  • a variant of a protein, polypeptide, or peptide may comprise one or more amino acid additions, deletions, or substitutions relative to (i.e., compared with) the corresponding protein or polypeptide.
  • a variant (substitution variant) of a protein, polypeptide, or peptide may comprise up to 70 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, 50, 60, or 70) conservative amino acid substitutions relative to (i.e., compared with) the corresponding protein or polypeptide; and/or a variant (substitution variant) of a protein, polypeptide, or peptide may comprise up to 20 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, or 19) non-conservative amino acid substitutions relative to (i.e., compared with) the corresponding protein or polypeptide.
  • a conservative amino acid substitution is a substitution of one amino acid for another with similar characteristics.
  • Conservative amino acid substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine.
  • the nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine.
  • the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine.
  • the positively charged (i.e., basic) amino acids include arginine, lysine and histidine.
  • the negatively charged (i.e., acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic, or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a non-conservative substitution is a substitution of one amino acid for another with dissimilar characteristics.
  • a variant (deletion variant) of a protein, polypeptide, or peptide may lack up to 20 amino acid segments (e.g., one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 segments) relative to (i.e., compared with) the corresponding protein or polypeptide.
  • the deletion segment(s) may each independently consist of one amino acid, two contiguous amino acids or three contiguous amino acids.
  • the deletion segments may be non-contiguous, or two or more or all of the deletion segments may be contiguous.
  • Reference to“fragment or variant” or“variant or fragment” of any marker, peptide, polypeptide, protein, or nucleic acid also encompasses fragments of variants of such marker, peptide, polypeptide, protein, or nucleic acid, and variants of fragments of such marker, peptide, polypeptide, protein, or nucleic acid.
  • a variant of a nucleic acid may comprise one or more nucleotide additions, deletions, or substitutions relative to (i.e., compared with) the corresponding nucleic acid.
  • fragments and/or variants of proteins, polypeptides or peptides this in particular denotes such fragments and/or variants which are biologically active.
  • biologically active is interchangeable with terms such as “functionally active” or“functional”, denoting that the fragment and/or variant at least partly retains the biological activity or intended functionality of the respective or corresponding protein, polypeptide, or peptide.
  • Reference to the“activity” of a protein, polypeptide, or peptide may generally encompass any one or more aspects of the biological activity of the protein, polypeptide, or peptide, such as without limitation any one or more aspects of its biochemical activity, enzymatic activity, signalling activity, interaction activity, ligand activity, and/or structural activity, e.g., within a cell, tissue, organ or an organism.
  • a functionally active fragment or variant may retain at least about 20%, e.g., at least about 25%, or at least 30%, or at least about 40%, or at least about 50%, e.g., at least 60%, more preferably at least about 70%, e.g., at least 80%, yet more preferably at least about 85%, still more preferably at least about 90%, and most preferably at least about 95% or even about 100% of the intended biological activity or functionality compared with the corresponding protein, polypeptide, or peptide ln certain embodiments, a functionally active fragment or variant may even display higher biological activity or functionality compared with the corresponding protein, polypeptide, or peptide, for example may display at least about 100%, or at least about 150%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500% of the intended biological activity or functionality compared with the corresponding protein, polypeptide, or peptide.
  • a functionally active fragment or variant of the protein, polypeptide, or peptide may produce a signal which is at least about 20%, or at least about 25%, or at least 30%, or at least about 40%, or at least about 50%, or at least 60%, more preferably at least about 70%, or at least 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 100%, or at least about 150%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500% of the signal produced by the corresponding protein, polypeptide, or peptide.
  • the activity of a given protein, polypeptide, or peptide may comprise binding of said protein, polypeptide, or peptide to a ligand and the strength of binding or affinity may be represented by the equilibrium constant for the dissociation (K D , moles per litre) of said protein, polypeptide, or peptide with said ligand.
  • the K D for the binding of the biologically active fragment or variant of said protein, polypeptide, or peptide with said ligand determined under substantially identical conditions may be no more than 3 orders of magnitude greater, preferably no more than 2 orders of magnitude greater, and more preferably no more than 1 order of magnitude greater than the K D for the binding of said protein, polypeptide, or peptide to said ligand ln other words, the strength of the binding of the biologically active fragment or variant of said protein, polypeptide, or peptide with said ligand as represented by K D may be at least 1/1000* , e.g., at least 1/750*, at least 1/500*, at least 1/250*, preferably at least 1/100*, e.g., at least 1/75*, at least 1/50*, at least 1/25*, more preferably at least 1/10*, e.g., 1/5*, l/3 rd or 1/2 of the strength of the binding of said protein, polypeptide, or peptide with said
  • a biologically active fragment or variant of a SRSF2 polypeptide or a mutated SRSF2 polypeptide as disclosed herein shall at least partly retain the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide. For example, it may retain one or more aspects of the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide.
  • reference to the activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide or functionally active fragment or variant thereof may particularly denote its ability to bind to a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C).
  • the mr5C-binding activity of SRSF2 or mutated SRSF2 or functionally active fragment or variant thereof can be measured essentially as described in the Examples.
  • reference to the activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide or functionally active fragment or variant thereof may particularly denote its ability to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C.
  • splicing activity can be assessed by existing methodologies of analysing RNA structure, such as RT-PCR analysis or RNA-sequencing.
  • mutated or“mutant” refers to a marker, peptide, polypeptide, protein, or nucleic acid comprising one or more mutations, i.e., comprising one or more amino acid sequence changes or nucleic acid sequence changes compared to respectively the amino acid sequence or nucleic acid sequence of the marker, peptide, polypeptide, protein, or nucleic acid that has not been so-mutated, such as, particularly, compared to the amino acid sequence or nucleic acid sequence of the wild- type marker, peptide, polypeptide, protein, or nucleic acid.
  • the term“wild-type” as applied to a marker, peptide, polypeptide, protein, or nucleic acid refers to a marker, peptide, polypeptide, protein, or nucleic acid that occurs in, or is produced by, a biological organism as that biological organism exists in nature ln certain embodiments, the term“wild-type” may refer to any form of a marker, peptide, polypeptide, protein, or nucleic acid present in or encoded by the germline (constitutional) DNA of a normal, healthy or typical specimen of a species, such as a healthy human or non-human mammal ln certain embodiments, the terms“mutant” or“mutated” may refer to any form of a marker, peptide, polypeptide, protein, or nucleic acid present in or encoded by the germline DNA or somatic DNA of an abnormal, diseased or non-typical specimen of a species, such as a diseased human or non-human mammal. Accordingly, the terms encompass germline mutations
  • suitable mutations may include deletions, insertions, and/or substitutions of one or more amino acids in a peptide, polypeptide, or protein, or may include deletions, insertions, and/or substitutions of one or more nucleotides in a nucleic acid.
  • the term“deletion” refers to a mutation wherein one or more amino acids or nucleotides, typically consecutive amino acids or nucleotides, are removed, i.e., deleted, from the peptide, polypeptide, or protein or from the nucleic acid.
  • insertion refers to a mutation wherein one or more amino acids or nucleotides, typically consecutive amino acids or nucleotides, are added, i.e., inserted, into the peptide, polypeptide, or protein, or into the nucleic acid.
  • substitution refers to a mutation wherein one or more amino acids of a peptide, polypeptide or protein, or one or more nucleotides of a nucleic acid, are each independently replaced, i.e., substituted, by another amino acid or nucleotide, respectively.
  • mutated or“mutant” as intended herein may encompass silent mutations, and may preferably encompass loss-of-function or gain- of- function mutations.
  • a mutation may introduce a premature in-frame stop codon into a sequence encoding a peptide, polypeptide, or protein, resulting in production of a C-terminally truncated form of said peptide, polypeptide, or protein or resulting in abolished production of said peptide, polypeptide, or protein.
  • a suitable insertion, deletion or substitution of one or more nucleotides in an open reading frame may introduce a premature in-frame stop codon.
  • a mutation may introduce a frame shift (e.g., +1 or +2 frame shift) in a sequence encoding a peptide, polypeptide, or protein.
  • a frame shift e.g., +1 or +2 frame shift
  • such frame shift may lead to a previously out-of-frame stop codon downstream of the mutation becoming an in- frame stop codon.
  • frame shift may lead to production of a form of the peptide, polypeptide, or protein having an alternative C-terminal portion and/or a C-terminally truncated form of said peptide, polypeptide, or protein, or may result in abolished production of said peptide, polypeptide, or protein.
  • a suitable insertion, deletion or substitution of one or more (not multiple of 3) nucleotides in an open reading frame may lead to a frame shift.
  • a mutation may delete at least a portion of a sequence encoding a peptide, polypeptide, or protein. Such deletion may lead to production of an N-terminally truncated form, a C-terminally truncated form and/or an internally deleted form of said peptide, polypeptide, or protein ln certain other embodiments, a mutation may be a substitution of one or more nucleotides in a sequence encoding a peptide, polypeptide, or protein resulting in substitution of one or more amino acids of said peptide, polypeptide, or protein.
  • Such mutation may typically preserve the production of the peptide, polypeptide, or protein and may affect some or all biological function(s) of the peptide, polypeptide, or protein ln certain other embodiments, a mutation may be a conservative or non-conservative substitution of one amino acid of a peptide, polypeptide, or protein for one another amino acid ln certain other embodiments, a mutation may be a substitution of one nucleotide in a sequence encoding a peptide, polypeptide, or protein resulting in a conservative or non-conservative substitution of one amino acid of said peptide, polypeptide, or protein for one another amino acid.
  • Various combinations of such exemplary types of mutations as mentioned above are foreseen herein.
  • one or more mutations comprised by a mutated SRSF2 polypeptide may alter, such as increase or decrease, the ability of the mutated SRSF2 polypeptide to bind to 5- methylcytosine(s) (mr5C) on an RNA molecule, compared with wild-type SRSF2.
  • one or more mutations comprised by a mutated SRSF2 polypeptide may alter, such as increase or decrease, the ability of the mutated SRSF2 polypeptide to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C, compared with wild-type SRSF2.
  • the one or more mutations in a mutated SRSF2 polypeptide may be germline mutations.
  • the one or more mutations in a mutated SRSF2 polypeptide may be somatic mutations.
  • the one or more mutations in a mutated SRSF2 polypeptide may be somatic mutations occurring in a neoplastic tissue.
  • the one or more mutations in a mutated SRSF2 polypeptide may be causative of or may contribute to a neoplastic disease.
  • Fig. 9 shows the frequency of non- synonymous single nucleotide variations (nsSNV), i.e., mutations resulting in altered amino acid sequence, in SRSF2 in various types of cancer.
  • Fig. 10 shows the frequency of nsSNV in SRSF2 across all cancers by SRSF2 amino acid position.
  • SRSF2 somatic mutations have been previously reported in neoplastic diseases (for each entry: position in SRSF2 nucleic acid sequence NM 003016.4 or NM 001195427.1, reference nucleotide, mutated nucleotide, position in SRSF2 amino acid sequence, reference amino acid, mutated amino acid, cancer type): 614, G, T, 205, R, L, Urinary bladder cancer; 402, T, C, 134, S, S, Thyroid cancer; 503, G, A, 168, R, K, Lung cancer; 560, C, A, 187, S, Y, Rectum cancer; 619, A, T, 207, K, X, Prostate cancer; 284, C, T, 95, P, L, Hematologic cancer; 618, G, T, 206, S, S, Prostate cancer; 284, C, G, 95, P, R, Hematologic cancer; 284, C, T, 95, P, L, Hematologic cancer; 284,
  • the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide. These positions have been reported as positions for post- translational modifications of the concerned amino acid, such as acetylation, phosphorylation, etc. A mutation, such as a conservative or non-conservative substitution of one amino acid for one another amino acid, at such position(s) can alter, such as increase or decrease, post-translational modification at the respective position(s).
  • the mutated SRSF2 polypeptide is mutated at amino acid position 95 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of amino acid 95 for one another amino acid, more preferably by a P95H substitution, as reported by Zhang et al. ⁇ supra).
  • the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of one amino acid for one another amino acid. Somatic single amino acid substitutions at these positions have been reported to occur in various types of cancers (see above).
  • the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of one amino acid for one another amino acid.
  • Amino acid sequence alignments with other known methyl-group binding protein have predicted these amino acids as implicated or contributing to the direct binding of SRSF2 to mr5C.
  • the present specification also describes a SRSF2 polypeptide mutated at one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide.
  • any one or more of the following characteristics may apply to the RNA molecule comprising one or more 5-methylcytosines (m5C) and configured for being bound by the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof:
  • m5C 5-methylcytosines
  • ribonucleosides each independently selected from A, G, C (at least one of which is 5-methylated), and U;
  • phosphodiester-linked ribonucleosides each independently selected from A, G, C (at least one of which is 5-methylated), and U;
  • m5C contains exactly one m5C; at least 5-nt long, for example, > 6-nt, > 7-nt, > 8-nt, > 9-nt, > lO-nt, > 1 l-nt, > l2-nt, > 13- nt, > l4-nt, > l5-nt, > l6-nt, > l7-nt, > l8-nt, > l9-nt, or > 20-nt long;
  • At most 50-nt long for example, ⁇ 45-nt, ⁇ 40-nt, ⁇ 35-nt, ⁇ 30-nt, or ⁇ 25-nt long;
  • 5-50-nt long, for example, 5-45-nt, 5-40-nt, 5-35-nt, 5-30-nt, 5-25-nt, l0-50-nt, lO-45-nt, l0-40-nt, lO-35-nt, l0-30-nt, lO-25-nt, 15-50-nt, 15-45-nt, 15-40-nt, 15-35-nt, 15-30-nt, or
  • sequence 5’-SSNG-3’ comprises the sequence 5’-SSNG-3’, wherein S is G or C, N is A, C, G or U, particularly providing that said 5’-SSNG-3’ sequence comprises at least one C, more particularly at least one C at the first two positions;
  • GC content 30-70% for example 40-70%, 50-70%, 55-70%, or 55-65%;
  • - displays GC content about 40%, about 45%, about 50%, about 55%, about 60%, or about
  • animal origin is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin;
  • a label such as a 5’-label and/or a 3’-label
  • a label such as a 5’-label and/or a 3’-label, said label being configured for detection using affinity separation, immunoaffinity separation, fluorescence resonance energy transfer, or bioluminescence resonance energy transfer;
  • a label such as a 5’-label and/or a 3’-label, wherein said label is biotin.
  • label refers to any atom, molecule, moiety or biomolecule that may be used to provide a detectable and preferably quantifiable read-out or property, and that may be attached to or made part of an entity of interest. Labels may be suitably detectable by for example mass spectrometric, spectroscopic, optical, colorimetric, magnetic, photochemical, biochemical, immunochemical or chemical means.
  • Labels include without limitation dyes; radiolabels such as P, P, S, I, I; electron-dense reagents; enzymes (e.g., horse-radish peroxidase or alkaline phosphatase as commonly used in immunoassays); binding moieties such as biotin-streptavidin; haptens such as digoxigenin; luminogenic, phosphorescent or fluorogenic moieties; mass tags; fluorescent dyes alone or in combination with moieties that may suppress or shift emission spectra by fluorescence resonance energy transfer (FRET).
  • FRET fluorescence resonance energy transfer
  • a label or tag may be utilised that permits detection with another agent.
  • tags may be, for example, biotin, streptavidin, his-tag, myc tag, maltose, maltose binding protein or any other kind of tag known in the art that has a binding partner.
  • associations which may be utilised include, for example, biotin: streptavidin, his-tag:metal ion (e.g., Ni 2+ ), maltose:maltose binding protein, etc.
  • detection agents include, but are not limited to, luminescent labels; colorimetric labels, such as dyes; fluorescent labels; or chemical labels, such as electroactive agents (e.g., ferrocyanide); enzymes; radioactive labels; or radiofrequency labels.
  • the detection agent may be a particle.
  • Such particles include, but are not limited to, colloidal gold particles; colloidal sulphur particles; colloidal selenium particles; colloidal barium sulfate particles; colloidal iron sulfate particles; metal iodate particles; silver halide particles; silica particles; colloidal metal (hydrous) oxide particles; colloidal metal sulfide particles; colloidal lead selenide particles; colloidal cadmium selenide particles; colloidal metal phosphate particles; colloidal metal ferrite particles; any of the above-mentioned colloidal particles coated with organic or inorganic layers; protein or peptide molecules; liposomes; or organic polymer latex particles, such as polystyrene latex beads.
  • Preferable particles may be colloidal gold particles.
  • methylation refers to the presence of a methyl moiety on a nucleotide (base), where the nucleotide (base) typically does not comprise a methyl moiety.
  • methylated ribonucleic acid molecule refers to a ribonucleic acid (RNA) molecule that contains one or more ribonucleotides that are methylated.
  • RNA molecule comprising at least one methylated ribonucleotide can be considered methylated.
  • An RNA molecule that does not comprise any methylated ribonucleotides can be considered unmethylated.
  • cytosine does not contain a methyl moiety on its pyrimidine ring.
  • 5-methylcytosine contains a methyl moiety at position 5 of the pyrimidine ring.
  • 5-methylcytosine may be denoted as “m5C”.
  • the abbreviation“mr5C” may be more commonly used to indicate 5-methylation of cytosine in RNA.
  • the structure of 5-methylcytosine is shown in Formula I below:
  • 5-methylcytidine a ribonucleoside unit containing 5-methylcytosine is shown in Formula II below:
  • the present specification may interchangeably refer to binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, or to a RNA molecule comprising one or more mr5C.
  • RNA molecules comprising one or more mr5C and configured to be bound by the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof may display variable or dissimilar nucleotide sequences.
  • the presence of the one or more mr5C may be the only structural commonality between such RNA molecules, their nucleotide sequences sharing no relevant sequence elements or significant identity.
  • such RNA molecules may comprise a consensus sequence, more particularly a consensus sequence encompassing the one or more mr5C.
  • consensus sequence may be 5’- SSNG-3’, wherein S is G or C, N is A, C, G or U, particularly providing that said 5’-SSNG-3’ sequence comprises at least one C; or may be 5’-SCNG-3’ (e.g., 5’-Sm5CNG-3’), wherein S is G or C, N is A, C, G or U; or may be 5’-Cm5CGG-3’.
  • the 5’-SSNG-3’ sequence has been reported as a preferred SRSF2 RNA-binding consensus sequence.
  • This sequences encompasses the alternative sequences 5’-CCNG, 5’-GCNG, 5’-CGNG and 5’-GGNG.
  • the 5’-CCNG, 5’-GCNG and 5’-CGNG sequences which comprise at least one C at the first two positions, are relevant in the context of SRSF2 m5C-mediated binding to RNA.
  • the inventors postulate that SRSF2 may bind with different degrees of specificity to these different sequences and/or the binding of SRSF2 may lead to different outcomes based on the particular sequence to which SRSF2 binds.
  • binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule particularly denotes a direct molecular interaction or molecular contact between the polypeptide and the RNA molecule, forming a molecular complex in which said components are physically associated or bound.
  • Said binding may particularly refer to non-covalent binding, i.e., binding mediated by non-covalent forces, such as for example, hydrogen bridges, dipolar interactions, van der Waals interactions, and the like.
  • Determination of the binding of a polypeptide and RNA molecule, and of the corresponding K A (or the dissociation constant, K D , the inverse of K A ) can be carried out by methods known in the art, such as for example, separation-based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis (e.g., electrophoretic mobility shift assays, EMSA), and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-Vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry.
  • separation-based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis (e.g., electrophoretic mobility shift assays, EMSA), and HPLC
  • mixture based techniques such as fluorescence intensity and anisotropy, UV-Vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry
  • the binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule particularly denotes specific binding, i.e., where the polypeptide binds to the RNA molecule comprising one or more mr5C substantially to the exclusion of other molecules which are random or unrelated.
  • SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule may bind to the RNA molecule comprising one or more mr5C with an affinity at least about 10-fold greater, such as at least 100-fold, 1000-fold, lxl0 4 -fold, lxl0 5 -fold, or lxlO 6 - fold greater than to an otherwise identical RNA molecule not comprising the one or more mr5C.
  • the term“agent” broadly refers to any chemical (e.g., inorganic or organic), biochemical or biological substance, molecule or macromolecule (e.g., biological macromolecule), a combination or mixture thereof, a sample of undetermined composition, or an extract made from biological materials such as bacteria, plants, fungi, or animal cells or tissues.
  • agents include nucleic acids, oligonucleotides, ribozymes, peptides, polypeptides, proteins, peptidomimetics, antibodies, antibody fragments, antibody-like protein scaffolds, aptamers, photoaptamers, spiegelmers, chemical substances, preferably organic molecules, more preferably small organic molecules, lipids, carbohydrates, polysaccharides, etc., and any combinations thereof.
  • the term“agent” may denote a“therapeutic agent” or“drug”, useful for or used in the treatment, cure, prevention, or diagnosis of a disease.
  • the agent such as the test agent or SRSF2-modulating agent may be selected from the group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, such as siRNA or shRNA, a soluble receptor, and combinations thereof.
  • the term“antibody” is used in its broadest sense and generally refers to any immunologic binding agent.
  • the term specifically encompasses intact monoclonal antibodies, polyclonal antibodies, multivalent (e.g., 2-, 3- or more-valent) and/or multi-specific antibodies (e.g., bi- or more-specific antibodies) formed from at least two intact antibodies, and antibody fragments insofar they exhibit the desired biological activity (particularly, ability to specifically bind an antigen of interest, i.e., antigen-binding fragments), as well as multivalent and/or multi specific composites of such fragments.
  • antibody is not only inclusive of antibodies generated by methods comprising immunisation, but also includes any polypeptide, e.g., a recombinantly expressed polypeptide, which is made to encompass at least one complementarity determining region (CDR) capable of specifically binding to an epitope on an antigen of interest. Hence, the term applies to such molecules regardless whether they are produced in vitro or in vivo.
  • CDR complementarity determining region
  • An antibody may be any of lgA, lgD, lgE, lgG and lgM classes, and preferably lgG class antibody.
  • An antibody may be a polyclonal antibody, e.g., an antiserum or immunoglobulins purified there from (e.g., affinity-purified).
  • An antibody may be a monoclonal antibody or a mixture of monoclonal antibodies.
  • Monoclonal antibodies can target a particular antigen or a particular epitope within an antigen with greater selectivity and reproducibility.
  • monoclonal antibodies may be made by the hybridoma method first described by Kohler et al.
  • Monoclonal antibodies may also be isolated from phage antibody libraries using techniques as described by Clackson et al. 1991 (Nature 352: 624-628) and Marks et al. 1991 (J Mol Biol 222: 581-597), for example.
  • Antibody binding agents may be antibody fragments.“Antibody fragments” comprise a portion of an intact antibody, comprising the antigen-binding or variable region thereof.
  • antibody fragments include Fab, Fab’, F(ab’)2, Fv and scFv fragments, single domain (sd) Fv, such as VH domains, VL domains and VHH domains; diabodies; linear antibodies; single-chain antibody molecules, in particular heavy-chain antibodies; and multivalent and/or multispecific antibodies formed from antibody fragment(s), e.g., dibodies, tribodies, and multibodies.
  • the above designations Fab, Fab’, F(ab’)2, Fv, scFv etc. are intended to have their art-established meaning.
  • antibody includes antibodies originating from or comprising one or more portions derived from any animal species, preferably vertebrate species, including, e.g., birds and mammals.
  • the antibodies may be chicken, turkey, goose, duck, guinea fowl, quail or pheasant.
  • the antibodies may be human, murine (e.g., mouse, rat, etc.), donkey, rabbit, goat, sheep, guinea pig, camel (e.g., Camelus bactrianus and Camelus dromaderius), llama (e.g., Lama paccos, Lama glama or Lama vicugna) or horse.
  • an antibody can include one or more amino acid deletions, additions and/or substitutions (e.g., conservative substitutions), insofar such alterations preserve its binding of the respective antigen.
  • An antibody may also include one or more native or artificial modifications of its constituent amino acid residues (e.g., glycosylation, etc.).
  • the agent may be a Nanobody®.
  • Nanobody® and “Nanobodies®” are trademarks of Ablynx NV (Belgium).
  • the term“Nanobody” is well-known in the art and as used herein in its broadest sense encompasses an immunological binding agent obtained (1) by isolating the V H H domain of a heavy-chain antibody, preferably a heavy-chain antibody derived from camelids; (2) by expression of a nucleotide sequence encoding a V H H domain; (3) by“humanization” of a naturally occurring V H H domain or by expression of a nucleic acid encoding a such humanized V HH domain; (4) by“camelization” of a V H domain from any animal species, and in particular from a mammalian species, such as from a human being, or by expression of a nucleic acid encoding such a camelized V H domain; (5) by“camelization” of a “domain antibody
  • “Camelids” as used herein comprise old world camelids ( Camelus bactrianus and Camelus dromaderius) and new world camelids (for example Lama paccos, Lama glama and Lama vicugna).
  • the antibody may be a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a humanized antibody, a primatized antibody, a human antibody, a Nanobody®, an intrabody, or mixtures thereof.
  • antibody-like protein scaffolds or“engineered protein scaffolds” broadly encompasses proteinaceous non-immunoglobulin specific -binding agents, typically obtained by combinatorial engineering (such as site-directed random mutagenesis in combination with phage display or other molecular selection techniques).
  • Such scaffolds are derived from robust and small soluble monomeric proteins (such as Kunitz inhibitors or lipocalins) or from a stably folded extra membrane domain of a cell surface receptor (such as protein A, fibronectin or the ankyrin repeat).
  • Such scaffolds have been extensively reviewed in Binz et al., Gebauer and Skerra, Gill and Damle, Skerra 2000, and Skerra 2007, and include without limitation affibodies, based on the Z-domain of staphylococcal protein A, a three-helix bundle of 58 residues providing an interface on two of its alpha-helices (Nygren); engineered Kunitz domains based on a small (ca. 58 residues) and robust, disulphide-crosslinked serine protease inhibitor, typically of human origin (e.g.
  • LACI-D1 which can be engineered for different protease specificities (Nixon and Wood); monobodies or adnectins based on the lOth extracellular domain of human fibronectin III (l0Fn3), which adopts an Ig-like beta-sandwich fold (94 residues) with 2-3 exposed loops, but lacks the central disulphide bridge (Koide and Koide); anticalins derived from the lipocalins, a diverse family of eight-stranded beta- barrel proteins (ca.
  • DARPins designed ankyrin repeat domains (166 residues), which provide a rigid interface arising from typically three repeated beta-turns (Stumpp et al.); avimers (multimerized LDLR-A module) (Silverman et al.); and cysteine-rich knottin peptides (Kolmar).
  • aptamer refers to single-stranded or double-stranded oligo-DNA, oligo-RNA or oligo- DNA/RNA or any analogue thereof that specifically binds to a target molecule such as a peptide.
  • aptamers display fairly high specificity and affinity (e.g., K A in the order lxlO 9 M 1 ) for their targets.
  • photoaptamer refers to an aptamer that contains one or more photoreactive functional groups that can covalently bind to or crosslink with a target molecule.
  • spiegelmer refers to an aptamer which includes L-DNA, L-RNA, or other left-handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides.
  • peptidomimetic refers to a non-peptide agent that is a topological analogue of a corresponding peptide. Methods of rationally designing peptidomimetics of peptides are known in the art.
  • the chemical substance is an organic molecule, preferably a small organic molecule.
  • small molecule refers to compounds, preferably organic compounds, with a size comparable to those organic molecules generally used in pharmaceuticals.
  • Preferred small organic molecules range in size up to about 5000 Da, e.g., up to about 4000, preferably up to 3000 Da, more preferably up to 2000 Da, even more preferably up to about 1000 Da, e.g., up to about 900, 800, 700, 600 or up to about 500 Da.
  • soluble receptor generally refers to the soluble (i.e., circulating, not bound to a cell) form of a cell-surface molecule, e.g., a cell-surface receptor, or a fragment or derivative thereof.
  • a cell-surface molecule can be made soluble by attaching a soluble fusion partner, e.g., an immunoglobulin (Ig) moiety, or a portion thereof, to the extracellular domain, or by removing its transmembrane domain.
  • a soluble fusion partner e.g., an immunoglobulin (Ig) moiety, or a portion thereof
  • Targeted genome modification is a powerful tool for genetic manipulation of cells and organisms, including mammals. Genome modification or gene editing, including insertion, deletion or replacement of DNA in the genome, can be carried out using a variety of known gene editing systems.
  • the term“gene editing system” or“genome editing system” as used herein refers to a tool to induce one or more nucleic acid modifications, such as DNA or RNA modifications, into a specific DNA or RNA sequence within a cell.
  • Gene editing systems typically make use of an agent capable of inducing a nucleic acid modification.
  • the agent capable of inducing a nucleic acid modification may be a (endo)nuclease or a variant thereof having altered or modified activity.
  • (endo)Nucleases typically comprise programmable, sequence-specific DNA- or RNA-binding modules linked to a nonspecific DNA or RNA cleavage domain. In DNA, these nucleases create site-specific double-strand breaks at desired locations in the genome. The induced double-stranded breaks are repaired through nonhomologous end-joining or homologous recombination, resulting in targeted mutations. In certain embodiments, said (endo)nuclease may be RNA-guided.
  • said (endo)nuclease can be engineered nuclease such as a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated (Cas) (endo)nuclease, such as Cas9, Cpfl, or C2c2, a (zinc finger nuclease (ZFN), a transcription factor like effector nuclease (TALEN), a meganuclease, or modifications thereof.
  • CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
  • Cas Clustered Regularly Interspaced Short Palindromic Repeats
  • ZFN zinc finger nuclease
  • TALEN transcription factor like effector nuclease
  • meganuclease or modifications thereof.
  • the nucleic acid SRSF2-modulating agent is an oligonucleotide.
  • oligonucleotide refers to a nucleic acid (including nucleic acid analogues and mimetics) oligomer or polymer as defined herein.
  • an oligonucleotide is (substantially) single-stranded.
  • Oligonucleotides as intended herein may be preferably between about 10 and about 100 nucleoside units (i.e., nucleotides or nucleotide analogues) in length, preferably between about 15 and about 50, more preferably between about 20 and about 40, also preferably between about 20 and about 30.
  • oligonucleotides as intended herein may comprise one or more or all non- naturally occurring heterocyclic bases and/or one or more or all non-naturally occurring sugar groups and/or one or more or all non-naturally occurring inter-nucleoside linkages, the inclusion of which may improve properties such as, for example, enhanced cellular uptake, increased stability in the presence of nucleases and increased hybridization affinity, increased tolerance for mismatches, etc.
  • oligonucleotides as intended herein may be configured to not activate RNAse H, accordance with known techniques (see, e.g., U.S. Pat. 5,149,797).
  • the oligonucleotide SRSF2-modulating agent is capable of specifically hybridising with an RNA molecule bound by the SRSF2 component, and said oligonucleotide SRSF2-modulating agent comprises one or more mr5C.
  • the formation of such duplex of, on the one hand, the RNA molecule bound by the SRSF2 component and, on the other hand, an mr5C- containing oligonucleotide agent can modulate, such as restore binding of the SRSF2 component (e.g., mutated SRSF2) to said RNA.
  • antisense generally refers to an agent (e.g., an oligonucleotide as defined elsewhere in the specification ) configured to specifically anneal with (hybridise to) a given sequence in a target nucleic acid, such as for example in a target DNA, hnRNA, pre-mRNA or mRNA, and typically comprises, consist essentially of or consist of a nucleic acid sequence that is complementary or substantially complementary to said target nucleic acid sequence.
  • Antisense agents suitable for use herein may typically be capable of annealing with (hybridising to) the respective target nucleic acid sequences at high stringency conditions, and capable of hybridising specifically to the target under physiological conditions.
  • nucleic acids refer to the normal binding of single-stranded nucleic acids under permissive salt (ionic strength) and temperature conditions by base pairing, preferably Watson-Crick base pairing.
  • base pairing preferably Watson-Crick base pairing.
  • complementary Watson-Crick base pairing occurs between the bases A and T, A and U or G and C.
  • sequence 5'-A-G-U-3' is complementary to sequence 5'-A-C-U-3'.
  • an antisense agent need not be 100% complementary to that of its target sequence to bind or hybridise specifically with the latter as defined elsewhere in the specification.
  • An antisense agent may be said to be specifically hybridisable when binding of the agent to a target nucleic acid molecule interferes with the normal function of the target nucleic acid such as to attain an intended outcome (e.g., loss of utility), and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense agent to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.
  • “specifically hybridisable” and“complementary” may indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between an antisense agent and a nucleic acid target.
  • the sequence of said antisense agents may be at least about 80% identical, preferably at least about 90% identical, more preferably at least about 95% identical, such as, e.g., about 96%, about 97%, about 98%, about 99% and up to 100% identical to the respective target sequence.
  • Antisense agents as intended herein preferably comprise or denote antisense molecules such as more preferably antisense nucleic acid molecules or antisense nucleic acid analogue molecules.
  • antisense agents may refer to antisense oligonucleotides or antisense oligonucleotide analogues.
  • Antisense agents such as oligonucleotides as taught herein may be further conjugated (e.g., covalently or non-covalently, directly or via a suitable linker) to one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide.
  • Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium l,2-di-0-hexadecyl- rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl- oxycholesterol moiety.
  • lipid moieties such as a cholesterol moiety, cholic acid, a thioether
  • antisense compounds that are chimeric compounds.“Chimeric” antisense compounds or“chimeras” are antisense molecules, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound.
  • oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the increased resistance to nuclease degradation, increased cellular uptake, and an additional region for increased binding affinity for the target nucleic acid.
  • RNA interference agent refers to ribonucleic acid sequences, modified ribonucleic acid sequences, or DNA sequences encoding said ribonucleic acid sequences, which cause RNA interference and thus decrease expression of the target gene.
  • RNAi (RNA interference) agent typically comprises, consists essentially of or consists of a double-stranded portion or region (notwithstanding the optional and potentially preferred presence of single-stranded overhangs) of annealed complementary strands, one of which has a sequence corresponding to a target nucleotide sequence (hence, to at least a portion of an mRNA) of the target gene to be down-regulated.
  • the other strand of the RNAi agent is complementary to said target nucleotide sequence.
  • RNAi agents are shRNAs, siRNAs, miRNAs, and DNA-RNA hybrids.
  • the number of mismatches between a target sequence and a nucleotide sequence of the RNAi agent is preferably no more than 1 in 5 bases, or 1 in 10 bases, or 1 in 20 bases, or 1 in 50 bases.
  • the sequence of said RNAi agents may be at least about 80% identical, preferably at least about 90% identical, more preferably at least about 95% identical, such as, e.g., about 96%, about 97%, about 98%, about 99% and up to 100% identical to the respective target sequence.
  • RNAi agent may be formed by separate sense and antisense strands or, alternatively, by a common strand providing for fold-back stem-loop or hairpin design where the two annealed strands of an RNAi agent are covalently linked.
  • An siRNA molecule may be typically produced, e.g., synthesised, as a double stranded molecule of separate, substantially complementary strands, wherein each strand is about 18 to about 35 bases long, preferably about 19 to about 30 bases, more preferably about 20 to about 25 bases and even more preferably about 21 to about 23 bases.
  • shRNA is in the form of a hairpin structure.
  • shRNA can be synthesized exogenously or can be formed by transcribing from RNA polymerase III promoters in vivo.
  • shRNAs can be engineered in host cells or organisms to ensure continuous and stable suppression of a desired gene. It is known that siRNA can be produced by processing a hairpin RNA in cells.
  • RNAi agents as intended herein may include any modifications as set out herein for nucleic acids and oligonucleotides, in order to improve their therapeutic properties.
  • At least one strand of an RNAi molecules may have a 3’ overhang from about 1 to about 6 bases in length, e.g., from 2 to 4 bases, more preferably from 1 to 3 bases.
  • one strand may have a 3’ overhang and the other strand may be either blunt-ended or may also have a 3’overhang.
  • the length of the overhangs may be the same or different for each strand.
  • the 3’ overhangs can be stabilised against degradation.
  • the RNA may be stabilised by including purine nucleotides, such as A or G nucleotides.
  • substitution of pyrimidine nucleotides by modified analogues e.g., substitution of U 3’ overhangs by 2’-deoxythymidine is tolerated and does not affect the efficiency of RNAi.
  • An exemplary but non-limiting siRNA molecule may by characterized by any one or more, and preferably by all of the following criteria:
  • mRNA having a sequence which targets an area of the target gene present in mature mRNA (e.g., an exon or alternatively spliced intron);
  • the exemplary siRNA may be further characterised by one or more or all of the following criteria: having a double-stranded nucleic acid length of between 16 to 30 bases and preferably of between 18 to 23 bases, and preferably of 19 nucleotides;
  • RNAi agents as intended herein may particularly comprise or denote (i.e., may be selected from a group comprising or consisting of) RNAi nucleic acid molecules or RNAi nucleic acid analogue molecules, such as preferably short interfering nucleic acids and short interfering nucleic acid analogues (siNA) such as short interfering RNA and short interfering RNA analogues (siRNA), and may further denote inter alia double-stranded RNA and double-stranded RNA analogues (dsRNA), 10 micro-RNA and micro-RNA analogues (miRNA), and short hairpin RNA and short hairpin RNA analogues (shRNA).
  • siNA short interfering nucleic acid analogues
  • siRNA short interfering nucleic acid analogues
  • dsRNA double-stranded RNA analogues
  • miRNA micro-RNA and micro-RNA analogues
  • shRNA short hairpin RNA and short
  • RNAi agents can be carried out by any processes known in the art, such as inter alia partly or entirely by chemical synthesis (e.g., routinely known solid phase synthesis; an exemplary an non-limiting method for synthesising oligonucleotides on a modified 15 solid support is described in US 4,458,066; in another example, diethyl-phosphoramidites are used as starting materials and may be synthesised as described by Beaucage el al. 1981 (Tetrahedron Letters 22: 1859-1862)), or partly or entirely by biochemical (enzymatic) synthesis, e.g.
  • chemical synthesis e.g., routinely known solid phase synthesis; an exemplary an non-limiting method for synthesising oligonucleotides on a modified 15 solid support is described in US 4,458,066; in another example, diethyl-phosphoramidites are used as starting materials and may be synthesised as described by Beaucage el al. 1981 (Tetrahedron Letter
  • nucleic acid construct template
  • suitable polymerase such as a T7 or SP6 RNA polymerase
  • nucleotide analogues can be introduced by in vitro chemical or biochemical synthesis.
  • the antisense agents of the invention are synthesised in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules.
  • modulate broadly denotes a qualitative and/or quantitative alteration, change or 25 variation in that which is being modulated. Where modulation can be assessed quantitatively - for example, where modulation comprises or consists of a change in a quantifiable variable such as a quantifiable property or where a quantifiable variable provides a suitable surrogate for the modulation - modulation specifically encompasses both increase (e.g., activation) or decrease (e.g., inhibition) in the measured variable.
  • the term encompasses any extent of such modulation, e.g., any extent of such increase or decrease, and may more particularly refer to statistically significant increase or decrease in the measured variable.
  • modulation may encompass an increase in the value of the measured variable by at least about 10%, e.g., by at least about 20%, preferably by at least about 30%, e.g., by at least about 40%, more preferably by at least about
  • modulation may encompass a decrease or reduction in the value of the measured variable by at least about 10%, e.g., by at least about 20%, by at least about
  • modulation may be specific or selective, hence, that which is being modulated may be changed or altered without modulated without substantially altering other (unintended, undesired, unrelated) targets, functions, properties or processes.
  • an agent may modulate one or more aspects of the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide, such as its ability to bind to an RNA molecule comprising one or more mr5C and/or its ability to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C.
  • determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule may typically involve measuring said binding in the presence (optionally at different concentrations of said test agent) vs. absence of said test agent and comparing said measurements to identify any difference or deviation there between.
  • first components such as one or more molecules, biological entities, cells, or materials
  • second components such as one or more molecules, biological entities, cells, or materials
  • modulation may occur either directly, i.e., by way of direct interaction between the first and second component(s); or indirectly, e.g., when the first component(s) interact with or modulate one or more further component(s), one or more of which in turn interact with or modulate the second component(s), or vice versa.
  • the term“contacting” may depending on the context be synonymous with“exposing”,“incubating”,“mixing”,“reacting”,“treating”, or the like.
  • contacting may be performed in a cell-free system or in a cell lysate or in isolated or cultured cells or in an isolated or cultured tissue.
  • Cell-free systems may be prepared, for example, by mixing the investigated components and optionally any other chemical and/or biological substances required for obtaining the investigated outcome, such as binding of the polypeptide and RNA molecule and modulation thereof by a test agent, to take place.
  • the components are combined in a suitable aqueous environment, such as in an aqueous solution comprising a buffer system.
  • Commonplace buffers include without limitation histidine-buffers, citrate-buffers, succinate-buffers, acetate-buffers, phosphate-buffers, formate buffers, benzoate buffers, TRIS (Tris(hydroxymethyl)-aminomethan) buffers or maleate buffers, or mixtures thereof.
  • the experimental conditions may be selected to approximate physiological conditions, e.g., temperature 25-38°C, pH 7.0-7.5, ionic strength 100-250 mM.
  • Cell lysates refer to cell suspensions or fractions thereof obtained by disruption or lysing of cells. Crude cell lysates (without further treatment) or cell lysate solutions (treated for example to remove or render inactive selected molecules) may be employed. Any method can be used to lyse cells in a cell sample. For example, osmotic shock, sonication, heating, physical disruption, microwave treatment, and enzymatic and/or alkaline lysis are methods that can be used to lyse cells.
  • isolated as used throughout this specification with reference to a particular component generally denotes that such component exists in separation from - for example, has been separated from or prepared and/or maintained in separation from - one or more other components of its natural environment. More particularly, the term“isolated” as used herein in relation to cells or tissues denotes that such cells or tissues do not form part of an animal or human body.
  • Isolated cells or tissues may be suitably cultured or cultivated in vitro.
  • the terms“culturing” or “cell culture” are common in the art and broadly refer to maintenance of cells and potentially expansion (proliferation, propagation) of cells in vitro.
  • animal cells such as mammalian cells, such as human cells, are cultured by exposing them to (i.e., contacting them with) a suitable cell culture medium in a vessel or container adequate for the purpose (e.g., a 96-, 24-, or 6-well plate, a T-25, T-75, T-150 or T-225 flask, or a cell factory), at art-known conditions conducive to in vitro cell culture, such as temperature of 37°C, 5% v/v CO2 and > 95% humidity.
  • medium broadly encompasses any cell culture medium conducive to maintenance of cells, preferably conducive to proliferation of cells.
  • the medium will be a liquid culture medium, which facilitates easy manipulation (e.g., decantation, pipetting, centrifugation, filtration, and such) thereof.
  • the medium will comprise a basal medium formulation as known in the art.
  • basal media formulations available, e.g., from the American Type Culture Collection, ATCC; or from lnvitrogen, Carlsbad, California
  • Compositions of basal media are generally known in the art and it is within the skill of one in the art to modify or modulate concentrations of media and/or media supplements as necessary for the cells cultured
  • basal media formulations contain ingredients necessary for mammalian cell development, which are known per se.
  • these ingredients may include inorganic salts (in particular salts containing Na, K, Mg, Ca, Cl, P and possibly Cu, Fe, Se and Zn), physiological buffers (e.g., HEPES, bicarbonate), nucleotides, nucleosides and/or nucleic acid bases, ribose, deoxyribose, amino acids, vitamins, antioxidants (e.g., glutathione) and sources of carbon (e.g., glucose, sodium pyruvate, sodium acetate), etc.
  • inorganic salts in particular salts containing Na, K, Mg, Ca, Cl, P and possibly Cu, Fe, Se and Zn
  • physiological buffers e.g., HEPES, bicarbonate
  • nucleotides e.g., nucleosides and/or nucleic acid bases
  • ribose e.g., deoxyribos
  • basal media can be supplied with one or more further components.
  • additional supplements can be used to supply the cells with the necessary trace elements and substances for optimal growth and expansion.
  • antioxidant supplements may be added, e.g., b-mercaptoethanol. While many basal media already contain amino acids, some amino acids may be supplemented later, e.g., L-glutamine, which is known to be less stable when in solution.
  • a medium may be further supplied with antibiotic and/or antimycotic compounds, such as, typically, mixtures of penicillin and streptomycin, and/or other compounds, exemplified but not limited to, amphotericin, ampicillin, gentamicin, bleomycin, hygromycin, kanamycin, mitomycin, mycophenolic acid, nalidixic acid, neomycin, nystatin, paromomycin, polymyxin, puromycin, rifampicin, spectinomycin, tetracycline, tylosin, and zeocin.
  • antibiotic and/or antimycotic compounds such as, typically, mixtures of penicillin and streptomycin, and/or other compounds, exemplified but not limited to, amphotericin, ampicillin, gentamicin, bleomycin, hygromycin, kanamycin, mitomycin, mycophenolic acid, nalidixic acid, neo
  • Lipids and lipid carriers can also be used to supplement cell culture media.
  • Such lipids and carriers can include, but are not limited to cyclodextrin, cholesterol, linoleic acid conjugated to albumin, linoleic acid and oleic acid conjugated to albumin, unconjugated linoleic acid, linoleic-oleic- arachidonic acid conjugated to albumin, oleic acid unconjugated and conjugated to albumin, among others.
  • Albumin can similarly be used in fatty-acid free formulations.
  • supplementation of cell culture media with mammalian plasma or sera. Plasma or sera often contain cellular factors and components that facilitate cell viability and expansion.
  • plasma or serum may be heat inactivated.
  • Heat inactivation is used in the art mainly to remove the complement. Heat inactivation typically involves incubating the plasma or serum at 56°C for 30 to 60min, e.g., 30min, with steady mixing, after which the plasma or serum is allowed to gradually cool to ambient temperature.
  • plasma or serum may be sterilised prior to storage or use.
  • Usual means of sterilisation may involve, e.g., filtration through one or more filters with pore size smaller than 1 pm, preferably smaller than 0.5 pm, e.g., smaller than 0.45pm, 0.40pm, 0.35pm, 0.30pm or 0.25pm, more preferably 0.2pm or smaller, e.g., 0.15pm or smaller, 0.10pm or smaller.
  • Suitable sera or plasmas for use in media as taught herein may include human serum or plasma, or serum or plasma from non-human animals, preferably non human mammals, such as, e.g., non-human primates (e.g., lemurs, monkeys, apes), foetal or adult bovine, horse, porcine, lamb, goat, dog, rabbit, mouse or rat serum or plasma, etc., or any combination of such.
  • a medium as taught herein may comprise bovine serum or plasma, preferably foetal bovine (calf) serum or plasma, more preferably foetal bovine (calf) serum (FCS or FBS).
  • media may preferably comprise human serum or plasma, such as autologous or allogeneic human serum or plasma, preferably human serum, such as autologous or allogeneic human serum, more preferably autologous human serum or plasma, even more preferably autologous human serum.
  • human serum or plasma such as autologous or allogeneic human serum or plasma
  • human serum such as autologous or allogeneic human serum, more preferably autologous human serum or plasma, even more preferably autologous human serum.
  • serum or plasma can be substituted in media by serum replacements, such as to provide for serum-free media (i.e., chemically defined media).
  • serum-free media i.e., chemically defined media
  • the provision of serum- free media may be advantageous particularly with view to administration of the media or fraction(s) thereof to subjects, especially to human subjects (e.g., improved bio-safety).
  • serum replacement it is broadly meant any a composition that may be used to replace the functions (e.g., cell maintenance and growth supportive function) of animal serum in a cell culture medium.
  • a conventional serum replacement may typically comprise vitamins, albumin, lipids, amino acids, transferrin, antioxidants, insulin and trace elements.
  • Many commercialized serum replacement additives such as KnockOut Serum Replacement (KOSR), N2, B27, lnsulin- Transferrin-Selenium Supplement (1TS), and G5 are well known and are readily available to those skilled in the art.
  • Plasma or serum or serum replacement may be comprised in media as taught herein at a proportion (volume of plasma or serum or serum replacement /volume of medium) between about 0.5% v/v and about 40.0% v/v, preferably between about 5.0% v/v and about 20.0% v/v, e.g., between about 5.0% v/v and about 15.0 % v/v, more preferably between about 8.0% v/v and about 12.0% v/v, e.g., about 10.0% v/v.
  • Suitable isolated or cultured cells may be without limitation bacterial cells, fungal cells, including yeast cells, plant cells, animal cells, mammalian cells, human cells, or non-human mammalian cells.
  • Animal cells such as mammalian cells, human cells, or non-human mammalian cells may be preferred.
  • Cells may include primary cells, secondary, tertiary etc. cells, or may include immortalised cell lines, including clonal cell lines.
  • Non-limiting examples of bacterial cells include Escherichia coli, Yersinia enterocolitica, Brucella sp., Salmonella tymphimurium, Serratia marcescens, or Bacillus subtilis.
  • Non-limiting examples of firngal cells include Yarrowia lipolytica, Arxula adeninivorans, Pichia pastoris, Hansenula polymorpha, Saccharomyces cerevisiae, or Schizosaccharomyces pombe.
  • Non-limiting examples of insect cells include cells derived from Drosophila melanogaster, such as Schneider 2 cells, cell lines derived from the army worm Spodoptera frugiperda, such as Sf9 and Sf2l cells, or cells derived from the cabbage looper Trichoplusia ni, such as High Five cells.
  • Non-limiting example of human cells include the human HeLa (cervical cancer) cell line.
  • human cell lines common in tissue culture practice include inter alia human embryonic kidney 293 cells (HEK cells), DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breast cancer), THP-l (acute myeloid leukemia), U87 (glioblastoma), SHSY5Y (neuroblastoma), or Saos-2 cells (bone cancer).
  • a non-limiting example of primate cells are Vero (African green monkey Chlorocebus kidney epithelial cell line) cells, and COS cells.
  • Non-limiting examples of rodent cells are rat GH3 (pituitary tumor), CHO (Chinese hamster ovary), PC12 (pheochromocytoma) cell lines, or mouse MC3T3 (embryonic calvarium) cell line.
  • rat GH3 pituitary tumor
  • CHO Choinese hamster ovary
  • PC12 pheochromocytoma
  • mouse MC3T3 embryonic calvarium cell line.
  • Such cells can be obtained from a variety of commercial sources and research resource facilities, such as, for example, the American Type Culture Collection (Rockville, MD).
  • the cells may have an intact cell membrane ln
  • the cell membrane may be permeabilised (transiently or permanently) to allow diffusion of components across the cell membrane which are not transported or are transported less effectively across an intact cell membrane.
  • Suitable detergents for cell membrane permeabilisation include without limitation saponins (e.g., digitonin), TritonTM X-100, or Polysorbate 20.
  • the cells may be live or viable, or may be non- viable.
  • the polypeptide and RNA molecule may be endogenous, i.e., endogenously produced by the cell; or the polypeptide may be endogenous and the RNA molecule or an expressible nucleic acid molecule encoding said RNA molecule may be introduced into the cell; or the polypeptide or an expressible nucleic acid molecule encoding said polypeptide may be introduced into the cell and the RNA molecule may be endogenous; or the polypeptide or an expressible nucleic acid molecule encoding said polypeptide and the RNA molecule or an expressible nucleic acid molecule encoding said RNA molecule may both be introduced into the cell.
  • Methods for introducing polypeptides and/or nucleic acids into viable cells are known to the person skilled in the art, and may include calcium phosphate co-precipitation, electroporation, micro injection, protoplast fusion, lipofection, exosome-mediated transfection, transfection employing polyamine transfection reagents, bombardment of cells by nucleic acid-coated tungsten micro projectiles, viral particle delivery, etc. Such introduction may also be referred to as delivery, transfection or transformation.
  • CPPs Cell penetrating peptides
  • CPPs may also be employed for delivering polypeptides or nucleic acids into cells.
  • CPP translocation may be classified into three main entry mechanisms: direct penetration in the membrane, endocytosis-mediated entry, and translocation through the formation of a transitory structure.
  • CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar/charged amino acids and non-polar, hydrophobic amino acids. These two types of structures are referred to as polycationic or amphipathic, respectively.
  • a third class of CPPs are the hydrophobic peptides, containing only apolar residues, with low net charge or have hydrophobic amino acid groups that are crucial for cellular uptake.
  • Tat trans-activating transcriptional activator
  • H1V-1 Human lmmunodeficiency Virus 1
  • R-AhX-R4 R-AhX-R4
  • CPPs can be conjugated or complex with the cargo as known in the art, e.g., via a thioether bond or via formation of particles.
  • Expressible nucleic acid molecules such as for example expression cassettes or expression vectors, encoding polypeptides or RNAs of interest can be provided as generally known in the art.
  • An expressible nucleic acid molecule may typically comprise a nucleic acid molecule encoding the polypeptide of interest and/or a nucleic acid molecule encoding the RNA molecule of interest and a promoter(s) operably linked to said nucleic acid molecule(s).
  • the promoter may be selected or configured to effect expression of the polypeptide and/or RNA of interest in a cell of interest, such as a bacterial cell, fungal cell, yeast cell, plant cell, animal cell, mammalian cell, human cell, or non-human mammalian cell.
  • expression vector refers to nucleic acid molecules, typically DNA, to which nucleic acid fragments, preferably the recombinant nucleic acid molecule as defined herein, may be inserted and cloned, i.e., propagated.
  • a vector will typically contain one or more unique restriction sites, and may be capable of autonomous replication in a defined cell or vehicle organism such that the cloned sequence is reproducible.
  • a vector may also preferably contain a selection marker, such as, e.g., an antibiotic resistance gene, to allow selection of recipient cells that contain the vector.
  • Vectors may include, without limitation, plasmids, phagemids, bacteriophages, bacteriophage-derived vectors, PAC, BAC, linear nucleic acids, e.g., linear DNA, transposons, viral vectors, etc., as appropriate (see, e.g., Sambrook et al., 1989; Ausubel 1992).
  • Viral vectors may include inter alia retroviral vectors, lentiviral vectors, adenoviral vectors, or adeno-associated viral vectors, for example, vectors based on H1V, SV40, EBV, HSV or BPV.
  • Expression vectors are generally configured to allow for and/or effect the expression of nucleic acids or open reading frames introduced thereto in a desired expression system, e.g., in vitro, in a cell, organ and/or organism.
  • expression vectors may advantageously comprise suitable regulatory sequences.
  • Factors of importance in selecting a particular vector include inter alia: choice of recipient cell, ease with which recipient cells that contain the vector may be recognised and selected from those recipient cells which do not contain the vector; the number of copies of the vector which are desired in particular recipient cells; whether it is desired for the vector to integrate into the chromosome or to remain extra-chromosomal in the recipient cells; and whether it is desirable to be able to“shuttle” the vector between recipient cells of different species.
  • Expression vectors can be autonomous or integrative.
  • a nucleic acid can be in introduced into a cell in the form of an expression vector such as a plasmid, phage, transposon, cosmid or virus particle.
  • the recombinant nucleic acid can be maintained extrachromosomally or it can be integrated into the cell chromosomal DNA.
  • Expression vectors can contain selection marker genes encoding proteins required for cell viability under selected conditions (e.g., URA3, which encodes an enzyme necessary for uracil biosynthesis, or LEU2, which encodes an enzyme required for leucine biosynthesis, or TRP1, which encodes an enzyme required for tryptophan biosynthesis) to permit detection and/or selection of those cells transformed with the desired nucleic acids.
  • Expression vectors can also include an autonomous replication sequence (ARS).
  • the ARS may comprise a centromere (CEN) and an origin of replication (OR1).
  • CEN centromere
  • OR1 origin of replication
  • Integrative vectors generally include a serially arranged sequence of at least a first insertable DNA fragment, a selectable marker gene, and a second insertable DNA fragment.
  • the first and second insertable DNA fragments are each about 200 (e.g., about 250, about 300, about 350, about 400, about 450, about 500, or about 1000 or more) nucleotides in length and have nucleotide sequences which are homologous to portions of the genomic DNA of the cell species to be transformed.
  • a nucleotide sequence containing a nucleic acid of interest for expression is inserted in this vector between the first and second insertable DNA fragments, whether before or after the marker gene.
  • Integrative vectors can be linearized prior to transformation to facilitate the integration of the nucleotide sequence of interest into the cell genome.
  • promoter refers to a DNA sequence that enables a gene to be transcribed.
  • a promoter is recognized by RNA polymerase, which then initiates transcription.
  • a promoter contains a DNA sequence that is either bound directly by, or is involved in the recruitment, of RNA polymerase.
  • a promoter sequence can also include“enhancer regions”, which are one or more regions of DNA that can be bound with proteins (namely the trans-acting factors) to enhance transcription levels of genes in a gene-cluster.
  • the enhancer while typically at the 5’ end of a coding region, can also be separate from a promoter sequence, e.g., can be within an intronic region of a gene or 3’ to the coding region of the gene.
  • An“operable linkage” is a linkage in which regulatory sequences and sequences sought to be expressed are connected in such a way as to permit said expression.
  • sequences such as, e.g., a promoter and an open reading frame (ORF)
  • ORF open reading frame
  • sequences such as, e.g., a promoter and an open reading frame (ORF)
  • ORF open reading frame
  • operably linked may mean incorporated into a genetic construct so that expression control sequences, such as a promoter, effectively control transcription / expression of a sequence of interest.
  • the promotor may be a constitutive or inducible (conditional) promoter.
  • a constitutive promoter is understood to be a promoter whose expression is constant under the standard culturing conditions.
  • Inducible promoters are promoters that are responsive to one or more induction cues.
  • an inducible promoter can be chemically regulated (e.g., a promoter whose transcriptional activity is regulated by the presence or absence of a chemical inducing agent such as an alcohol, tetracycline, a steroid, a metal, or other small molecule) or physically regulated (e.g., a promoter whose transcriptional activity is regulated by the presence or absence of a physical inducer such as light or high or low temperatures).
  • An inducible promoter can also be indirectly regulated by one or more transcription factors that are themselves directly regulated by chemical or physical cues.
  • promoters include T7, U6, Hl, retroviral Rous sarcoma virus (RSV) LTR promoter, the cytomegalovirus (CMV) promoter, the SV40 promoter, the dihydrofolate reductase promoter, the b-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EFla promoter.
  • the vectors Prior to introducing the vectors into a cell of interest, the vectors can be grown (e.g., amplified) in bacterial cells such as Escherichia coli ( E . coli).
  • the vector DNA can be isolated from bacterial cells by any of the methods known in the art which result in the purification of vector DNA from the bacterial milieu.
  • the purified vector DNA can be extracted extensively with phenol, chloroform, and ether, to ensure that no E. coli proteins are present in the plasmid DNA preparation, since these proteins can be toxic to mammalian cells.
  • the evaluation of the binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof with the RNA molecule comprising one or more mr5C may in certain embodiments involve measuring either the so-bound SRSF2 component or the so-bound RNA component or both, after said components have been contacted to allow for their binding to take place.
  • “Measuring” as used throughout the present specification broadly refers to any means of detecting or determining the presence or absence and/or quantity of that which is“measured”, such as a marker, peptide, polypeptide, protein, or nucleic acid, or such as binding, activity, function, etc.
  • Any existing, available or conventional separation, detection and/or quantification methods may be used to measure the presence or absence and/or quantity of any marker, peptide, polypeptide, protein, or nucleic acid, as discussed herein, such as of the SRSF2 and/or RNA components.
  • such methods may include biochemical assay methods, including inter alia assays of enzymatic activity, membrane channel activity, substance-binding activity, gene regulatory activity, or cell signaling activity of a marker, peptide, polypeptide, protein, or nucleic acid.
  • such methods may include affinity-based assay methods, wherein the ability of an assay to separate, detect and/or quantify a marker, peptide, polypeptide, protein, or nucleic acid is conferred by specific binding between a separable, detectable and/or quantifiable binding agent and i) the marker peptide, polypeptide, protein, or nucleic acid, or ii) a label or tag comprised by (e.g., covalently bound to or conjugated with) the marker peptide, polypeptide, protein, or nucleic acid.
  • the binding agent may be an immunological binding agent (antibody) or a non- immunological binding agent.
  • antibodies capable of binding to human SRSF2 include without limitation those available from the following vendors (“#” stands for catalogue number): OriGene (#APl2450PU-N, #APl8l94PU-N, rabbit polyclonals); Invitrogen (#RA5-12402, #PA5- 62086, rabbit polyclonals); GeneTex (#GTXl l826, mouse monoclonal); ProteoGenix (#PTGX-SC- 4F11, mouse monoclonal); and Santa Cruz (#sc-535l8, mouse monoclonal).
  • i) include anti-myc antibodies, which specifically bind to a myc tag (EQKLISEEDL), or anti-FLAG antibodies, which specifically bind to a FLAG tag (DYKDDDDK).
  • Non-limiting examples of ii) include streptavidin, which specifically binds to biotin; metal ion (e.g., Ni 2+ ), which specifically binds to his-tag; and maltose binding protein (MBP), which specifically binds maltose.
  • MBP maltose binding protein
  • Affinity- based assay methods include without limitation immunohistochemistry, immunocytochemistry, flow cytometry, mass cytometry, fluorescence activated cell sorting (FACS), fluorescence microscopy, fluorescence based cell sorting using microfluidic systems, (immuno)affinity adsorption based techniques such as affinity chromatography, magnetic particle separation, magnetic activated cell sorting or bead based cell sorting using microfluidic systems, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA) and ELISPOT based techniques, radioimmunoassay (RIA), Western blot, etc.
  • FACS fluorescence activated cell sorting
  • FACS fluorescence activated cell sorting
  • microscopy fluorescence based cell sorting using microfluidic systems
  • immunoprecipitation enzyme-linked immunosorbent assay (ELISA) and ELISPOT based techniques
  • RIA radioimmunoassay
  • such methods may include mass spectrometry analysis methods.
  • mass spectrometric (MS) techniques that are capable of obtaining precise information on the mass of peptides, and preferably also on fragmentation and/or (partial) amino acid sequence of selected peptides (e.g., in tandem mass spectrometry, MS/MS; or in post source decay, TOF MS), may be useful herein for separation, detection and/or quantification of markers, peptides, polypeptides, or proteins, or nucleic acid (such as, preferably, peptides, polypeptides, or proteins).
  • Suitable peptide MS and MS/MS techniques and systems are well-known per se (see, e.g., Methods in Molecular Biology, vol.
  • MS arrangements, instruments and systems suitable for peptide analysis may include, without limitation, matrix-assisted laser desorption/ionisation time- of- flight (MALD1-TOF) MS; MALD1-TOF post-source-decay (PSD); MALD1-TOF/TOF; surface- enhanced laser desorption/ionization time-of-flight mass spectrometry (SELD1-TOF) MS; electrospray ionization mass spectrometry (ES1-MS); ES1-MS/MS; ES1- MS/(MS)n (n is an integer greater than zero); ES1 3D or linear (2D) ion trap MS; ES1 triple quadrupole MS; ES1 quadrupole orthogonal TOF (Q-TOF); ES1 Fourier transform MS systems; desorption/ionization on silicon (DlOS); secondary ion mass spectrometry (S1MS); atmospheric pressure chemical ionization mass spectrometry (APC1-MS); APC1-MS/
  • MS/MS Peptide ion fragmentation in tandem MS
  • CID collision induced dissociation
  • Detection and quantification of markers by mass spectrometry may involve multiple reaction monitoring (MRM), such as described among others by Kuhn et al. 2004 (Proteomics 4: 1175-86).
  • MS peptide analysis methods may be advantageously combined with upstream peptide or protein separation or fractionation methods, such as for example with the chromatographic and other methods.
  • such methods may include chromatography methods.
  • chromatography encompasses methods for separating substances, such as chemical or biological substances, e.g., peptides, polypeptides, proteins, or nucleic acids, referred to as such and vastly available in the art.
  • chromatography refers to a process in which a mixture of substances (analytes) carried by a moving stream of liquid or gas (“mobile phase”) is separated into components as a result of differential distribution of the analytes, as they flow around or over a stationary liquid or solid phase (“stationary phase”), between said mobile phase and said stationary phase.
  • the stationary phase may be usually a finely divided solid, a sheet of filter material, or a thin film of a liquid on the surface of a solid, or the like. Chromatography is also widely applicable for the separation of chemical compounds of biological origin.
  • Chromatography may be preferably columnar (i.e., wherein the stationary phase is deposited or packed in a column), preferably liquid chromatography, and yet more preferably HPLC. While particulars of chromatography are well known in the art, for further guidance see, e.g., Meyer M., 1998, ISBN: 047198373X, and“Practical HPLC Methodology and Applications”, Bidlingmeyer, B. A., John Wiley & Sons Inc., 1993.
  • Exemplary types of chromatography include, without limitation, high-performance liquid chromatography (HPLC), normal phase HPLC (NP-HPLC), reversed phase HPLC (RP-HPLC), ion exchange chromatography (IEC), such as cation or anion exchange chromatography, hydrophilic interaction chromatography (HILIC), hydrophobic interaction chromatography (HIC), size exclusion chromatography (SEC) including gel filtration chromatography or gel permeation chromatography, chromatofocusing, affinity chromatography such as immunoaffinity, immobilised metal affinity chromatography, and the like.
  • HPLC high-performance liquid chromatography
  • NP-HPLC normal phase HPLC
  • RP-HPLC reversed phase HPLC
  • IEC ion exchange chromatography
  • HILIC hydrophilic interaction chromatography
  • HIC hydrophobic interaction chromatography
  • SEC size exclusion chromatography
  • gel filtration chromatography or gel permeation chromatography chromatofocusing
  • affinity chromatography such as immunoaffinity,
  • Such methods include, without limitation, chemical extraction partitioning, isoelectric focusing (IEF) including capillary isoelectric focusing (CIEF), capillary isotachophoresis (CITP), capillary electrochromatography (CEC), and the like, one-dimensional polyacrylamide gel electrophoresis (PAGE), two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), capillary gel electrophoresis (CGE), capillary zone electrophoresis (CZE), micellar electrokinetic chromatography (MEKC), free flow electrophoresis (FFE), etc.
  • IEF isoelectric focusing
  • CITP capillary isotachophoresis
  • CEC capillary electrochromatography
  • PAGE polyacrylamide gel electrophoresis
  • 2D-PAGE two-dimensional polyacrylamide gel electrophoresis
  • CGE capillary gel electrophoresis
  • CZE capillary zone electrophoresis
  • MEKC micellar electrokinetic chromatography
  • Non limiting examples include hybridisation-based analysis, microarray analysis, RNA-in-situ hybridisation (RISH), Northern-blot analysis and the like; PCR, RT-PCR, RT-qPCR, end-point PCR, digital PCR or the like; supported oligonucleotide detection, pyrosequencing, polony cyclic sequencing by synthesis, simultaneous bi-directional sequencing, single-molecule sequencing, single molecule real time sequencing, true single molecule sequencing, hybridization-assisted nanopore sequencing, sequencing by synthesis, single-cell RNA sequencing (sc-RNA seq), or the like.
  • RISH RNA-in-situ hybridisation
  • Non-limiting examples employing techniques such as discussed above include without limitation the following.
  • An embodiment employs RNA pull-down assay.
  • endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line.
  • endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line.
  • the RNA component is produced synthetically and conjugated with a tag configured for specific binding to a binding agent.
  • the tag is biotin and the binding agent is streptavidin.
  • the so-tagged RNA component is captured onto streptavidin-conjugated (magnetic) beads, and a known quantity of the beads having the RNA component displayed thereon are contacted with a known quantity of the SRSF2 component, under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, the unbound SRSF2 component is washed away.
  • the beads are collected (such as magnetically or by centrifugation), and the RNA-beads-bound SRSF2 component is optionally eluted and is suitably detected / quantified, such as by Western blotting, dot blotting, EL1SA, or MS.
  • SRSF2 component is recombinantly produced in and isolated from a cell line.
  • human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line.
  • the SRSF2 component is recombinantly fused to a tag configured for specific binding to a binding agent.
  • the tag is a FLAG tag, such as N-terminal or C-terminal FLAG tag, and the binding agent is anti-FLAG antibody.
  • the RNA component is produced synthetically.
  • the RNA component is unlabelled or labelled (e.g., radioactive ly labelled, such as 32 P- or 33 P-labelled, or fluorescently- or chemiluminescently-labelled).
  • the so-tagged SRSF2 component is captured onto anti-FLAG antibody-conjugated (magnetic) beads, and a known quantity of the beads having the SRSF2 component displayed thereon are contacted with a known quantity of the RNA component, under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, the unbound RNA component is washed away.
  • the beads are collected (such as magnetically or by centrifugation), and the SRSF2-beads-bound RNA component is optionally eluted and suitably detected / quantified, such as by Northern blotting, dot blotting, scintillation counting, fluorescent signal detection, chemiluminiscence signal detection, or sequencing.
  • RNA electrophoretic mobility shift assay employs RNA electrophoretic mobility shift assay (RNA EMSA).
  • endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line.
  • endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line.
  • the RNA component is produced synthetically and is labelled (e.g., radioactively labelled, such as 32 P- or 33 P-labelled, or fluorescently- or chemiluminescently-labelled).
  • SRSF2 and RNA components are contacted under conditions conducive to the binding of the SRSF2 and RNA components.
  • the binding reaction is then separated by non- denaturing polyacrylamide gel electrophoresis (PAGE), or the SRSF2-RNA complex is crosslinked and the binding reaction is separated by denaturing PAGE.
  • PAGE polyacrylamide gel electrophoresis
  • the SRSF2-bound RNA component displays a migration shift relative to the unbound RNA component.
  • the SRSF2-bound RNA is quantified, typically following transfer onto a nylon membrane, by quantification of the label provided on the RNA component.
  • the evaluation of the binding of the SRSF2 component with the RNA component may in further embodiments rely on the detection of spatial proximity of moieties conjugated to the SRSF2 and RNA components, such as moieties configured to provide for fluorescence resonance energy transfer (FRET) or bioluminescence resonance energy transfer (BRET).
  • FRET fluorescence resonance energy transfer
  • BRET bioluminescence resonance energy transfer
  • An embodiment employs FRET.
  • endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line.
  • endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line.
  • the RNA component is produced synthetically.
  • the SRSF2 component is labelled with a donor fluorophore and the RNA component is labelled with an acceptor fluorophore, wherein when the donor and acceptor fluorophores are in spatial proximity (typically in the range of 1-10 nm), the donor fluorophore in its excited state non-radiatively transfers its excitation energy to the neighbouring acceptor fluorophore, thereby causing the acceptor fluorophore to emit its characteristic fluorescence, which can be detected.
  • the SRSF2 component is labelled with the acceptor fluorophore and the RNA component is labelled with the donor fluorophore.
  • the SRSF2 component may be recombinantly fused to the FP.
  • Suitable FRET pairs include without limitation Alexa Fluor 405 - Alexa Fluor 430, Cy2 - Cy3, Cy3 - Cy5, FITC (fluorescein isothiocyanate) - TRITC (tetramethylrhodamine), PE (phycoerythrin) - APC (allophycocyanin), Alexa Fluor 488 - Alexa Fluor 514/532/546/610, Alexa Fluor 647 - Alexa Fluor 680/700/750.
  • Suitable FRET FP pairs include without limitation CFP (cyan FP) - YFP (yellow FP), cerulean FP - YFP, GFP (green FP)- YFP, GFP - mRFP (monomeric red FP).
  • Known quantities of the SRSF2 and RNA components are contacted (e.g., in solution or in permeabilised cells) under conditions conducive to the binding of the SRSF2 and RNA components.
  • the binding reaction is illuminated at a frequency configured to excite the donor fluorophore, and the light emitted by the acceptor fluorophore is suitably detected / quantified, such as using a fluorescent microscope or reader.
  • Detailed guidance to performing FRET can be found inter alia in Bajar et al. (Sensors (Basel). 2016, vol. 16(9), 1488).
  • Another embodiment employs BRET ln BRET bioluminescence provides the light source (donor) for the excitation of the acceptor fluorophore, thus avoiding external illumination.
  • a bioluminescent luciferase such as a bioluminescent luciferase from Renilla reniformis or from Oplophorus gracilirostris, may be used.
  • the bioluminescent luciferase is recombinantly fused to one of the interaction partners ln an example, luciferase from Renilla reniformis may be used in conjunction with YFP as acceptor ln another example, luciferase from Oplophorus gracilirostris may be used in conjunction with a chloroalkane derivative of nonchloro TOM (NCT) dye with peak light emission at 635 nm as acceptor (see Machleidt et al. ACS Chem Biol. 2015, vol. 10(8), 1797-804).
  • NCT nonchloro TOM
  • a BRET system based on luciferase from Oplophorus gracilirostris (NanoLuc®) and a HaloTag® protein- fluorophore conjugate has been described in Machleidt et al. ⁇ supra) and is commercialised by Promega Corp under the designation NanoBRETTM (see also Fig. 6).
  • endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line.
  • endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line.
  • the RNA component is produced synthetically.
  • the SRSF2 component is recombinantly fused to a bioluminescent luciferase, such as Renilla reniformis luciferase or NanoLuc® luciferase.
  • the RNA component is conjugated with YFP or with Alexa-594, respectively.
  • SRSF2 and RNA components are contacted (e.g., in solution or in permeabilised cells) under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, a suitable luciferase substrate is added and the light emitted by the acceptor fluorophore is suitably detected / quantified, such as using a fluorescent microscope or reader.
  • the SRSF2-modulating agent may be capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to said one or more mr5C on the RNA molecule.
  • the binding between the SRSF2 and RNA components may be reduced or decreased by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said SRSF2-modulating agent.
  • Said percentage may refer to the value of a quantifiable variable representative of said binding, such as without limitation the quantitative a signal or read-out in an RNA pull-down, EMSA, FRET, BRET, or similar experiment.
  • inclusion of such SRSF2-modulating agent at a given concentration in a binding reaction may lead to apparent decrease in K A / increase in K D of binding between the SRSF2 and RNA components by > 1 order of magnitude (lOx), such as > 2 (100c), > 3 (IOOOc), > 4 (lxlO 4 ), or > 5 (lxl 0 5 ) orders of magnitude.
  • the lC 5 o of the SRSF2-modulating agent for modulating such as reducing the binding between the SRSF2 and RNA components may be 0.1 nM and 10 mM, preferably between 0.1 nM and 5 mM, more preferably between 0.1 nM and 1 mM, even more preferably between 0.1 nM and 100 nM, e.g., between 10-100 nM, preferably between 1.0-10 nM, more preferably between 0.1-5.0 nM, even more preferably between 0.1-1.0 nM.
  • the present methods may further comprise determining whether the SRSF2-modulating agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
  • the effect of the SRSF2-modulating agent on said quantity and/or activity may be determined in a cell-free system, in cell lysates, in isolated or cultured cells or tissues, or in non-human animal model organisms.
  • the SRSF2-modulating agent reduces said quantity and/or activity
  • such may be reduced or decreased by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said SRSF2-modulating agent.
  • Said percentage may refer to the value of a quantifiable variable representative of said quantity and/or activity, such as without limitation the quantitative a signal or read-out in a Western blot, EL1SA, MS, or similar experiment.
  • the present methods may further comprise determining whether the SRSF2-modulating agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant, such as specifically bind to the mr5C- binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
  • Specific binding particularly denotes that the SRSF2-modulating agent binds to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant substantially to the exclusion of other molecules which are random or unrelated.
  • Specificity of binding may be determined, for example, in a cell-free system (e.g., including a suitable control protein, such as bovine serum albumin or casein), in cell lysates, or in isolated or cultured cells or tissues, such as cell lysates, cells and tissues of human origin.
  • SRSF2-modulating agent displaying such specific binding may have affinity for the SRSF2 target under the conditions of binding at least about 100-fold, or at least about 1000-fold, or at least about 10 4 -fold, or at least about 10 5 -fold, or at least about 10 6 -fold or more greater, than its affinity for a non-target molecule.
  • An exemplary, non- limiting way for evaluating the specificity of binding of a SRSF2-modulating agent to the SRSF2 component may be pull-down of proteins from a cell lysate, such as human cell lysate, using the agent conjugated to (magnetic) beads, and identifying the pulled-down proteins by for example MS, to determine the abundance / enrichment of SRSF2 and the presence of other ‘contaminating’ proteins.
  • An exemplary, non- limiting way for evaluating the specificity of binding of a SRSF2-modulating agent to the mr5C-binding site of the SRSF2 component may involve a computational protein modelling analysis modelling the agent into said site.
  • the RNA molecule may be susceptible to splicing and the present methods may further comprise determining whether the SRSF2-modulating agent can alter the splicing of said RNA molecule.
  • splicing denotes the process and means of removing intervening sequences (introns) from pre- mRNA in the process of producing mature mRNA.
  • the reference to splicing particularly aims at native splicing such as occurs under normal physiological conditions.
  • pre-mRNA and “transcript” are used herein to denote RNA species that precede mature mRNA, such as in particular a primary RNA transcript and any partially processed forms thereof.
  • Sequence elements required for splicing refer particularly to cis elements in the sequence of pre-mRNA which direct the cellular splicing machinery (spliceosome) towards correct and precise removal of introns from the pre-mRNA. Sequence elements involved in splicing are generally known per se and can be further determined by known techniques including inter alia mutation or deletion analysis. By means of further explanation,“splice donor site” or“5' splice site” generally refer to a conserved sequence immediately adjacent to an exon-intron boundary at the 5’ end of an intron.
  • a splice donor site may contain a dinucleotide GU, and may involve a consensus sequence of about 8 bases at about positions +2 to -6.“Splice acceptor site” or“3' splice site” generally refers to a conserved sequence immediately adjacent to an intron-exon boundary at the 3’ end of an intron. Commonly, a splice acceptor site may contain a dinucleotide AG, and may involve a consensus sequence of about 16 bases at about positions -14 to +2.
  • An exemplary, non-limiting way for evaluating the impact of an SRSF2-modulating agent on the splicing of an RNA molecule may comprise i) providing or being provided with cells expressing SRSF2 (endogenously or recombinantly) and expressing an RNA molecule (endogenously or recombinantly), wherein said RNA molecule is susceptible to splicing and SRSF2 plays a role in said splicing, ii) contacting said cells with said SRSF2-modulating agent, and iii) determining whether the splicing of said RNA molecule has been altered.
  • Altered splicing may manifest as, for example, diminished quantity of the RNA molecule or of a protein encoded by said RNA molecule and/or as production of alternatively-spliced species of said RNA molecule. Such alteration can be detected by conventional techniques, such as Northern blotting or RNA sequencing.
  • the present methods may further comprise determining whether the SRSF2-modulating agent displays anti-neoplastic property, such as anti-cancer property.
  • anti-neoplastic property such as anti-cancer property.
  • anti-neoplastic properties may particularly include, cytostatic effects on neoplastic cells or tissues.
  • a further aspect provides an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
  • a related aspect provides a method of treating a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation in a subject, comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule.
  • a further related aspect provides the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
  • a further related aspect provides the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
  • the agent is capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to the one or more mr5C on the RNA molecule;
  • the agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant;
  • the agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant; and/or
  • the RNA molecule is susceptible to splicing and the agent can alter the splicing of said RNA molecule.
  • non-human animals preferably warm-blooded animals, even more preferably mammals, such as, e.g., non-human primates, rodents, canines, felines, equines, ovines, porcines, and the like.
  • non-human animals includes all vertebrates, e.g., mammals, such as non-human primates, (particularly higher primates), sheep, dog, rodent (e.g. mouse or rat), guinea pig, goat, pig, cat, rabbits, cows, and non-mammals such as chickens, amphibians, reptiles etc.
  • the subject is a non-human mammal. In certain preferred embodiments, the subject is human. In other embodiments, the subject is an experimental animal or animal substitute as a disease model.
  • the term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. Examples of subjects include humans, dogs, cats, cows, goats, and mice. The term subject is further intended to include transgenic species.
  • the subject may be a human subject, and said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of human origin.
  • the terms“therapy” or“treatment” refer to the alleviation or measurable lessening of one or more symptoms or measurable markers of a pathological condition such as a disease or disorder.
  • the terms encompass primary treatments as well as neo-adjuvant treatments, adjuvant treatments and adjunctive therapies.
  • prophylactically effective amount refers to an amount of an active compound or pharmaceutical agent that inhibits or delays in a subject the onset of a disorder as being sought by a researcher, veterinarian, medical doctor or other clinician.
  • therapeutically effective amount refers to an amount of active compound or pharmaceutical agent that elicits the biological or medicinal response in a subject that is being sought by a researcher, veterinarian, medical doctor or other clinician, which may include inter alia alleviation of the symptoms of the disease or condition being treated. Methods are known in the art for determining therapeutically and prophylactically effective doses for the pharmaceutical formulation as taught herein.
  • dysregulation refers to an abnormality, deviation, or alteration in the value or quantity of a variable that is said to be dysregulated in one or more cells or tissues of a subject from the value or quantity of said variable in corresponding one or more cells or tissues of a healthy subject.
  • the term may particularly denote a statistically significant deviation or alteration.
  • values representing dysregulation may fall outside of error margins of reference values in a healthy population (as expressed, for example, by standard deviation or standard error, or by a predetermined multiple thereof, e.g., ⁇ lxSD or ⁇ 2xSD or ⁇ 3xSD, or ⁇ lxSE or ⁇ 2xSE or ⁇ 3xSE).
  • values representing dysregulation may fall outside of a reference range defined by reference values in a healthy population (for example, outside of a range which comprises >40%, > 50%, >60%, >70%, >75% or >80% or >85% or >90% or >95% or even >100% of values in said population).
  • Dysregulation specifically encompasses both increase (e.g., increased expression and/or activity) or decrease (e.g., decreased expression and/or activity) in the variable that is said to be dysregulated.
  • the term encompasses any extent of such increase or decrease.
  • any one or more of the several successive molecular mechanisms involved in the expression of SRSF2 may be dysregulated and may lead to dysregulation of the quantity of SRSF2 produced by one or more cells or tissues of a subject.
  • these may include alterations in the gene sequence (e.g., the polypeptide-encoding, non-coding and/or regulatory portions of the gene sequence), the transcription of the gene into RNA, the polyadenylation and where applicable splicing and/or other post-transcriptional modifications of the RNA into mRNA, the localisation of the mRNA into cell cytoplasm, where applicable other post-transcriptional modifications of the mRNA, the translation of the mRNA into a polypeptide chain, where applicable post-translational modifications of the polypeptide, and/or folding of the polypeptide chain into the mature conformation of the polypeptide.
  • compartmentalised polypeptides such as secreted polypeptides and transmembrane polypeptides
  • this may further include targeting trafficking of the polypeptides, i.e., the cellular mechanism by which polypeptides are transported to the appropriate sub-cellular compartment or organelle, membrane, e.g. the plasma membrane, or outside the cell.
  • any one or more aspects of SRSF2 activity or function may be dysregulated in one or more cells or tissues of a subject.
  • the binding of SRSF2 to RNAs comprising one or more mr5C may be dyregulated, or modulation of splicing of RNAs or mRNAs, particularly RNAs or mRNAs comprising one or more mr5C, by SRSF2 may be dyregulated, or both.
  • dyregulated binding of SRSF2 to an RNA comprising one or more mr5C may alter the corresponding equilibrium constant for the dissociation (K D ) by > 1 order of magnitude (lOx), such as > 2 (IOOc), > 3 (IOOOc), > 4 (lx lO 4 ), or > 5 (lx l 0 5 ) orders of magnitude, compared to normal or reference binding.
  • the dysregulation of SRSF2 expression and/or activity may be due to a mutation in SRSF2.
  • Any types of mutations and particular are contemplated herein, inter alia SRSF2 mutations and mutated SRSF2 as described elsewhere in this specification.
  • RNA mr5C methylation may be dysregulated in one or more cells or tissues of a subject.
  • the extent or quantity of mr5C methylation of an RNA molecule or of a population of RNA molecules or of transcriptome may be expressed by a convenient variable, such as the ratio of 5-methylated cytosines to all cytosines, or the quantity of 5-methylated cytosines per given quantity of RNA (w/w), or the quantity of 5-methylated cytosines per given quantity of cells or tissue (w/w), or similar.
  • Methods for measuring mr5C are available, and typically rely on either separation according to physicochemical properties, differential enzymatic turnover or differential chemical reactivity. Suitable methods and assays are reviewed for example in Motorin et al. (Nucleic Acids Research. 2010, vol. 38, 1415-1430) and Helm and Motorin (Nature Reviews Genetics. 2017, vol. 18, 275-291).
  • the disease is a neoplastic disease.
  • RNA molecule for use in the treatment of a neoplastic disease; a method of treating a neoplastic disease in a subject, comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule; use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of a neoplastic disease;
  • the disease is cancer.
  • a method of treating cancer in a subject comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule;
  • an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of cancer;
  • neoplastic disease generally refers to any disease or disorder characterized by neoplastic cell growth and proliferation, whether benign (not invading surrounding normal tissues, not forming metastases), pre-malignant (pre-cancerous), or malignant (invading adjacent tissues and capable of producing metastases).
  • the term neoplastic disease generally includes all transformed cells and tissues and all cancerous cells and tissues. Neoplastic diseases or disorders include, but are not limited to abnormal cell growth, benign tumors, premalignant or precancerous lesions, malignant tumors, and cancer.
  • neoplastic diseases or disorders are benign, pre-malignant, or malignant neoplasms located in any tissue or organ, such as in the prostate, colon, abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, or urogenital tract.
  • tissue or organ such as in the prostate, colon, abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, or urogenital tract.
  • the neoplastic disease may be a tumor or may be characterized by the presence of a tumor.
  • tumor or tumor tissue refer to an abnormal mass of tissue that results from excessive cell division.
  • a tumor or tumor tissue comprises tumor cells which are neoplastic cells with abnormal growth properties and no useful bodily function. Tumors, tumor tissue and tumor cells may be benign, pre-malignant or malignant, or may represent a lesion without any cancerous potential.
  • a tumor or tumor tissue may also comprise tumor-associated non-tumor cells, e.g., vascular cells which form blood vessels to supply the tumor or tumor tissue. Non-tumor cells may be induced to replicate and develop by tumor cells, for example, the induction of angiogenesis in a tumor or tumor tissue.
  • the tumor including any metastases of the tumor
  • the tumor may be of epithelial origin ln certain embodiments, the tumor, including any metastases of the tumor, may originate from glial cells, astrocytes, oligodendrocyte progenitor cells or neural stem cells.
  • Tumors of epithelial origin include any tumors originated from epithelial tissue in any of several sites, such as without limitation breast, lung, bladder, cervix, intestine, colon, skin, head and neck (including lips, oral cavity, salivary glands, nasal cavity, nasopharynx, paranasal sinuses, pharynx, throat, larynx, and associated structures), esophagus, thyroid, kidney, liver, pancreas, penis, testes, prostate, vagina, or anus.
  • sites such as without limitation breast, lung, bladder, cervix, intestine, colon, skin, head and neck (including lips, oral cavity, salivary glands, nasal cavity, nasopharynx, paranasal sinuses, pharynx, throat, larynx, and associated structures), esophagus, thyroid, kidney, liver, pancreas, penis, testes, prostate, vagina, or anus.
  • the term“cancer” refers to a malignant neoplasm characterized by deregulated or unregulated cell growth.
  • the term“cancer” includes primary malignant cells or tumors (e.g., those whose cells have not migrated to sites in the subject’s body other than the site of the original malignancy or tumor) and secondary malignant cells or tumors (e.g., those arising from metastasis, the migration of malignant cells or tumor cells to secondary sites that are different from the site of the original tumor).
  • the term“metastatic” or“metastasis” generally refers to the spread of a cancer from one organ or tissue to another non-adjacent organ or tissue. The occurrence of the neoplastic disease in the other non-adjacent organ or tissue is referred to as metastasis.
  • cancer examples include but are not limited to carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More particular examples of such cancers include without limitation: squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung and large cell carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioma, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulvar cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as CNS cancer,
  • cancers or malignancies include, but are not limited to: Acute Childhood Lymphoblastic Leukemia, Acute Lymphoblastic Leukemia, Acute Lymphocytic Leukemia, Acute Myeloid Leukemia, Adrenocortical Carcinoma, Adult (Primary) Hepatocellular Cancer, Adult (Primary) Liver Cancer, Adult Acute Lymphocytic Leukemia, Adult Acute Myeloid Leukemia, Adult Hodgkin's Disease, Adult Hodgkin's Lymphoma, Adult Lymphocytic Leukemia, Adult Non- Hodgkin's Lymphoma, Adult Primary Liver Cancer, Adult Soft Tissue Sarcoma, AIDS-Related Lymphoma, AIDS-Related Malignancies, Anal Cancer, Astrocytoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Brain Stem Glioma, Brain Tumors, Breast Cancer, Cancer of the Renal Pelvis and Urethra, Central Nervous
  • the disease may be myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML).
  • MDS myelodysplastic syndrome
  • AML acute myeloid leukemia
  • one or more agents as taught herein may be formulated into and administered as pharmaceutical formulations or compositions.
  • Such pharmaceutical formulations or compositions may be comprised in a kit of parts.
  • pharmaceutically acceptable as used herein is consistent with the art and means compatible with the other ingredients of a pharmaceutical composition and not deleterious to the recipient thereof.
  • “carrier” or“excipient” includes any and all solvents, diluents, buffers (such as, e.g., neutral buffered saline or phosphate buffered saline), solubilisers, colloids, dispersion media, vehicles, fillers, chelating agents (such as, e.g., EDTA or glutathione), amino acids (such as, e.g., glycine), proteins, disintegrants, binders, lubricants, wetting agents, emulsifiers, sweeteners, colorants, flavourings, aromatisers, thickeners, agents for achieving a depot effect, coatings, antifungal agents, preservatives, antioxidants, tonicity controlling agents, absorption delaying agents, and the like.
  • buffers such as, e.g., neutral buffered saline or phosphate buffered saline
  • solubilisers such as, e.g., EDTA or
  • Illustrative, non-limiting carriers for use in formulating the pharmaceutical compositions include, for example, oil-in-water or water-in-oil emulsions, aqueous compositions with or without inclusion of organic co-solvents suitable for intravenous (IV) use, liposomes or surfactant- containing vesicles, microspheres, microbeads and microsomes, powders, tablets, capsules, suppositories, aqueous suspensions, aerosols, and other carriers apparent to one of ordinary skill in the art.
  • compositions as intended herein may be formulated for essentially any route of administration, such as without limitation, oral administration (such as, e.g., oral ingestion or inhalation), intranasal administration (such as, e.g., intranasal inhalation or intranasal mucosal application), parenteral administration (such as, e.g., subcutaneous, intravenous, intramuscular, intraperitoneal or intrastemal injection or infusion), transdermal or transmucosal (such as, e.g., oral, sublingual, intranasal) administration, topical administration, rectal, vaginal or intra-tracheal instillation, and the like.
  • oral administration such as, e.g., oral ingestion or inhalation
  • intranasal administration such as, e.g., intranasal inhalation or intranasal mucosal application
  • parenteral administration such as, e.g., subcutaneous, intravenous, intramus
  • compositions may be formulated in the form of pills, tablets, lacquered tablets, coated (e.g., sugar-coated) tablets, granules, hard and soft gelatin capsules, aqueous, alcoholic or oily solutions, syrups, emulsions or suspensions.
  • preparation of oral dosage forms may be is suitably accomplished by uniformly and intimately blending together a suitable amount of the active compound in the form of a powder, optionally also including finely divided one or more solid carrier, and formulating the blend in a pill, tablet or a capsule.
  • Exemplary but non-limiting solid carriers include calcium phosphate, magnesium stearate, talc, sugars (such as, e.g., glucose, mannose, lactose or sucrose), sugar alcohols (such as, e.g., mannitol), dextrin, starch, gelatin, cellulose, polyvinylpyrrolidine, low melting waxes and ion exchange resins.
  • Compressed tablets containing the pharmaceutical composition can be prepared by uniformly and intimately mixing the active ingredient with a solid carrier such as described above to provide a mixture having the necessary compression properties, and then compacting the mixture in a suitable machine to the shape and size desired.
  • Moulded tablets maybe made by moulding in a suitable machine, a mixture of powdered compound moistened with an inert liquid diluent.
  • Suitable carriers for soft gelatin capsules and suppositories are, for example, fats, waxes, semisolid and liquid polyols, natural or hardened oils, etc.
  • compositions may be formulated with illustrative carriers, such as, e.g., as in solution with saline, polyethylene glycol or glycols, DPPC, methylcellulose, or in mixture with powdered dispersing agents, further employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilising or dispersing agents known in the art.
  • illustrative carriers such as, e.g., as in solution with saline, polyethylene glycol or glycols, DPPC, methylcellulose, or in mixture with powdered dispersing agents, further employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilising or dispersing agents known in the art.
  • Suitable pharmaceutical formulations for administration in the form of aerosols or sprays are, for example, solutions, suspensions or emulsions of the agents as taught herein or their physiologically tolerable salts in a pharmaceutically acceptable solvent, such as ethanol or water, or a mixture of such solvents.
  • a pharmaceutically acceptable solvent such as ethanol or water, or a mixture of such solvents.
  • the formulation can also additionally contain other pharmaceutical auxiliaries such as surfactants, emulsifiers and stabilizers as well as a propellant.
  • delivery may be by use of a single-use delivery device, a mist nebuliser, a breath-activated powder inhaler, an aerosol metered-dose inhaler (MDI) or any other of the numerous nebuliser delivery devices available in the art.
  • MDI aerosol metered-dose inhaler
  • mist tents or direct administration through endotracheal tubes may also be used.
  • Examples of carriers for administration via mucosal surfaces depend upon the particular route, e.g., oral, sublingual, intranasal, etc.
  • illustrative examples include pharmaceutical grades of mannitol, starch, lactose, magnesium stearate, sodium saccharide, cellulose, magnesium carbonate and the like, with mannitol being preferred.
  • illustrative examples include polyethylene glycol, phospholipids, glycols and glycolipids, sucrose, and/or methylcellulose, powder suspensions with or without bulking agents such as lactose and preservatives such as benzalkonium chloride, EDTA.
  • the phospholipid 1,2 dipalmitoyl-sn-glycero-3-phosphocholine is used as an isotonic aqueous carrier at about 0.01-0.2% for intranasal administration of the compound of the subject invention at a concentration of about 0.1 to 3.0 mg/ml.
  • compositions may be advantageously formulated as solutions, suspensions or emulsions with suitable solvents, diluents, solubilisers or emulsifiers, etc.
  • suitable solvents are, without limitation, water, physiological saline solution or alcohols, e.g. ethanol, propanol, glycerol, in addition also sugar solutions such as glucose, invert sugar, sucrose or mannitol solutions, or alternatively mixtures of the various solvents mentioned.
  • the injectable solutions or suspensions may be formulated according to known art, using suitable non-toxic, parenterally-acceptable diluents or solvents, such as mannitol, l,3-butanediol, water, Ringer's solution or isotonic sodium chloride solution, or suitable dispersing or wetting and suspending agents, such as sterile, bland, fixed oils, including synthetic mono- or diglycerides, and fatty acids, including oleic acid.
  • suitable non-toxic, parenterally-acceptable diluents or solvents such as mannitol, l,3-butanediol, water, Ringer's solution or isotonic sodium chloride solution, or suitable dispersing or wetting and suspending agents, such as sterile, bland, fixed oils, including synthetic mono- or diglycerides, and fatty acids, including oleic acid.
  • suitable dispersing or wetting and suspending agents such as sterile, bland, fixed oils, including synthetic
  • a carrier for intravenous use includes a mixture of 10% USP ethanol, 40% USP propylene glycol or polyethylene glycol 600 and the balance USP Water for Injection (WFI).
  • Other illustrative carriers for intravenous use include 10% USP ethanol and USP WFI; 0.01-0.1% triethanolamine in USP WFI; or 0.01-0.2% dipalmitoyl diphosphatidylcholine in USP WFI; and 1-10% squalene or parenteral vegetable oil-in-water emulsion.
  • Illustrative examples of carriers for subcutaneous or intramuscular use include phosphate buffered saline (PBS) solution, 5% dextrose in WFI and 0.01- 0.1% triethanolamine in 5% dextrose or 0.9% sodium chloride in USP WFI, or a 1 to 2 or 1 to 4 mixture of 10% USP ethanol, 40% propylene glycol and the balance an acceptable isotonic solution such as 5% dextrose or 0.9% sodium chloride; or 0.01-0.2% dipalmitoyl diphosphatidylcholine in USP WFI and 1 to 10% squalene or parenteral vegetable oil- in- water emulsions.
  • PBS phosphate buffered saline
  • aqueous formulations may comprise one or more surfactants.
  • the composition can be in the form of a micellar dispersion comprising at least one suitable surfactant, e.g., a phospholipid surfactant.
  • phospholipids include diacyl phosphatidyl glycerols, such as dimyristoyl phosphatidyl glycerol (DPMG), dipalmitoyl phosphatidyl glycerol (DPPG), and distearoyl phosphatidyl glycerol (DSPG), diacyl phosphatidyl cholines, such as dimyristoyl phosphatidylcholine (DPMC), dipalmitoyl phosphatidylcholine (DPPC), and distearoyl phosphatidylcholine (DSPC); diacyl phosphatidic acids, such as dimyristoyl phosphatidic acid (DPMA), dipahnitoyl phosphatidic acid (DPPA), and distearoyl phosphatidic acid (DSPA); and diacyl phosphatidyl ethanolamines such as dimyristoyl phosphatidyl ethanolamine (DPME), dipalmitoyl phosphatid
  • a surfactant: active substance molar ratio in an aqueous formulation will be from about 10:1 to about 1 :10, more typically from about 5:1 to about 1 :5, however any effective amount of surfactant may be used in an aqueous formulation to best suit the specific objectives of interest.
  • these formulations When rectally administered in the form of suppositories, these formulations may be prepared by mixing the compounds according to the invention with a suitable non-irritating excipient, such as cocoa butter, synthetic glyceride esters or polyethylene glycols, which are solid at ordinary temperatures, but liquidify and/or dissolve in the rectal cavity to release the drug.
  • a suitable non-irritating excipient such as cocoa butter, synthetic glyceride esters or polyethylene glycols, which are solid at ordinary temperatures, but liquidify and/or dissolve in the rectal cavity to release the drug.
  • Suitable carriers for microcapsules, implants or rods are, for example, copolymers of glycolic acid and lactic acid.
  • Suitable carriers for microcapsules, implants or rods are, for example, copolymers of glycolic acid and lactic acid.
  • One skilled in this art will recognize that the above description is illustrative rather than exhaustive. Indeed, many additional formulations techniques and pharmaceutically-acceptable excipients and carrier solutions are well-known to those skilled in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens.
  • the dosage or amount of the present active agents used, optionally in combination with one or more other active compound to be administered depends on the individual case and is, as is customary, to be adapted to the individual circumstances to achieve an optimum effect. Thus, it depends on the nature and the severity of the disorder to be treated, and also on the sex, age, body weight, general health, diet, mode and time of administration, and individual responsiveness of the human or animal to be treated, on the route of administration, efficacy, metabolic stability and duration of action of the compounds used, on whether the therapy is acute or chronic or prophylactic, or on whether other active compounds are administered in addition to the agent(s) as taught herein.
  • a typical daily dosage of an agent as disclosed herein, or combinations of two or more such agents might range from about 1 pg/kg to 1 g/kg of body weight or more, depending on the factors mentioned above.
  • a daily dosage of the agent(s) may range from about 1 mg/kg to 1 g/kg of body weight.
  • a preferred dosage of the agent(s) may be in the range from about 10.0 mg/kg to about 500 mg/kg of body weight.
  • one or more doses of about 10.0 mg/kg, 20.0 mg/kg, 50.0 mg/kg, 100 mg/kg, 200 mg/kg, 300 mg/kg, 400 mg/kg, or 500 mg/kg (or any combination thereof) may be administered to the patient.
  • Such doses may be administered intermittently, e.g., every day, every week or every two or three weeks.
  • the agent(s) may be administered daily during the treatment. In certain embodiments, the agent(s) may be administered at least once a day during the treatment, for example the agent(s) may be administered at least twice a day during the treatment, for example the agent(s) may be administered at least three times a day during the treatment. In certain embodiments, the agent(s) may be administered continuously during the treatment for instance in an aqueous drinking solution.
  • the agent(s) or pharmaceutical formulation as taught herein may be used alone or in combination with one or more active compounds that are suitable in the treatment of diseases as disclosed herein, such as neoplastic diseases, such as cancer (i.e., combination therapy).
  • the latter can be administered before, after, or simultaneously with the administration of the agent(s) or pharmaceutical formulation as taught herein.
  • Non-limiting examples of anti-cancer therapies include surgery, radiotherapy, chemotherapy, biological therapy, and combinations thereof, as generally known in the art.
  • SRSF2 is a reader capable of recognising the mr5C modification also allows the detection and/or quantification of mr5C on RNA or RNA comprising mr5C, using a SRSF2 reagent as a‘detection tool’.
  • an aspect provides an in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
  • RNA molecule comprising one or more mr5C, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof, the binding of the SRSF2 and RNA components and the methods for detection and/or quantification thereof, apply mutatis mutandis to this aspects.
  • sample or“biological sample” as used throughout this specification include any biological specimen obtained (isolated, removed) from a subject.
  • Samples may include without limitation organ tissue (e.g., primary or metastatic tumor tissue), whole blood, plasma, serum, whole blood cells, red blood cells, white blood cells (e.g., peripheral blood mononuclear cells), saliva, urine, stool (feces), tears, sweat, sebum, nipple aspirate, ductal lavage, tumor exudates, synovial fluid, cerebrospinal fluid, lymph, fine needle aspirate, amniotic fluid, any other bodily fluid, exudate or secretory fluid, cell lysates, cellular secretion products, inflammation fluid, semen and vaginal secretions.
  • organ tissue e.g., primary or metastatic tumor tissue
  • whole blood plasma
  • serum whole blood cells
  • red blood cells e.g., white blood mononuclear cells
  • saliva urine
  • stool feces
  • tears sweat
  • a sample may be readily obtainable by non-invasive or minimally invasive methods, such as blood collection (‘liquid biopsy’), urine collection, feces collection, tissue (e.g., tumor tissue) biopsy or fine-needle aspiration, allowing the provision / removal / isolation of the sample from a subject.
  • tissue e.g., tumor tissue
  • tissue as used herein encompasses all types of cells of the body including cells of organs but also including blood and other body fluids recited above.
  • the tissue may be healthy or affected by pathological alterations, e.g., tumor tissue.
  • the tissue may be from a living subject or may be cadaveric tissue.
  • Particularly useful samples may be those known to comprise, or expected or predicted to comprise, or known to potentially comprise, or expected or predicted to potentially comprise cells having dysregulation of RNA mr5C methylation, or tumor or cancer cells.
  • Any suitable weight or volume of a sample may be removed from a subject for analysis.
  • a liquid sample may have a volume between 1 ml and 20 ml, such as 5 ml, 7.5 ml, 10 ml, 15 ml or 20 ml.
  • a solid sample may have a weight of between 1 g and 20 g, such as 5 g, 7.5 g, 10 g, 15 g or 20 g.
  • the biological sample may be any sample in which the quantity, activity and/or methylation level of a relevant marker can be determined.
  • the biological sample is a neoplastic tissue sample, such as a tumor sample, e.g., a primary or metastatic tumor sample.
  • the biological sample may also be derived from a biological fluid or bodily fluid, for example, whole blood, blood, urine, lymph fluid, serum, plasma, nipple aspirate, ductal fluid, and tumor exudate ft has been shown in the literature that cancer or tumor cells often release genomic DNA in circulating or other bodily fluids. Since said genomic DNA has the same methylation profile of the DNA inside the tumor or cancer cell, said methylation profile can be detected in the circulating or other bodily fluid sample.
  • the sample is a bodily fluid comprising neoplastic cells.
  • SRSF2 is a reader capable of recognising the mr5C modification also allows to predict or evaluate whether a given mutation in SRSF2 may be causative of or may contribute to a neoplastic disease.
  • SRSF2 mutation may be a mutation discovered or identified in a subject having a neoplastic disease.
  • SRSF2 mutation may be a germline mutation discovered or identified in a subject having a neoplastic disease.
  • such SRSF2 mutation may be a somatic mutation discovered or identified in a subject having a neoplastic disease, particularly in one or more neoplastic cells of said subject.
  • This prediction or evaluation is based on the premise that mutations which affect the binding of SRSF2 to mr5C on RNA are likely or probable to be causative of or contributory to neoplastic diseases, such as likely or probable to facilitate the emergence and/or maintenance of the neoplastic phenotype of cells.
  • an aspect provides an in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
  • SRSF2 is a reader capable of recognising the mr5C modification, and that mutations which affect the binding of SRSF2 to mr5C on RNA may cause or contribute to neoplastic diseases, also allows to diagnose neoplastic diseases in subjects.
  • an aspect provides a method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
  • diagnosis are commonplace and well-understood in medical practice.
  • diagnosis generally refers to the process or act of recognizing, deciding on or concluding on a disease or condition in a subject on the basis of symptoms and signs and/or from results of various diagnostic procedures (such as, for example, from knowing the presence, absence and/or quantity of one or more biomarkers characteristic of the diagnosed disease or condition).
  • RNA ribonucleic acid
  • mr5C 5-methylcytosines
  • said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant binds to said one or more mr5C on the RNA molecule, with a test agent; and determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
  • test agent identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
  • Statement 2 The method according to Statement 1, wherein the SRSF2-modulating agent can reduce the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
  • Statement 3 The method according to Statement 1 or 2, further comprising determining whether the SRSF2-modulating agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
  • Statement 4 The method according to any one of Statements 1 to 3, further comprising determining whether the SRSF2-modulating agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
  • Statement 6 The method according to any one of Statements 1 to 5, further comprising determining whether the SRSF2-modulating agent displays anti-neoplastic property, such as anti-cancer property.
  • Statement 7 The method according to any one of Statements 1 to 6, wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant and/or the RNA molecule is of human origin.
  • Statement 8 The method according to any one of Statements 1 to 7, wherein the amino acid sequence of said SRSF2 polypeptide is as set forth in GenBank accession no. NP 001182356.1.
  • Statement 10 The method according to any one of Statements 1 to 9, wherein the method is performed in a cell- free system or in a cell lysate or in isolated or cultured cells or in an isolated or cultured tissue.
  • test agent is selected from the group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof.
  • Statement 12 The method according to Statement 11, wherein the chemical substance is an organic molecule, preferably a small organic molecule, or wherein the nucleic acid is an oligonucleotide.
  • An agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
  • Statement 15 The agent for use according to Statement 14, wherein the agent is capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to the one or more mr5C on the RNA molecule.
  • Statement 16 The agent for use according to Statement 14 or 15, wherein the agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant.
  • Statement 17 The agent for use according to any one of Statements 14 to 16, wherein the agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
  • Statement 18 The agent for use according to any one of Statements 14 to 17, wherein said RNA molecule is susceptible to splicing and said agent can alter the splicing of said RNA molecule.
  • Statement 19 The agent for use according to any one of Statements 14 to 18, wherein the dysregulation of SRSF2 expression and/or activity is due to a mutation in SRSF2.
  • Statement 20 The agent for use according to any one of Statements 14 to 19, wherein the disease is a neoplastic disease, such as cancer.
  • Statement 21 The agent for use according to any one of Statements 14 to 20, wherein the disease is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML).
  • MDS myelodysplastic syndrome
  • AML acute myeloid leukemia
  • Statement 22 The agent for use according to any one of Statements 14 to 21 in a human subject, wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of human origin.
  • Statement 24 The agent for use according to any one or Statements 14 to 23, wherein the agent is selected from a group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof.
  • Statement 25 The agent for use according to Statement 24, wherein the chemical substance is an organic molecule, preferably a small organic molecule, or wherein the nucleic acid is an oligonucleotide.
  • Statement 26 The agent for use according to Statement 25, wherein said oligonucleotide is capable of specifically hybridising with said RNA molecule and comprises one or more mr5C.
  • a method for diagnosing a neoplastic disease in a subject comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
  • RNA affinity approach involving biotinylated-RNA pull-down assay schematically illustrated in Fig. 1, using methylated and control versions of RNA baits followed by mass spectrometry (MS) or Western blotting (WB), was used to identify novel mr5C-binding proteins.
  • MS mass spectrometry
  • WB Western blotting
  • the 5’-GACU-3’ consensus sequence-containing A and mr6A probes have been reported to be bound by the YTH family proteins (as seen for YTHDF2).
  • the cytosine (C), 5-methylcytosine (mr5C) and 5- hydroxymethylcytosine (hmr5C) probes contain a 5’-CCGG-3’ sequence corresponding to the reported SSNG consensus sequence (where S is G or C, N is A, C, G or U).
  • 5’-SSNG-3’ was reported as RNA-binding consensus sequence for SRSF2 and was implicated in disease where altered binding of targets was observed when SRSF2 was mutated (see Daubner et al. EMBO J. 2012, vol. 31(1), 162-74; Pandit et al. Mol Cell. 2013, vol. 50(2), 223-235; Kim et al. Cancer Cell. 2015, vol. 27(5), 617-630; Zhang et al. Proc Natl Acad Sci USA. 2015, vol. 112(34), E4726- E4734).
  • a probe (A) (SEQ ID NO: 1):
  • mr6A probe (m6A) (SEQ ID NO: 2):
  • C probe (C) (SEQ ID NO: 3):
  • mr5C probe (mC) (SEQ ID NO: 4):
  • hmr5C probe (hmC) (SEQ ID NO: 5):
  • the 5’-GACU-3’ consensus sequence in A and mr6A probes and the 5’-CCGG-3’ sequence in the C, mr5C and hmr5C probes are underlined.
  • RNA affinity chromatography approach involving biotinylated-RNA pull-down assay followed by MS identified SRSF2 as a specific mr5C-reader (Fig. 2).
  • Affinity pulldown assays of biotinylated RNA for detection of protein-RNA complexes are described inter alia in Panda et al. (Bio Protoc. 2016, vol. 6(24)).
  • source of protein was endogenous SRSF2 from Hela cell extract. lOxlO 6 cells were used per pulldown condition.
  • the biotinylated- RNA pulldown assay protocol used in the present examples was as follows: 1.
  • Hela cells were harvested at 70-80% confluence, washed with PBS and lysed in (500 ul/lOxlO 6 cells) lysis buffer (lOmM NaCl, 2mM EDTA, 0.5% Triton X-100, 0.5mM DTT, lOmM Tris-HCl, pH7.5) containing complete protease inhibitor cocktail (Roche) and phosphatase inhibitor cocktail 2 (Sigma- Aldrich). 2.
  • Lysates were separated from insoluble cell debris by centrifugation (l0,000g for 15 min at 4 °C) and pre-cleared for 1 h at 4 °C by incubation with 20 ul streptavidin-conjugated agarose beads (Sigma- Aldrich) in (+500ul/cond) binding buffer (l50mM KC1, l.5mM MgCf, 0.05% (v/v) NP- 40, 0.5mM DTT, lOmMTris-HCl pH7.5). Final volume: lml/cond. 3.
  • Biotinylated RNA baits (2ug) were incubated with pre-cleared cell lysates supplemented with 0.4 units/ul RNasin (Promega) for 30 min at room temperature followed by lh30 incubation at 4°C. The mixture was then added to streptavidin-conjugated agarose beads pre-blocked (lh30) with BSA (1%) and tRNA (50ug/ml) fol h at 4 °C. 4. RNA-protein complexes were pulled-down and washed extensively (4-5x with Binding buffer).
  • RNA affinity approach involving biotinylated-RNA pull-down assay followed by WB confirmed SRSF2 as a specific mr5C-reader (Fig. 4).
  • samples were separated on 15% (w/v) polyacrylamide Bis-Tris gels (Invitrogen) and transferred onto nitrocellulose membrane.
  • Membrane was blocked in 5% milk, 0.05% Tween-20 in PBS for 1 h, and then incubated overnight at 4 °C with anti-YTHDF2 polyclonal antibody (Abeam, ab 170118 ) diluted 1 :500 or anti-SRSF2 monoclonal antibody (Abeam, ab2049l6) diluted 1 :2000 in 5% milk.
  • Panel A of Fig. 4 shows technical efficiency validation of our approach through Western blotting of known YTHDF2 binding to the mr6A bait versus the unmethylated (A) bait.
  • RNA affinity approach involving biotinylated-RNA pull-down assay followed by WB confirmed SRSF2 as a specific and direct mr5C-reader (Fig. 5).
  • Myc-tagged SRSF2 was overexpressed in Hela cells.
  • Vector used was pcDNA3.l-SC35-cMyc purchased from Addgene, plasmid #44721, Myc tag was C- terminal on backbone. Plasmid DNA was transfected in Hela cells using Lipofectamine 2000 transfection reagent from Invitrogen by Life technologies using provider’s protocol.
  • Anti-cMyc monoclonal antibody from Santa Cruz (sc-40) was used at 1 :1000 dilution in 5% milk PBS-T solution.
  • Panels B and C which show Biotin-RNA pulldown followed by WB of recombinant GST-tagged SRSF2 (commercial GST-tagged (N-term) SRSF2 was purchased from MyBioSource.com catalog # MBS961916; lug of GST-SRSF2 was loaded per biotinylated-RNA pulldown condition; anti-GST antibody was purchased from Abeam) or His-tagged SRSF2 (Ffis- tagged SRSF2 recombinant protein was produced and purified in-house.
  • Vector pET-30a(+)-His- SRSF2., His tag N-term.
  • BL21 E.coli bacteria were transformed with plasmid using heat shock technique, grown in LB with antibiotic overnight and then induced for protein production using 1PTG during a 4h incubation. Bacteria pellet was resuspended in a TBS/triton/lOmM lmidazole/anti-proteases solution for sonication. The protein containing supernatant discarded from cellular debris by centrifugation was exposed to Ni-NTA beads and incubated for lhour.
  • Protein- bound beads were then washed 3x with TBS/Triton/40 mM Imidazole prior to TBS/l50mM lmidazole elution of recombinant His-tagged SRSF2 proteins.
  • Equiloading Western blot was performed.
  • the NanoBRETTM platform uses NanoLuc® Luciferase as a BRET energy donor, and HaloTag® protein labelled with the NanoBRETTM 618 fluorophore as the energy acceptor to measure the interaction of specific protein pairs.
  • the NanoBRETTM technology enables sensitive, reproducible detection of protein interactions (PP1) in the natural cellular environment.
  • PP1 protein interactions
  • the use of full-length proteins expressed at low levels enables PPI monitoring and screening studies that reflect true cellular physiology.
  • Fig. 6 schematically illustrates the operation of the NanoBRETTM platform for detecting PPL
  • NanoLuc®-SRSF2 protein was expressed in mammalian cells, which were subsequently permeabilised with digitonin and exposed to Alexa- 594-labelled bait RNA.
  • NanoBRET signal was measured only when there was a direct protein- RNA interaction.
  • Fig. 7 schematically illustrates the operation of the modified NanoBRETTM platform for detecting protein-RNA interactions.
  • the NanoBRETTM-based proteimRNA interaction assay showed a higher affinity of SRSF2 for the methylated tracer RNA (mrC) in comparison with the unmethylated version (C) (panel A).
  • the assay shown in panel B used corresponding‘cold’ RNA oligos and demonstrated the specificity of the detected NanoBRET signal.
  • the detected NanoBRETTM signal has dropped to half of the original detected signal in absence of cold RNA.
  • Panel C shows NanoBRETTM competition assays with cold RNA at diverse concentrations and demonstrated the specificity of the detected signal and the higher affinity of SRSF2 for the methylated RNA.

Abstract

The application discloses serine and arginine rich splicing factor 2 (SRSF2) as an RNA epigenetic factor, more particularly as a reader capable of recognising 5-methylcytosine (mr5C) on RNA, such as mRNA. Various aspects make use of the interaction between SRSF2 and mr5C on RNA for the purposes of inter alia SRSF2 detection, phenotypic characterisation of SRSF2 mutations, discovery of SRSF2 modulating agents, and diagnosis or treatment of SRSF2-related diseases, such as neoplastic diseases.

Description

SRSF2 AS RNA EPIGENETIC FACTOR
FIELD
The invention relates to biomarkers and targets for diseases and conditions in subjects, in particular for neoplastic diseases, and to related methods, uses, kits and therapeutic agents.
BACKGROUND
With an estimated 23.6 million new cases each year by 2030, cancer is clearly one of the main human, socio-economic, medical and scientific challenges at the beginning of the 21 st century. In Europe, there are 2.9 million new cases of cancer per year that regrettably include 1.7 million deaths. Cancer continues to be the primary cause of death in men and in women under 65 years of age.
RNA modifications, more than 100 kinds of which have been reported in different RNA species, are involved in diverse biological and physiological processes. Post-transcriptional RNA modifications or“RNA epigenetics” are becoming increasingly recognised as the third pillar of epigenetics, in addition to histone modifications and DNA modifications.
Enzymes involved in methylation of adenosine in RNA have been shown to be elevated in tumours and to be associated with increased cancer risk, including breast cancers. N6-Methyadenosine (m6A), the most abundant modification on higher eukaryote mRNAs, is recognized by YTHDF2 (YTH domain family 2), a specific m6A reader implicated in mRNA degradation. Recently, the association between YTHDF2, m6A deregulation and malignancy of hepatocellular carcinoma (HCC), has been reported. Besides the well-characterised m6A RNA modification, methylation and hydroxymethylation of cytosine on RNA have recently been reported.
RNA epigenetic events are dynamic and reversible, providing attractive targets for the development of new anti-cancer therapies. For instance, agents capable of modulating disease-associated RNA epigenetic factors, such as RNA readers, could be employed as therapeutic agents in the presence of mutated or otherwise transformed RNA epigenetic factors or altered epitranscriptomic landscape.
Recurrent somatic mutations in genes encoding splicing factors have been identified in a substantial proportion of patients with myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Somatic mutations in genes encoding components of the spliceosome have been identified in about 60% of patients with MDS. The incidence of MDS approximates 3 to 4 cases per 100,000 population per year, with 30 cases per 100,000 population per year in patients more than 70 years old. It is estimated that approximately 10,000 to 15,000 new cases are diagnosed annually in the United States. Data analysis on MDS from 2001 through 2008 suggested that the observed 3-year survival rate was of 42% and the 5-year survival rate of 29%. Serine and arginine rich splicing factor 2 (SRSF2) has been implicated in RNA-binding and mRNA precursor splicing. Mutations in SRSF2 have been reported to lead to dysregulated splicing events of target transcripts, including some transcripts with relevance to diseases. SRSF2 mutations occur in 20-30% of MDS and about 50% of chronic myelomonocytic leukaemia (CMML) patients.
More generally, recent studies have highlighted the abundant altered splicing patterns of key cancer-associated genes with enriched mutations in genes encoding spliceosomal proteins in many different cancer types. Consequently, the spliceosome has emerged as a novel therapeutic target in diseases, in particular neoplastic diseases. However, currently marketed anti-tumour drugs which manipulate the altered splicing machinery, such as TG003 (( 1 Z)- 1 -(3-Ethyl-5-mcthoxy-2(3//)- benzothiazolylidene)-2-propanone), mainly act by inhibiting kinase-mediated phosphorylation of the target splicing factors. Such kinase inhibitors tend to have pleiotropic actions which detracts from the drugs’ specificity and increases the risk of unwanted side effects.
The importance of devising novel and/or improved manners to detect, characterise, diagnose and/or combat diseases, such as neoplastic diseases, such as cancer, is self-evident.
SUMMARY
The present inventors have unexpectedly realised and demonstrated that serine and arginine rich splicing factor 2 (SRSF2) is capable of specific binding to 5-methylcytosine (mr5C) on RNA, especially mRNA. Hence, the present inventors identified SRSF2 as an RNA epigenetic factor, a reader, capable of recognising the mr5C modification. This realisation opens new avenues for exploiting the interaction of SRSF2 with mr5C on RNA inter alia for SRSF2 detection, mr5C- containing RNA detection, phenotypic characterisation of SRSF2 mutations, drug discovery, and diagnosis or treatment of diseases, such as neoplastic diseases.
For example, screening of SRSF2 mutations for their ability to alter SRSF2’s mr5C reader ability and splicing factor function can reveal mutations which cause or contribute to diseases, such as neoplastic diseases, and can be employed to identify diseased subjects carrying such mutations. Specifically targeting SRSF2’s mr5C reader function and splicing events dependent thereon can provide novel therapeutic avenues in diseases, such as neoplastic diseases. By means of an example, certain subjects may be heterozygous for mutated SRSF2 which binds with altered (such as increased) specificity or strength to RNA sequence elements in mRNAs with dysregulated splicing lnterfering with such binding of the mutated SRSF2 may restore normal SRSF2 function owing to SRSF2 encoded by the wild-type allele and/or owing to the activity of other SR family members with redundant functions. Further, where dysregulated mr5C landscape alters the functioning of SRSF2's, oligonucleotide therapy with mr5C-enriched oligonucleotides designed to hybridise to SRSF2 targets could be used to direct SRSF2 binding to mRNAs with altered mr5C landscape, thereby also avoiding pathologic splicing events.
Accordingly, an aspect of the invention relates to an in vitro method for identifying a serine and arginine rich splicing factor 2 (SRSF2)-modulating agent, said method comprising:
contacting a SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof and a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C), wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant binds to said one or more mr5C on the RNA molecule, with a test agent; and
determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
A further aspect relates to an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
Another aspect relates to an in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
A further aspect relates to an in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
(a) measuring the binding of SRSF2 polypeptide or biologically active fragment thereof comprising said mutation to an RNA molecule comprising one or more mr5C;
(b) determining that the mutation causes or contributes to the neoplastic disease when the binding as measured in (a) differs from binding of an SRSF2 polypeptide or a biologically active fragment thereof not comprising said mutation to the RNA molecule. Another aspect relates to a method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
These and further aspects and preferred embodiments of the invention are described in the following sections and in the appended claims. The subject-matter of the appended claims is hereby specifically incorporated in this specification.
BRIEF DESCRIPTION OF DRAWINGS
Fig. 1 schematically illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay used to identify novel mr5C-binding proteins.
Fig. 2 illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay, followed by mass spectrometry (MS) to identify novel mr5C-binding proteins.
Fig. 3 illustrates a control RNA affinity approach involving biotinylated-RNA pull-down assay for known mr6A-readers of YTH family proteins.
Fig. 4 illustrates an RNA affinity approach involving biotinylated-RNA pull-down assay, followed by Western blotting (WB) to validate novel mr5C-binding proteins.
Fig. 5 illustrates an RNA affinity approach involving biotinylated-labelled-RNA pull-down assay, followed by WB to validate SRSF2 as a specific and direct mr5C-reader.
Fig. 6 schematically illustrates the operation of the NanoBRET™ platform for detecting protein- protein interactions (PPI). The illustration depicts energy transfer from a NanoLuc®-Protein A fusion (energy donor) to a fluorescently labelled HaloTag®-Protein B fusion (energy acceptor) upon interaction of Protein A and Protein B.
Fig. 7 schematically illustrates the operation of the modified NanoBRET™ platform for detecting protein-RNA interactions.
Fig. 8 illustrates validation of SRSF2 as a specific and direct mr5C-reader using the modified NanoBRET™ platform for detecting protein-RNA interactions in cellulo.
Fig. 9 illustrates the frequency of non-synonymous single nucleotide variations (nsSNV) in SRSF2 in various types of cancer.
Fig. 10 illustrates the frequency of nsSNV in SRSF2 across all cancers by SRSF2 amino acid position. DESCRIPTION OF EMBODIMENTS
As used herein, the singular forms“a”,“an”, and“the” include both singular and plural referents unless the context clearly dictates otherwise.
The terms“comprising”,“comprises” and“comprised of’ as used herein are synonymous with “including”,“includes” or“containing”,“contains”, and are inclusive or open-ended and do not exclude additional, non-recited members, elements or method steps. The terms also encompass “consisting of’ and“consisting essentially of’, which enjoy well-established meanings in patent terminology.
The recitation of numerical ranges by endpoints includes all numbers and fractions subsumed within the respective ranges, as well as the recited endpoints.
The terms“about” or“approximately” as used herein when referring to a measurable value such as a parameter, an amount, a temporal duration, and the like, are meant to encompass variations of and from the specified value, such as variations of +/-l0% or less, preferably +/- 5% or less, more preferably +1-1% or less, and still more preferably +/-0.l% or less of and from the specified value, insofar such variations are appropriate to perform in the disclosed invention. It is to be understood that the value to which the modifier“about” refers is itself also specifically, and preferably, disclosed.
Whereas the terms“one or more” or“at least one”, such as one or more members or at least one member of a group of members, is clear per se, by means of further exemplification, the term encompasses inter alia a reference to any one of said members, or to any two or more of said members, such as, e.g., any >3, >4, >5, >6 or >7 etc. of said members, and up to all said members. In another example,“one or more” or“at least one” may refer to 1, 2, 3, 4, 5, 6, 7 or more.
The discussion of the background to the invention herein is included to explain the context of the invention. This is not to be taken as an admission that any of the material referred to was published, known, or part of the common general knowledge in any country as of the priority date of any of the claims.
Throughout this disclosure, various publications, patents and published patent specifications are referenced by an identifying citation. All documents cited in the present specification are hereby incorporated by reference in their entirety. In particular, the teachings or sections of such documents herein specifically referred to are incorporated by reference.
Unless otherwise defined, all terms used in disclosing the invention, including technical and scientific terms, have the meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. By means of further guidance, term definitions are included to better appreciate the teaching of the invention. When specific terms are defined in connection with a particular aspect of the invention or a particular embodiment of the invention, such connotation is meant to apply throughout this specification, i.e., also in the context of other aspects or embodiments of the invention, unless otherwise defined.
In the following passages, different aspects or embodiments of the invention are defined in more detail. Each aspect or embodiment so defined may be combined with any other aspect(s) or embodiment(s) unless clearly indicated to the contrary. In particular, any feature indicated as being preferred or advantageous may be combined with any other feature or features indicated as being preferred or advantageous.
Reference throughout this specification to“one embodiment”,“an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, appearances of the phrases“in one embodiment” or“in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment, but may. Furthermore, the particular features, structures or characteristics may be combined in any suitable manner, as would be apparent to a person skilled in the art from this disclosure, in one or more embodiments. Furthermore, while some embodiments described herein include some but not other features included in other embodiments, combinations of features of different embodiments are meant to be within the scope of the invention, and form different embodiments, as would be understood by those in the art. For example, in the appended claims, any of the claimed embodiments can be used in any combination.
The present inventors have identified serine and arginine rich splicing factor 2 (SRSF2) as an RNA reader capable of specifically recognising 5-methylcytosine (mr5C) on RNA, and realised novel methods, uses, kits and therapeutic agents exploiting the interaction of SRSF2 with mr5C on RNA.
Accordingly, an aspect provides an in vitro method for identifying SRSF2-modulating agent, said method comprising:
contacting a SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof and a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C), wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant binds to said one or more mr5C on the RNA molecule, with a test agent; and
determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule; identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
For reasons of brevity, and unless another meaning is apparent from the context, SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof may also be referred to throughout this specification as“SRSF2 component”, and the RNA molecule comprising one or more mr5C and capable of being bound by SRSF2 may also be referred to throughout this specification as “RNA component”. These terms are used to denote said components both when separate and when bound or complexed together.
The term“in vitro” generally denotes outside, or external to, a body, e.g., an animal or human body. The term also encompasses“ex vivo”.
The reference to“serine and arginine rich splicing factor 2” or“SRSF2” denotes the SRSF2 marker, peptide, polypeptide, protein, or nucleic acid, as commonly known under said designation in the art. By means of additional guidance, SRSF2 is also known as protein PR264, splicing component 35 kDa, splicing factor SC35, SC-35, and splicing factor arginine/serine-rich 2. The terms denote SRSF2 nucleic acids, as well as SRSF2 peptides, polypeptides and proteins, as apparent from the context. The term“SRSF2 polypeptide” as used herein is synonymous with “SRSF2 protein”.
By means of an example, human SRSF2 mRNA is annotated under NCBI Genbank (http://www.ncbi.nlm.nih.gov/) accession numbers NM 003016.4 (“transcript variant 1”), NM 001195427.1 (“transcript variant 2”), or XM 017024942.1 (“predicted transcript variant XI”) Nucleotides 252 (start codon) to 917 (stop codon) of NM 003016.4 and NM 001195427.1, and nucleotides 272 to 937 of XM 017024942.1 constitute the SRSF2 coding sequence. By means of an example, nucleotides 252 to 917 of NM 003016.4 are reproduced below (SEQ ID NO: 6)
ATGAGCTACGGCCGCCCCCCTCCCGATGTGGAGGGTATGACCTCCCTCAAGGTGGACA
ACCTGACCTACCGCACCTCGCCCGACACGCTGAGGCGCGTCTTCGAGAAGTACGGGCG
CGTCGGCGACGTGTACATCCCGCGGGACCGCTACACCAAGGAGTCCCGCGGCTTCGCC
TTCGTTCGCTTTCACGACAAGCGCGACGCTGAGGACGCTATGGATGCCATGGACGGGG
CCGTGCTGGACGGCCGCGAGCTGCGGGTGCAAATGGCGCGCTACGGCCGCCCCCCGG
ACTCACACCACAGCCGCCGGGGACCGCCACCCCGCAGGTACGGGGGCGGTGGCTACG
GACGCCGGAGCCGCAGCCCTAGGCGGCGTCGCCGCAGCCGATCCCGGAGTCGGAGCC
GTTCCAGGTCTCGCAGCCGATCTCGCTACAGCCGCTCGAAGTCTCGGTCCCGCACTCGT
TCTCGATCTCGGTCGACCTCCAAGTCCAGATCCGCACGAAGGTCCAAGTCCAAGTCCT
CGTCGGTCTCCAGATCTCGTTCGCGGTCCAGGTCCCGGTCTCGGTCCAGGAGTCCTCCC CCAGTGTCCAAGAGGGAATCCAAATCCAGGTCGCGATCGAAGAGTCCCCCCAAGTCTC CT GAAGAGGAAGGAGCGGT GTCCT CTTAA
By means of an example, human SRSF2 protein sequence is annotated under NCBI Genbank accession numbers NP 003007.2, NP 001182356.1, and XP 016880431.1, and Uniprot (www.uniprot.org) accession number Q01130-1, and is further reproduced below (SEQ ID NO: 7):
MSY GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY GRVGDVYIPRDRYTKESRGFAFV RFHDKRDAEDAMDAMDGAVLDGRELRVQMARY GRPPDSHHSRRGPPPRRY GGGGY GRR SRSPRRRRRSRSRSRSRSRSRSRSRYSRSKSRSRTRSRSRSTSKSRSARRSKSKSSSVSRSRSR SRSRSRSRSPPPVSKRESKSRSRSKSPPKSPEEEGAVSS
In certain embodiments, the amino acid sequence of said SRSF2 polypeptide is as set forth in GenBank accession no. NP 001182356.1.
By means of an example, human SRSF2 gene is annotated under NCBI Genbank Gene ID 6427.
A skilled person can appreciate that any sequences represented in sequence databases or in the present specification may be of precursors of markers, peptides, polypeptides, proteins, or nucleic acids and may include parts which are processed away from mature molecules.
The term“marker” is widespread in the art and commonly broadly denotes a biological molecule, more particularly an endogenous biological molecule, and/or a detectable portion thereof, whose qualitative and/or quantitative evaluation in a tested object (e.g., in or on a cell, cell population, tissue, organ, or organism, e.g., in a biological sample of a subject) is predictive or informative with respect to one or more aspects of the tested object’s phenotype and/or genotype. The terms “marker” and“biomarker” may be used interchangeably throughout this specification.
Preferably, markers as intended herein may be peptide-, polypeptide- and/or protein-based, or may be nucleic acid-based. For example, a marker may be comprised of peptide(s), polypeptide(s) and/or protein(s) encoded by a given gene, or of detectable portions thereof. Further, whereas the term“nucleic acid” generally encompasses DNA, RNA and DNA/RNA hybrid molecules, in the context of markers the term may typically refer to heterogeneous nuclear RNA (hnRNA), pre- mRNA, messenger RNA (mRNA), or copy DNA (cDNA), or detectable portions thereof. Such nucleic acid species are particularly useful as markers, since they contain qualitative and/or quantitative information about the expression of the gene. Particularly preferably, a nucleic acid- based marker may encompass mRNA of a given gene, or cDNA made of the mRNA, or detectable portions thereof.
The term“protein” as used throughout this specification generally encompasses macromolecules comprising one or more polypeptide chains, i.e., polymeric chains of amino acid residues linked by peptide bonds. The term may encompass naturally, recombinantly, semi-synthetically or synthetically produced proteins. The term also encompasses proteins that carry one or more co- or post-expression-type modifications of the polypeptide chain(s), such as, without limitation, glycosylation, acetylation, phosphorylation, sulfonation, methylation, ubiquitination, signal peptide removal, N-terminal Met removal, conversion of pro-enzymes or pre-hormones into active forms, etc. The term further also includes protein variants or mutants which carry amino acid sequence variations vis-a-vis a corresponding native proteins, such as, e.g., amino acid deletions, additions and/or substitutions. The term contemplates both full-length proteins and protein parts or fragments, e.g., naturally- occurring protein parts that ensue from processing of such full-length proteins.
The term“polypeptide” as used throughout this specification generally encompasses polymeric chains of amino acid residues linked by peptide bonds. Hence, especially when a protein is only composed of a single polypeptide chain, the terms“protein” and“polypeptide” may be used interchangeably herein to denote such a protein. The term is not limited to any minimum length of the polypeptide chain. The term may encompass naturally, recombinantly, semi-synthetically or synthetically produced polypeptides. The term also encompasses polypeptides that carry one or more co- or post-expression-type modifications of the polypeptide chain, such as, without limitation, glycosylation, acetylation, phosphorylation, sulfonation, methylation, ubiquitination, signal peptide removal, N-terminal Met removal, conversion of pro-enzymes or pre-hormones into active forms, etc. The term further also includes polypeptide variants or mutants which carry amino acid sequence variations vis-a-vis a corresponding native polypeptide, such as, e.g., amino acid deletions, additions and/or substitutions. The term contemplates both full-length polypeptides and polypeptide parts or fragments, e.g., naturally- occurring polypeptide parts that ensue from processing of such full-length polypeptides.
The term“peptide” as used throughout this specification preferably refers to a polypeptide as used herein consisting essentially of 50 amino acids or less, e.g., 45 amino acids or less, preferably 40 amino acids or less, e.g., 35 amino acids or less, more preferably 30 amino acids or less, e.g., 25 or less, 20 or less, 15 or less, 10 or less or 5 or less amino acids.
Without limitation, protein, polypeptides or peptides can be produced recombinantly by a suitable host or host cell expression system and isolated therefrom (e.g., a suitable bacterial, yeast, fungal, plant or animal host or host cell expression system), or produced recombinantly by cell-free transcription and/or translation, or non-biological protein, polypeptide or peptide synthesis.
The term“nucleic acid” as used throughout this specification typically refers to a polymer (preferably a linear polymer) of any length composed essentially of nucleoside units. A nucleoside unit commonly includes a heterocyclic base and a sugar group. Heterocyclic bases may include inter alia purine and pyrimidine bases such as adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) which are widespread in naturally- occurring nucleic acids, other naturally- occurring bases (e.g., xanthine, inosine, hypoxanthine) as well as chemically or biochemically modified (e.g., methylated), non-natural or derivatised bases. Exemplary modified nucleobases include without limitation 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. In particular, 5- methylcytosine substitutions have been shown to increase nucleic acid duplex stability and may be preferred base substitutions in for example antisense agents, even more particularly when combined with 2'-0-methoxyethyl sugar modifications. Sugar groups may include inter alia pentose (pentofuranose) groups such as preferably ribose and/or 2-deoxyribose common in naturally- occurring nucleic acids, or arabinose, 2-deoxyarabinose, threose or hexose sugar groups, as well as modified or substituted sugar groups (such as without limitation 2'-0-alkylated, e.g., 2'-0- methylated or 2'-0-ethylated sugars such as ribose; 2'-0-alkyloxyalkylated, e.g., 2’-0- methoxyethylated sugars such as ribose; or 2'-0,4'-C-alkylene-linked, e.g., 2'-0,4'-C-methylene- linked or 2'-0,4'-C-ethylene-linked sugars such as ribose; 2’-fluoro-arabinose, etc.). Nucleic acid molecules comprising at least one ribonucleoside unit may be typically referred to as ribonucleic acids or RNA. Such ribonucleoside unit(s) comprise a 2'-OH moiety, wherein -H may be substituted as known in the art for ribonucleosides (e.g., by a methyl, ethyl, alkyl, or alkyloxyalkyl). Preferably, ribonucleic acids or RNA may be composed primarily of ribonucleoside units, for example, > 80%, > 85%, > 90%, > 95%, > 96%, > 97%, > 98%, > 99% or even 100% (by number) of nucleoside units constituting the nucleic acid molecule may be ribonucleoside units. Nucleic acid molecules comprising at least one deoxyribonucleoside unit may be typically referred to as deoxyribonucleic acids or DNA. Such deoxyribonucleoside unit(s) comprise 2'-H. Preferably, deoxyribonucleic acids or DNA may be composed primarily of deoxyribonucleoside units, for example, > 80%, > 85%, > 90%, > 95%, > 96%, > 97%, > 98%, > 99% or even 100% (by number) of nucleoside units constituting the nucleic acid molecule may be deoxyribonucleoside units. Nucleoside units may be linked to one another by any one of numerous known inter-nucleoside linkages, including inter alia phosphodiester linkages common in naturally-occurring nucleic acids, and further modified phosphate- or phosphonate-based linkages such as phosphorothioate, alkyl phosphorothioate such as methyl phosphorothioate, phosphorodithioate, alkylphosphonate such as methylphosphonate, alkylphosphonothioate, phosphotriester such as alkylphosphotriester, phosphoramidate, phosphoropiperazidate, phosphoromorpholidate, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate; and further siloxane, carbonate, sulfamate, carboalkoxy, acetamidate, carbamate such as 3’-N-carbamate, morpholino, borano, thioether, 3’-thioacetal, and sulfone intemucleoside linkages. Preferably, inter-nucleoside linkages may be phosphate-based linkages including modified phosphate-based linkages, such as more preferably phosphodiester, phosphorothioate or phosphorodithioate linkages or combinations thereof. The term“nucleic acid” also encompasses any other nucleobase containing polymers such as nucleic acid mimetics, including, without limitation, peptide nucleic acids (PNA), peptide nucleic acids with phosphate groups (PHONA), locked nucleic acids (LNA), morpholino phosphorodiamidate-backbone nucleic acids (PMO), cyclohexene nucleic acids (CeNA), tricyclo- DNA (tcDNA), and nucleic acids having backbone sections with alkyl linkers or amino linkers (see, e.g., Kurreck 2003 (Eur J Biochem 270: 1628-1644)).“Alkyl” as used herein particularly encompasses lower hydrocarbon moieties, e.g., C1-C4 linear or branched, saturated or unsaturated hydrocarbon, such as methyl, ethyl, ethenyl, propyl, 1 -propenyl, 2-propenyl, and isopropyl. Nucleic acids as intended herein may include naturally occurring nucleosides, modified nucleosides or mixtures thereof. A modified nucleoside may include a modified heterocyclic base, a modified sugar moiety, a modified inter-nucleoside linkage or a combination thereof.
The term“nucleic acid” further preferably encompasses DNA, RNA and DNA/RNA hybrid molecules, specifically including hnRNA, pre-mRNA, mRNA, cDNA, genomic DNA, amplification products, oligonucleotides, and synthetic (e.g., chemically synthesised) DNA, RNA or DNA/RNA hybrids. RNA is inclusive of RNAi (inhibitory RNA), dsRNA (double stranded RNA), siRNA (small interfering RNA), mRNA (messenger RNA), mi RNA (micro-RNA), tRNA (transfer RNA, whether charged or discharged with a corresponding acylated amino acid), and cRNA (complementary RNA). A nucleic acid can be naturally occurring, e.g., present in or isolated from nature, can be recombinant, i.e., produced by recombinant DNA technology, and/or can be, partly or entirely, chemically or biochemically synthesised. Without limitation, nucleic acids can be produced recombinantly by a suitable host or host cell expression system and isolated therefrom (e.g., a suitable bacterial, yeast, fungal, plant or animal host or host cell expression system), or produced recombinantly by cell-free transcription, or non-biological nucleic acid synthesis. A nucleic acid can be double-stranded, partly double stranded, or single-stranded. Where single- stranded, the nucleic acid can be the sense strand or the antisense strand ln addition, nucleic acid can be circular or linear.
The reference to any marker, peptide, polypeptide, protein, or nucleic acid, corresponds to the marker, peptide, polypeptide, protein, or nucleic acid, commonly known under the respective designations in the art. The terms encompass such markers peptides, polypeptides, proteins, or nucleic acids, of any organism where found, and particularly of animals, preferably warm-blooded animals, more preferably vertebrates, yet more preferably mammals, including humans and non human mammals, still more preferably of humans. In certain embodiments, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
In certain embodiments, the RNA molecule is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
In certain embodiments, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant and the RNA molecule are of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin.
The terms particularly encompass such markers, peptides, polypeptides, proteins, or nucleic acids, with a native sequence, i.e., ones of which the primary sequence is the same as that of the markers, peptides, polypeptides, proteins, or nucleic acids found in or derived from nature. A skilled person understands that native sequences may differ between different species due to genetic divergence between such species. Moreover, native sequences may differ between or within different individuals of the same species due to normal genetic diversity (variation) within a given species. Also, native sequences may differ between or even within different individuals of the same species due to somatic mutations, or post-transcriptional or post-translational modifications. Any such variants or isoforms of markers, peptides, polypeptides, proteins, or nucleic acids are intended herein. Accordingly, all sequences of markers, peptides, polypeptides, proteins, or nucleic acids found in or derived from nature are considered“native”. The terms encompass the markers, peptides, polypeptides, proteins, or nucleic acids when forming a part of a living organism, organ, tissue or cell, when forming a part of a biological sample, as well as when at least partly isolated from such sources. The terms also encompass markers, peptides, polypeptides, proteins, or nucleic acids when produced by recombinant or synthetic means.
In certain embodiments, markers, peptides, polypeptides, proteins, or nucleic acids, may be human, i.e., their primary sequence may be the same as a corresponding primary sequence of or present in a naturally occurring human markers, peptides, polypeptides, proteins, or nucleic acids. Hence, the qualifier“human” in this connection relates to the primary sequence of the respective markers, peptides, polypeptides, proteins, or nucleic acids, rather than to their origin or source. For example, such markers, peptides, polypeptides, proteins, or nucleic acids may be present in or isolated from samples of human subjects or may be obtained by other means (e.g., by recombinant expression, cell- free transcription or translation, or non-biological nucleic acid or peptide synthesis). Unless otherwise apparent from the context, reference herein to any marker, peptide, polypeptide, protein, or nucleic acid, or fragment thereof may generally also encompass modified forms of said marker, peptide, polypeptide, protein, or nucleic acid, or fragment thereof, such as bearing post expression modifications including, for example, phosphorylation, glycosylation, lipidation, methylation, cysteinylation, sulphonation, glutathionylation, acetylation, oxidation of methionine to methionine sulphoxide or methionine sulphone, and the like.
Fragments of any marker, peptide, polypeptide, protein, or nucleic acid, are also envisaged herein.
Hence, for example, the reference herein to measuring (or measuring the quantity of) any one marker, peptide, polypeptide, protein, or nucleic acid, may encompass measuring the marker, peptide, polypeptide, protein, or nucleic acid, and/or measuring one or more fragments thereof. For example, any marker, peptide, polypeptide, protein, or nucleic acid, and/or one or more fragments thereof may be measured collectively, such that the measured quantity corresponds to the sum amounts of the collectively measured species ln another example, any marker, peptide, polypeptide, protein, or nucleic acid, and/or one or more fragments thereof may be measured each individually.
The term“fragment” as used throughout this specification with reference to a peptide, polypeptide, or protein generally denotes a portion of the peptide, polypeptide, or protein, such as typically an N- and/or C-terminally truncated form of the peptide, polypeptide, or protein. Preferably, a fragment may comprise at least about 30%, e.g., at least about 50% or at least about 70%, preferably at least about 80%, e.g., at least about 85%, more preferably at least about 90%, and yet more preferably at least about 95% or even about 99% of the amino acid sequence length of said peptide, polypeptide, or protein. For example, insofar not exceeding the length of the full-length peptide, polypeptide, or protein, a fragment may include a sequence of > 5 consecutive amino acids, or > 10 consecutive amino acids, or > 20 consecutive amino acids, or > 30 consecutive amino acids, e.g., >40 consecutive amino acids, such as for example > 50 consecutive amino acids, e.g., > 60, > 70, > 80, > 90, > 100, > 200, > 300, > 400, > 500 or > 600 consecutive amino acids of the corresponding full-length peptide, polypeptide, or protein.
For example, a fragment of SRSF2 polypeptide may include a sequence of > 5 consecutive amino acids, or > 10 consecutive amino acids, or > 20 consecutive amino acids, or > 30 consecutive amino acids, e.g., >40 consecutive amino acids, such as for example > 50 consecutive amino acids, e.g., > 60, > 70, > 80, > 90, > 100, > 110, > 120, > 130, > 140, > 150, > 160, > 170, > 180, > 190, > 200, or > 210 consecutive amino acids of the corresponding full-length SRSF2 polypeptide. The term“fragment” with reference to a nucleic acid (polynucleotide) generally denotes a 5’- and/or 3’-truncated form of a nucleic acid. Preferably, a fragment may comprise at least about 30%, e.g., at least about 50% or at least about 70%, preferably at least about 80%, e.g., at least about 85%, more preferably at least about 90%, and yet more preferably at least about 95% or even about 99% of the nucleic acid sequence length of said nucleic acid. For example, insofar not exceeding the length of the full-length nucleic acid, a fragment may include a sequence of > 5 consecutive nucleotides, or > 10 consecutive nucleotides, or > 20 consecutive nucleotides, or > 30 consecutive nucleotides, e.g., >40 consecutive nucleotides, such as for example > 50 consecutive nucleotides, e.g., > 60, > 70, > 80, > 90, > 100, > 200, > 300, > 400, > 500 or > 600 consecutive nucleotides of the corresponding full-length nucleic acid.
The terms encompass fragments arising by any mechanism, in vivo and/or in vitro, such as, without limitation, by alternative transcription or translation, exo- and/or endo-proteolysis, exo- and/or endo-nucleolysis, or degradation of the peptide, polypeptide, protein, or nucleic acid, such as, for example, by physical, chemical and/or enzymatic proteolysis or nucleolysis.
Variants of any marker, peptide, polypeptide, protein, or nucleic acid, are also envisaged herein.
The term“variant” of a protein, polypeptide, peptide, or nucleic acid generally refers to proteins, polypeptides or peptides the amino acid sequence of which, or nucleic acids the nucleotide sequence of which, is substantially identical (i.e., largely but not wholly identical) to the sequence of the protein, polypeptide, peptide, or nucleic acid, e.g., at least about 80% identical or at least about 85% identical, e.g., preferably at least about 90% identical, e.g., at least 91% identical, 92% identical, more preferably at least about 93% identical, e.g., at least 94% identical, even more preferably at least about 95% identical, e.g., at least 96% identical, yet more preferably at least about 97% identical, e.g., at least 98% identical, and most preferably at least 99% identical to the sequence of the recited protein, polypeptide, peptide, or nucleic acid. Preferably, a variant may display such degrees of identity to a recited protein, polypeptide, peptide or nucleic acid when the whole sequence of the recited protein, polypeptide, peptide or nucleic acid is queried in the sequence alignment (i.e., overall sequence identity). Sequence identity may be determined using suitable algorithms for performing sequence alignments and determination of sequence identity as know per se. Exemplary but non-limiting algorithms include those based on the Basic Local Alignment Search Tool (BLAST) originally described by Altschul et al. 1990 (J Mol Biol 215: 403-10), such as the“Blast 2 sequences” algorithm described by Tatusova and Madden 1999 (FEMS Microbiol Lett 174: 247-250), for example using the published default settings or other suitable settings (such as, e.g., for the BLASTN algorithm: cost to open a gap = 5, cost to extend a gap = 2, penalty for a mismatch = -2, reward for a match = 1, gap x dropoff = 50, expectation value = 10.0, word size = 28; or for the BLASTP algorithm: matrix = Blosum62 (Henikoff et al., 1992, Proc. Natl. Acad. Sci., 89:10915-10919), cost to open a gap = 11, cost to extend a gap = 1, expectation value = 10.0, word size = 3).
An example procedure to determine the percent identity between a particular amino acid sequence and the amino acid sequence of a query polypeptide will entail aligning the two amino acid sequences using the Blast 2 sequences (B12seq) algorithm, available as a web application or as a standalone executable programme (BLAST version 2.2.31+) at the NCBI web site (www.nchi.nlm.nih.gov), using suitable algorithm parameters. An example of suitable algorithm parameters include: matrix = Blosum62, cost to open a gap = 11, cost to extend a gap = 1, expectation value = 10.0, word size = 3). If the two compared sequences share homology, then the output will present those regions of homology as aligned sequences. If the two compared sequences do not share homology, then the output will not present aligned sequences. Once aligned, the number of matches will be determined by counting the number of positions where an identical amino acid residue is presented in both sequences. The percent identity is determined by dividing the number of matches by the length of the query polypeptide, followed by multiplying the resulting value by 100. The percent identity value may, but need not, be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 may be rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 may be rounded up to 78.2. It is further noted that the detailed view for each segment of alignment as outputted by B12seq already conveniently includes the percentage of identities.
A variant of a protein, polypeptide, peptide, or nucleic acid may be a homologue (e.g., orthologue or paralogue) of said protein, polypeptide, peptide, or nucleic acid. As used herein, the term “homology” generally denotes structural similarity between two macromolecules from same or different taxons, wherein said similarity is due to shared ancestry.
A variant of a protein, polypeptide, or peptide may comprise one or more amino acid additions, deletions, or substitutions relative to (i.e., compared with) the corresponding protein or polypeptide.
For example, a variant (substitution variant) of a protein, polypeptide, or peptide may comprise up to 70 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, 50, 60, or 70) conservative amino acid substitutions relative to (i.e., compared with) the corresponding protein or polypeptide; and/or a variant (substitution variant) of a protein, polypeptide, or peptide may comprise up to 20 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, or 19) non-conservative amino acid substitutions relative to (i.e., compared with) the corresponding protein or polypeptide. A conservative amino acid substitution is a substitution of one amino acid for another with similar characteristics. Conservative amino acid substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (i.e., basic) amino acids include arginine, lysine and histidine. The negatively charged (i.e., acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic, or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a non-conservative substitution is a substitution of one amino acid for another with dissimilar characteristics.
Alternatively or in addition, for example, a variant (deletion variant) of a protein, polypeptide, or peptide may lack up to 20 amino acid segments (e.g., one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 segments) relative to (i.e., compared with) the corresponding protein or polypeptide. The deletion segment(s) may each independently consist of one amino acid, two contiguous amino acids or three contiguous amino acids. The deletion segments may be non-contiguous, or two or more or all of the deletion segments may be contiguous.
Reference to“fragment or variant” or“variant or fragment” of any marker, peptide, polypeptide, protein, or nucleic acid, also encompasses fragments of variants of such marker, peptide, polypeptide, protein, or nucleic acid, and variants of fragments of such marker, peptide, polypeptide, protein, or nucleic acid.
A variant of a nucleic acid may comprise one or more nucleotide additions, deletions, or substitutions relative to (i.e., compared with) the corresponding nucleic acid.
Where the present specification refers to or encompasses fragments and/or variants of proteins, polypeptides or peptides, this in particular denotes such fragments and/or variants which are biologically active. The term “biologically active” is interchangeable with terms such as “functionally active” or“functional”, denoting that the fragment and/or variant at least partly retains the biological activity or intended functionality of the respective or corresponding protein, polypeptide, or peptide. Reference to the“activity” of a protein, polypeptide, or peptide may generally encompass any one or more aspects of the biological activity of the protein, polypeptide, or peptide, such as without limitation any one or more aspects of its biochemical activity, enzymatic activity, signalling activity, interaction activity, ligand activity, and/or structural activity, e.g., within a cell, tissue, organ or an organism.
Preferably, a functionally active fragment or variant may retain at least about 20%, e.g., at least about 25%, or at least 30%, or at least about 40%, or at least about 50%, e.g., at least 60%, more preferably at least about 70%, e.g., at least 80%, yet more preferably at least about 85%, still more preferably at least about 90%, and most preferably at least about 95% or even about 100% of the intended biological activity or functionality compared with the corresponding protein, polypeptide, or peptide ln certain embodiments, a functionally active fragment or variant may even display higher biological activity or functionality compared with the corresponding protein, polypeptide, or peptide, for example may display at least about 100%, or at least about 150%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500% of the intended biological activity or functionality compared with the corresponding protein, polypeptide, or peptide. By means of an example, where the activity of a given protein, polypeptide, or peptide can be readily measured in an assay with a quantitative output, for example an enzymatic assay or a binding assay producing a quantifiable signal, a functionally active fragment or variant of the protein, polypeptide, or peptide may produce a signal which is at least about 20%, or at least about 25%, or at least 30%, or at least about 40%, or at least about 50%, or at least 60%, more preferably at least about 70%, or at least 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 100%, or at least about 150%, or at least about 200%, or at least about 300%, or at least about 400%, or at least about 500% of the signal produced by the corresponding protein, polypeptide, or peptide.
ln one example, the activity of a given protein, polypeptide, or peptide may comprise binding of said protein, polypeptide, or peptide to a ligand and the strength of binding or affinity may be represented by the equilibrium constant for the dissociation (KD, moles per litre) of said protein, polypeptide, or peptide with said ligand. The KD for the binding of the biologically active fragment or variant of said protein, polypeptide, or peptide with said ligand determined under substantially identical conditions may be no more than 3 orders of magnitude greater, preferably no more than 2 orders of magnitude greater, and more preferably no more than 1 order of magnitude greater than the KD for the binding of said protein, polypeptide, or peptide to said ligand ln other words, the strength of the binding of the biologically active fragment or variant of said protein, polypeptide, or peptide with said ligand as represented by KD may be at least 1/1000* , e.g., at least 1/750*, at least 1/500*, at least 1/250*, preferably at least 1/100*, e.g., at least 1/75*, at least 1/50*, at least 1/25*, more preferably at least 1/10*, e.g., 1/5*, l/3rd or 1/2 of the strength of the binding of said protein, polypeptide, or peptide with said ligand as represented by KD. By means of an example and not limitation, a biologically active fragment or variant of a SRSF2 polypeptide or a mutated SRSF2 polypeptide as disclosed herein shall at least partly retain the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide. For example, it may retain one or more aspects of the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide. By means of an example and not limitation, reference to the activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide or functionally active fragment or variant thereof may particularly denote its ability to bind to a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C). For example, the mr5C-binding activity of SRSF2 or mutated SRSF2 or functionally active fragment or variant thereof can be measured essentially as described in the Examples. By means of an example and not limitation, reference to the activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide or functionally active fragment or variant thereof may particularly denote its ability to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C. For example, splicing activity can be assessed by existing methodologies of analysing RNA structure, such as RT-PCR analysis or RNA-sequencing.
The term“mutated” or“mutant” refers to a marker, peptide, polypeptide, protein, or nucleic acid comprising one or more mutations, i.e., comprising one or more amino acid sequence changes or nucleic acid sequence changes compared to respectively the amino acid sequence or nucleic acid sequence of the marker, peptide, polypeptide, protein, or nucleic acid that has not been so-mutated, such as, particularly, compared to the amino acid sequence or nucleic acid sequence of the wild- type marker, peptide, polypeptide, protein, or nucleic acid. As used herein, the term“wild-type” as applied to a marker, peptide, polypeptide, protein, or nucleic acid refers to a marker, peptide, polypeptide, protein, or nucleic acid that occurs in, or is produced by, a biological organism as that biological organism exists in nature ln certain embodiments, the term“wild-type” may refer to any form of a marker, peptide, polypeptide, protein, or nucleic acid present in or encoded by the germline (constitutional) DNA of a normal, healthy or typical specimen of a species, such as a healthy human or non-human mammal ln certain embodiments, the terms“mutant” or“mutated” may refer to any form of a marker, peptide, polypeptide, protein, or nucleic acid present in or encoded by the germline DNA or somatic DNA of an abnormal, diseased or non-typical specimen of a species, such as a diseased human or non-human mammal. Accordingly, the terms encompass germline mutations as well as somatic mutations.
Any types of mutations are contemplated herein. For example, suitable mutations may include deletions, insertions, and/or substitutions of one or more amino acids in a peptide, polypeptide, or protein, or may include deletions, insertions, and/or substitutions of one or more nucleotides in a nucleic acid. The term“deletion” refers to a mutation wherein one or more amino acids or nucleotides, typically consecutive amino acids or nucleotides, are removed, i.e., deleted, from the peptide, polypeptide, or protein or from the nucleic acid. The term“insertion” refers to a mutation wherein one or more amino acids or nucleotides, typically consecutive amino acids or nucleotides, are added, i.e., inserted, into the peptide, polypeptide, or protein, or into the nucleic acid. The term “substitution” refers to a mutation wherein one or more amino acids of a peptide, polypeptide or protein, or one or more nucleotides of a nucleic acid, are each independently replaced, i.e., substituted, by another amino acid or nucleotide, respectively.
The terms“mutated” or“mutant” as intended herein may encompass silent mutations, and may preferably encompass loss-of-function or gain- of- function mutations. Without limitation, a mutation may introduce a premature in-frame stop codon into a sequence encoding a peptide, polypeptide, or protein, resulting in production of a C-terminally truncated form of said peptide, polypeptide, or protein or resulting in abolished production of said peptide, polypeptide, or protein. For example, a suitable insertion, deletion or substitution of one or more nucleotides in an open reading frame may introduce a premature in-frame stop codon. Further without limitation, a mutation may introduce a frame shift (e.g., +1 or +2 frame shift) in a sequence encoding a peptide, polypeptide, or protein. Typically, such frame shift may lead to a previously out-of-frame stop codon downstream of the mutation becoming an in- frame stop codon. Hence, such frame shift may lead to production of a form of the peptide, polypeptide, or protein having an alternative C-terminal portion and/or a C-terminally truncated form of said peptide, polypeptide, or protein, or may result in abolished production of said peptide, polypeptide, or protein. For example, a suitable insertion, deletion or substitution of one or more (not multiple of 3) nucleotides in an open reading frame may lead to a frame shift. Further without limitation, a mutation may delete at least a portion of a sequence encoding a peptide, polypeptide, or protein. Such deletion may lead to production of an N-terminally truncated form, a C-terminally truncated form and/or an internally deleted form of said peptide, polypeptide, or protein ln certain other embodiments, a mutation may be a substitution of one or more nucleotides in a sequence encoding a peptide, polypeptide, or protein resulting in substitution of one or more amino acids of said peptide, polypeptide, or protein. Such mutation may typically preserve the production of the peptide, polypeptide, or protein and may affect some or all biological function(s) of the peptide, polypeptide, or protein ln certain other embodiments, a mutation may be a conservative or non-conservative substitution of one amino acid of a peptide, polypeptide, or protein for one another amino acid ln certain other embodiments, a mutation may be a substitution of one nucleotide in a sequence encoding a peptide, polypeptide, or protein resulting in a conservative or non-conservative substitution of one amino acid of said peptide, polypeptide, or protein for one another amino acid. Various combinations of such exemplary types of mutations as mentioned above are foreseen herein. In certain embodiments, one or more mutations comprised by a mutated SRSF2 polypeptide may alter, such as increase or decrease, the ability of the mutated SRSF2 polypeptide to bind to 5- methylcytosine(s) (mr5C) on an RNA molecule, compared with wild-type SRSF2. In certain embodiments, one or more mutations comprised by a mutated SRSF2 polypeptide may alter, such as increase or decrease, the ability of the mutated SRSF2 polypeptide to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C, compared with wild-type SRSF2. The one or more mutations in a mutated SRSF2 polypeptide may be germline mutations. The one or more mutations in a mutated SRSF2 polypeptide may be somatic mutations.
The one or more mutations in a mutated SRSF2 polypeptide may be somatic mutations occurring in a neoplastic tissue. The one or more mutations in a mutated SRSF2 polypeptide may be causative of or may contribute to a neoplastic disease. For example, Fig. 9 shows the frequency of non- synonymous single nucleotide variations (nsSNV), i.e., mutations resulting in altered amino acid sequence, in SRSF2 in various types of cancer. For example, Fig. 10 shows the frequency of nsSNV in SRSF2 across all cancers by SRSF2 amino acid position. For example, the following individual SRSF2 somatic mutations have been previously reported in neoplastic diseases (for each entry: position in SRSF2 nucleic acid sequence NM 003016.4 or NM 001195427.1, reference nucleotide, mutated nucleotide, position in SRSF2 amino acid sequence, reference amino acid, mutated amino acid, cancer type): 614, G, T, 205, R, L, Urinary bladder cancer; 402, T, C, 134, S, S, Thyroid cancer; 503, G, A, 168, R, K, Lung cancer; 560, C, A, 187, S, Y, Rectum cancer; 619, A, T, 207, K, X, Prostate cancer; 284, C, T, 95, P, L, Hematologic cancer; 618, G, T, 206, S, S, Prostate cancer; 284, C, G, 95, P, R, Hematologic cancer; 284, C, T, 95, P, L, Hematologic cancer; 468, A, G, 156, R, R, Kidney cancer; 284, C, A, 95, P, H, Hematologic cancer; 284, C, A, 95, P, H, Hematologic cancer; 283, C, A, 95, P, T, Hematologic cancer; 284, C, T, 95, P, L, Hematologic cancer; 284, C, A, 95, P, H, Hematologic cancer; 651, A, C, 217, G, G, Liver cancer; 385, C, T, 129, R, X, Kidney cancer; 296, A, T, 99, H, L, Hematologic cancer; 386, G, T, 129, R, L, Urinary bladder cancer; 284, C, G, 95, P, R, Hematologic cancer; 367, A, T, 123, R, W, Lung cancer; 614, G, T, 205, R, L, Urinary bladder cancer; 500, G, A, 167, R, Q, Urinary bladder cancer; 386, G, T, 129, R, L, Urinary bladder cancer; 385, C, G, 129, R, G, Pharynx cancer; 468, A, G, 156, R, R, Kidney cancer; 468, A, G, 156, R, R, Kidney cancer; 385, C, T, 129, R, X, Kidney cancer; 625, C, A, 209, P, T, Brain cancer; 625, C, A, 209, P, T, Brain cancer; 284, C, T, 95, P, L, Hematologic cancer; 583, G, C, 195, V, L, Lung cancer; 536, C, G, 179, S, C, Lung cancer; 240, G, C, 80, L, L, Lung cancer; 177, C, T, 59, F, F, Lung cancer; 9, C, T, 3, Hematologic cancer; 407, C, G, 136, S, C, Breast cancer; 329, A, G, 110, Y, C, Lung cancer; 320, C, A, 107, P, H, Hematologic cancer; 284, C, A, 95, P, H, Hematologic cancer; 659, C, G, 220, S, C, Thyroid cancer; 651, A, C, 217, G, G, Liver cancer; 619, A, T, 207, K, X, Prostate cancer; 618, G, T, 206, S, S, Prostate cancer; 614, G, T, 205, R, L, Urinary bladder cancer; 583, G, C, 195, V, L, Lung cancer; 536, C, G, 179, S, C, Lung cancer; 500, G, A, 167, R, Q, Urinary bladder cancer; 468, A, G, 156, R, R, Kidney cancer; 445, T, C, 149, S, P, Skin cancer; 407, C, G, 136, S, C, Breast cancer; 402, T, C, 134, S, S, Thyroid cancer; 386, G, T, 129, R, L, Urinary bladder cancer; 385, C, T, 129, R, X, Kidney cancer; 303, C, T, 101, S, S, Liver cancer; 280, C, T, 94, R, C, Skin cancer; 177, C, T, 59, F, F, Lung cancer; 156, G, C, 52, K, N, Breast cancer; 152, C, T, 51, T, I, Skin cancer; 44, C, T, 15, S, F, Skin cancer; 9, C, T, 3, Y, Y, Hematologic cancer; 1, A, C, 1, M, L, Hematologic cancer; 284, C, T, 95, P, L, Hematologic cancer; 595, G, A, 199, E, K, Melanoma; 579, C, T, 193, P, P, Melanoma; 659, C, G, 220, S, C, Thyroid cancer; 177, C, T, 59, F, F, Lung cancer; 536, C, G, 179, S, C, Lung cancer; 44, C, T, 15, S, F, Skin cancer; 152, C, T, 51, T, I, Skin cancer; 445, T, C, 149, S, P, Skin cancer; 280, C, T, 94, R, C, Skin cancer; 303, C, T, Liver cancer; 619, A, T, 207, K, X, Prostate cancer; 618, G, T, 206, S, S, Prostate cancer; 144, C, T, 48, D, D, Pancreatic cancer; 536, C, G, 179, S, C, Lung cancer; 583, G, C, 195, V, L, Lung cancer; 177, C, T, 59, F, F, Lung cancer; 288, G, A, 96, P, P, Liver cancer; 468, A, G, 156, R, R, Kidney cancer; 385, C, T, 129, R, X, Kidney cancer; 385, C, G, 129, R, G, Head and neck cancer; 140, G, T, 47, R, L, Head and neck cancer; 399, G, A, 133, R, R, Head and neck cancer; 500, G, T, 167, R, L, Head and neck cancer; 625, C, A, 209, P, T, Malignant glioma; 393, G, C, 131, R, R, Cervical cancer; 311, G, A, 104, G, E, Cervical cancer; 171, C, T, 57, F, F, Cervical cancer; 205, G, A, 69, E, K, Cervical cancer; 156, G, C, 52, K, N, Breast cancer; 407, C, G, 136, S, C, Breast cancer; 103, G, C, 35, E, Q, Breast cancer; 500, G, A, 167, R, Q, Urinary bladder cancer; 386, G, T, 129, R, L, Urinary bladder cancer; 614, G, T, 205, R, L, Urinary bladder cancer; 284, C, A, 95, P, H, Hematologic cancer; 500, G, A, 167, R, Q, Urinary bladder cancer; 283, C, G, 95, P, A, Hematologic cancer; 240, G, C, 80, L, L, Lung cancer; 39, G, C, 13, M, I, Lung cancer; 1, A, C, 1, M, L, Hematologic cancer; 407, C, G, 136, S, C, Breast cancer; 583, G, C, 195, V, L, Lung cancer; 417, C, T, 139, R, R, Lung cancer. Further, P95H has been reported as disease-associated (cancer) mutation of SRSF2 (Zhang et al. Proc Natl Acad Sci USA. 2015, vol. 112, E4726-34).
In certain embodiments, the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide. These positions have been reported as positions for post- translational modifications of the concerned amino acid, such as acetylation, phosphorylation, etc. A mutation, such as a conservative or non-conservative substitution of one amino acid for one another amino acid, at such position(s) can alter, such as increase or decrease, post-translational modification at the respective position(s). In certain embodiments, the mutated SRSF2 polypeptide is mutated at amino acid position 95 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of amino acid 95 for one another amino acid, more preferably by a P95H substitution, as reported by Zhang et al. {supra).
In certain embodiments, the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of one amino acid for one another amino acid. Somatic single amino acid substitutions at these positions have been reported to occur in various types of cancers (see above).
In certain embodiments, the mutated SRSF2 polypeptide is mutated at one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide, preferably by a conservative or non-conservative substitution of one amino acid for one another amino acid. Amino acid sequence alignments with other known methyl-group binding protein have predicted these amino acids as implicated or contributing to the direct binding of SRSF2 to mr5C. Accordingly, the present specification also describes a SRSF2 polypeptide mutated at one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide.
Any combinations of two or more SRSF2 mutations as exemplified in the preceding sections are also envisaged.
In certain non-limiting embodiments, any one or more of the following characteristics may apply to the RNA molecule comprising one or more 5-methylcytosines (m5C) and configured for being bound by the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof:
composed of a single RNA strand;
composed of ribonucleosides each independently selected from A, G, C (at least one of which is 5-methylated), and U;
composed of phosphodiester-linked ribonucleosides each independently selected from A, G, C (at least one of which is 5-methylated), and U;
contains exactly 1, 2, 3, 4 or 5 m5C;
contains exactly one m5C; at least 5-nt long, for example, > 6-nt, > 7-nt, > 8-nt, > 9-nt, > lO-nt, > 1 l-nt, > l2-nt, > 13- nt, > l4-nt, > l5-nt, > l6-nt, > l7-nt, > l8-nt, > l9-nt, or > 20-nt long;
at most 50-nt long, for example, < 45-nt, < 40-nt, < 35-nt, < 30-nt, or < 25-nt long;
5-50-nt long, for example, 5-45-nt, 5-40-nt, 5-35-nt, 5-30-nt, 5-25-nt, l0-50-nt, lO-45-nt, l0-40-nt, lO-35-nt, l0-30-nt, lO-25-nt, 15-50-nt, 15-45-nt, 15-40-nt, 15-35-nt, 15-30-nt, or
15-25-nt long;
l5-nt, l6-nt, l7-nt, l8-nt, l9-nt, 20-nt, 2l-nt, 22-nt, 23-nt, 24-nt or 25-nt long;
20-nt long;
comprises the sequence 5’-SSNG-3’, wherein S is G or C, N is A, C, G or U, particularly providing that said 5’-SSNG-3’ sequence comprises at least one C, more particularly at least one C at the first two positions;
comprises the sequence 5’-Sm5CNG-3’, wherein S is G or C, N is A, C, G or U;
comprises the sequence 5’-Cm5CGG-3’;
comprises said 5’-SSNG-3’ (particularly providing that said 5’-SSNG-3’ sequence comprises at least one C, more particularly at least one C at the first two positions), 5’-
Sm5CNG-3’ or 5’-Cm5CGG-3’ sequence centrally or substantially centrally located, for example, the lengths of the 5’- and 3’-flanks of said sequence are the same or differ by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2, or l-nt;
displays GC content 30-70%, for example 40-70%, 50-70%, 55-70%, or 55-65%;
- displays GC content about 40%, about 45%, about 50%, about 55%, about 60%, or about
65%;
displays GC content about 60%;
- displays the sequence 5’-UUUCAGCUCm5CGGUCACGCUC-3’ (SEQ 1D NO: 8);
displays a sequence differing with no more than three, no more than two, or at most one single-nucleotide substitution, deletion and/or insertion from SEQ 1D NO: 8;
is of animal origin, preferably warm-blooded animal origin, more preferably vertebrate origin, yet more preferably mammalian origin, including human origin and non-human mammalian origin, still more preferably human origin;
comprises a label, such as a 5’-label and/or a 3’-label; comprises a label, such as a 5’-label and/or a 3’-label, said label being configured for detection using affinity separation, immunoaffinity separation, fluorescence resonance energy transfer, or bioluminescence resonance energy transfer; and/or
comprises a label, such as a 5’-label and/or a 3’-label, wherein said label is biotin.
The term“label” refers to any atom, molecule, moiety or biomolecule that may be used to provide a detectable and preferably quantifiable read-out or property, and that may be attached to or made part of an entity of interest. Labels may be suitably detectable by for example mass spectrometric, spectroscopic, optical, colorimetric, magnetic, photochemical, biochemical, immunochemical or chemical means. Labels include without limitation dyes; radiolabels such as P, P, S, I, I; electron-dense reagents; enzymes (e.g., horse-radish peroxidase or alkaline phosphatase as commonly used in immunoassays); binding moieties such as biotin-streptavidin; haptens such as digoxigenin; luminogenic, phosphorescent or fluorogenic moieties; mass tags; fluorescent dyes alone or in combination with moieties that may suppress or shift emission spectra by fluorescence resonance energy transfer (FRET).
In some embodiments, a label or tag may be utilised that permits detection with another agent. Such tags may be, for example, biotin, streptavidin, his-tag, myc tag, maltose, maltose binding protein or any other kind of tag known in the art that has a binding partner. Examples of associations which may be utilised include, for example, biotin: streptavidin, his-tag:metal ion (e.g., Ni2+), maltose:maltose binding protein, etc.
Examples of detection agents include, but are not limited to, luminescent labels; colorimetric labels, such as dyes; fluorescent labels; or chemical labels, such as electroactive agents (e.g., ferrocyanide); enzymes; radioactive labels; or radiofrequency labels. The detection agent may be a particle. Examples of such particles include, but are not limited to, colloidal gold particles; colloidal sulphur particles; colloidal selenium particles; colloidal barium sulfate particles; colloidal iron sulfate particles; metal iodate particles; silver halide particles; silica particles; colloidal metal (hydrous) oxide particles; colloidal metal sulfide particles; colloidal lead selenide particles; colloidal cadmium selenide particles; colloidal metal phosphate particles; colloidal metal ferrite particles; any of the above-mentioned colloidal particles coated with organic or inorganic layers; protein or peptide molecules; liposomes; or organic polymer latex particles, such as polystyrene latex beads. Preferable particles may be colloidal gold particles.
The term“methylation” as used herein refers to the presence of a methyl moiety on a nucleotide (base), where the nucleotide (base) typically does not comprise a methyl moiety. The phrase “methylated ribonucleic acid molecule” refers to a ribonucleic acid (RNA) molecule that contains one or more ribonucleotides that are methylated. An RNA molecule comprising at least one methylated ribonucleotide can be considered methylated. An RNA molecule that does not comprise any methylated ribonucleotides can be considered unmethylated.
For example, cytosine does not contain a methyl moiety on its pyrimidine ring. 5-methylcytosine contains a methyl moiety at position 5 of the pyrimidine ring. 5-methylcytosine may be denoted as “m5C”. The abbreviation“mr5C” may be more commonly used to indicate 5-methylation of cytosine in RNA. Hence, the structure of 5-methylcytosine is shown in Formula I below:
Figure imgf000026_0001
Formula I
The structure of 5-methylcytidine, a ribonucleoside unit containing 5-methylcytosine is shown in Formula II below:
Figure imgf000026_0002
Formula II
The present specification may interchangeably refer to binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, or to a RNA molecule comprising one or more mr5C. RNA molecules comprising one or more mr5C and configured to be bound by the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof may display variable or dissimilar nucleotide sequences. In certain embodiments, the presence of the one or more mr5C may be the only structural commonality between such RNA molecules, their nucleotide sequences sharing no relevant sequence elements or significant identity. In certain embodiments, such RNA molecules may comprise a consensus sequence, more particularly a consensus sequence encompassing the one or more mr5C. In certain embodiments, such consensus sequence may be 5’- SSNG-3’, wherein S is G or C, N is A, C, G or U, particularly providing that said 5’-SSNG-3’ sequence comprises at least one C; or may be 5’-SCNG-3’ (e.g., 5’-Sm5CNG-3’), wherein S is G or C, N is A, C, G or U; or may be 5’-Cm5CGG-3’. The 5’-SSNG-3’ sequence has been reported as a preferred SRSF2 RNA-binding consensus sequence. This sequences encompasses the alternative sequences 5’-CCNG, 5’-GCNG, 5’-CGNG and 5’-GGNG. In particular, the 5’-CCNG, 5’-GCNG and 5’-CGNG sequences, which comprise at least one C at the first two positions, are relevant in the context of SRSF2 m5C-mediated binding to RNA. The inventors postulate that SRSF2 may bind with different degrees of specificity to these different sequences and/or the binding of SRSF2 may lead to different outcomes based on the particular sequence to which SRSF2 binds.
The binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule particularly denotes a direct molecular interaction or molecular contact between the polypeptide and the RNA molecule, forming a molecular complex in which said components are physically associated or bound. Said binding may particularly refer to non-covalent binding, i.e., binding mediated by non-covalent forces, such as for example, hydrogen bridges, dipolar interactions, van der Waals interactions, and the like. The formation of such molecular complex may be favoured, such as in particular under physiological conditions (e.g., temperature 25-38°C, pH 7.0-7.5, ionic strength 100-250 mM), for example, the polypeptide and the RNA molecule may bind with an equilibrium affinity constant (KA) of such binding KA ³ lxlO5 M4, KA ³ lxlO6 M4, KA > lxlO7 M4, KA > lxlO8 M4, KA > lxlO9 M 1, KA > lxlO10 M 1, or KA > lxlO11 M 1, wherein KA = [P_R]/[P][R], P denotes the polypeptide, R denotes the RNA molecule. Determination of the binding of a polypeptide and RNA molecule, and of the corresponding KA (or the dissociation constant, KD, the inverse of KA) can be carried out by methods known in the art, such as for example, separation-based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis (e.g., electrophoretic mobility shift assays, EMSA), and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-Vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry. The binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule particularly denotes specific binding, i.e., where the polypeptide binds to the RNA molecule comprising one or more mr5C substantially to the exclusion of other molecules which are random or unrelated. Further, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to one or more mr5C on an RNA molecule may bind to the RNA molecule comprising one or more mr5C with an affinity at least about 10-fold greater, such as at least 100-fold, 1000-fold, lxl04-fold, lxl05-fold, or lxlO6- fold greater than to an otherwise identical RNA molecule not comprising the one or more mr5C. As used herein, the term“agent” broadly refers to any chemical (e.g., inorganic or organic), biochemical or biological substance, molecule or macromolecule (e.g., biological macromolecule), a combination or mixture thereof, a sample of undetermined composition, or an extract made from biological materials such as bacteria, plants, fungi, or animal cells or tissues. Preferred though non limiting “agents” include nucleic acids, oligonucleotides, ribozymes, peptides, polypeptides, proteins, peptidomimetics, antibodies, antibody fragments, antibody-like protein scaffolds, aptamers, photoaptamers, spiegelmers, chemical substances, preferably organic molecules, more preferably small organic molecules, lipids, carbohydrates, polysaccharides, etc., and any combinations thereof. Depending on the context, the term“agent” may denote a“therapeutic agent” or“drug”, useful for or used in the treatment, cure, prevention, or diagnosis of a disease.
ln certain embodiments, the agent such as the test agent or SRSF2-modulating agent may be selected from the group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, such as siRNA or shRNA, a soluble receptor, and combinations thereof.
As used herein, the term“antibody” is used in its broadest sense and generally refers to any immunologic binding agent. The term specifically encompasses intact monoclonal antibodies, polyclonal antibodies, multivalent (e.g., 2-, 3- or more-valent) and/or multi-specific antibodies (e.g., bi- or more-specific antibodies) formed from at least two intact antibodies, and antibody fragments insofar they exhibit the desired biological activity (particularly, ability to specifically bind an antigen of interest, i.e., antigen-binding fragments), as well as multivalent and/or multi specific composites of such fragments. The term“antibody” is not only inclusive of antibodies generated by methods comprising immunisation, but also includes any polypeptide, e.g., a recombinantly expressed polypeptide, which is made to encompass at least one complementarity determining region (CDR) capable of specifically binding to an epitope on an antigen of interest. Hence, the term applies to such molecules regardless whether they are produced in vitro or in vivo.
An antibody may be any of lgA, lgD, lgE, lgG and lgM classes, and preferably lgG class antibody. An antibody may be a polyclonal antibody, e.g., an antiserum or immunoglobulins purified there from (e.g., affinity-purified). An antibody may be a monoclonal antibody or a mixture of monoclonal antibodies. Monoclonal antibodies can target a particular antigen or a particular epitope within an antigen with greater selectivity and reproducibility. By means of example and not limitation, monoclonal antibodies may be made by the hybridoma method first described by Kohler et al. 1975 (Nature 256: 495), or may be made by recombinant DNA methods (e.g., as in US 4,816,567). Monoclonal antibodies may also be isolated from phage antibody libraries using techniques as described by Clackson et al. 1991 (Nature 352: 624-628) and Marks et al. 1991 (J Mol Biol 222: 581-597), for example.
Antibody binding agents may be antibody fragments.“Antibody fragments” comprise a portion of an intact antibody, comprising the antigen-binding or variable region thereof. Examples of antibody fragments include Fab, Fab’, F(ab’)2, Fv and scFv fragments, single domain (sd) Fv, such as VH domains, VL domains and VHH domains; diabodies; linear antibodies; single-chain antibody molecules, in particular heavy-chain antibodies; and multivalent and/or multispecific antibodies formed from antibody fragment(s), e.g., dibodies, tribodies, and multibodies. The above designations Fab, Fab’, F(ab’)2, Fv, scFv etc. are intended to have their art-established meaning.
The term antibody includes antibodies originating from or comprising one or more portions derived from any animal species, preferably vertebrate species, including, e.g., birds and mammals. Without limitation, the antibodies may be chicken, turkey, goose, duck, guinea fowl, quail or pheasant. Also without limitation, the antibodies may be human, murine (e.g., mouse, rat, etc.), donkey, rabbit, goat, sheep, guinea pig, camel (e.g., Camelus bactrianus and Camelus dromaderius), llama (e.g., Lama paccos, Lama glama or Lama vicugna) or horse.
A skilled person will understand that an antibody can include one or more amino acid deletions, additions and/or substitutions (e.g., conservative substitutions), insofar such alterations preserve its binding of the respective antigen. An antibody may also include one or more native or artificial modifications of its constituent amino acid residues (e.g., glycosylation, etc.).
Methods of producing polyclonal and monoclonal antibodies as well as fragments thereof are well known in the art, as are methods to produce recombinant antibodies or fragments thereof (see for example, Harlow and Lane,“Antibodies: A Laboratory Manual”, Cold Spring Harbour Laboratory, New York, 1988; Harlow and Lane,“Using Antibodies: A Laboratory Manual”, Cold Spring Harbour Laboratory, New York, 1999, 1SBN 0879695447;“Monoclonal Antibodies: A Manual of Techniques”, by Zola, ed., CRC Press 1987, 1SBN 0849364760;“Monoclonal Antibodies: A Practical Approach”, by Dean & Shepherd, eds., Oxford University Press 2000, 1SBN 0199637229; Methods in Molecular Biology, vol. 248:“Antibody Engineering: Methods and Protocols”, Lo, ed., Humana Press 2004, 1SBN 1588290921).
ln certain embodiments, the agent may be a Nanobody®. The terms “Nanobody®” and “Nanobodies®” are trademarks of Ablynx NV (Belgium). The term“Nanobody” is well-known in the art and as used herein in its broadest sense encompasses an immunological binding agent obtained (1) by isolating the VHH domain of a heavy-chain antibody, preferably a heavy-chain antibody derived from camelids; (2) by expression of a nucleotide sequence encoding a VHH domain; (3) by“humanization” of a naturally occurring VHH domain or by expression of a nucleic acid encoding a such humanized VHH domain; (4) by“camelization” of a VH domain from any animal species, and in particular from a mammalian species, such as from a human being, or by expression of a nucleic acid encoding such a camelized VH domain; (5) by“camelization” of a “domain antibody” or“dAb” as described in the art, or by expression of a nucleic acid encoding such a camelized dAb; (6) by using synthetic or semi-synthetic techniques for preparing proteins, polypeptides or other amino acid sequences known per se; (7) by preparing a nucleic acid encoding a Nanobody using techniques for nucleic acid synthesis known per se, followed by expression of the nucleic acid thus obtained; and/or (8) by any combination of one or more of the foregoing. “Camelids” as used herein comprise old world camelids ( Camelus bactrianus and Camelus dromaderius) and new world camelids (for example Lama paccos, Lama glama and Lama vicugna).
In certain embodiments, the antibody may be a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a humanized antibody, a primatized antibody, a human antibody, a Nanobody®, an intrabody, or mixtures thereof.
The term“antibody-like protein scaffolds” or“engineered protein scaffolds” broadly encompasses proteinaceous non-immunoglobulin specific -binding agents, typically obtained by combinatorial engineering (such as site-directed random mutagenesis in combination with phage display or other molecular selection techniques). Usually, such scaffolds are derived from robust and small soluble monomeric proteins (such as Kunitz inhibitors or lipocalins) or from a stably folded extra membrane domain of a cell surface receptor (such as protein A, fibronectin or the ankyrin repeat).
Such scaffolds have been extensively reviewed in Binz et al., Gebauer and Skerra, Gill and Damle, Skerra 2000, and Skerra 2007, and include without limitation affibodies, based on the Z-domain of staphylococcal protein A, a three-helix bundle of 58 residues providing an interface on two of its alpha-helices (Nygren); engineered Kunitz domains based on a small (ca. 58 residues) and robust, disulphide-crosslinked serine protease inhibitor, typically of human origin (e.g. LACI-D1), which can be engineered for different protease specificities (Nixon and Wood); monobodies or adnectins based on the lOth extracellular domain of human fibronectin III (l0Fn3), which adopts an Ig-like beta-sandwich fold (94 residues) with 2-3 exposed loops, but lacks the central disulphide bridge (Koide and Koide); anticalins derived from the lipocalins, a diverse family of eight-stranded beta- barrel proteins (ca. 180 residues) that naturally form binding sites for small ligands by means of four structurally variable loops at the open end, which are abundant in humans, insects, and many other organisms (Skerra 2008); DARPins, designed ankyrin repeat domains (166 residues), which provide a rigid interface arising from typically three repeated beta-turns (Stumpp et al.); avimers (multimerized LDLR-A module) (Silverman et al.); and cysteine-rich knottin peptides (Kolmar). The term“aptamer” refers to single-stranded or double-stranded oligo-DNA, oligo-RNA or oligo- DNA/RNA or any analogue thereof that specifically binds to a target molecule such as a peptide. Advantageously, aptamers display fairly high specificity and affinity (e.g., KA in the order lxlO9 M 1) for their targets. Aptamer production is described inter alia in US 5,270,163; Ellington & Szostak 1990 (Nature 346: 818-822); Tuerk & Gold 1990 (Science 249: 505-510); or“The Aptamer Handbook: Functional Oligonucleotides and Their Applications”, by Klussmann, ed., Wiley-VCH 2006, ISBN 3527310592, incorporated by reference herein. The term“photoaptamer” refers to an aptamer that contains one or more photoreactive functional groups that can covalently bind to or crosslink with a target molecule. The term“spiegelmer” refers to an aptamer which includes L-DNA, L-RNA, or other left-handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides. The term “peptidomimetic” refers to a non-peptide agent that is a topological analogue of a corresponding peptide. Methods of rationally designing peptidomimetics of peptides are known in the art. For example, the rational design of three peptidomimetics based on the sulphated 8-mer peptide CCK26-33, and of two peptidomimetics based on the l l-mer peptide Substance P, and related peptidomimetic design principles, are described in Horwell 1995 (Trends Biotechnol 13: 132-134).
In certain embodiments, the chemical substance is an organic molecule, preferably a small organic molecule. The term“small molecule” refers to compounds, preferably organic compounds, with a size comparable to those organic molecules generally used in pharmaceuticals. The term excludes biological macromolecules (e.g., proteins, peptides, nucleic acids, etc.). Preferred small organic molecules range in size up to about 5000 Da, e.g., up to about 4000, preferably up to 3000 Da, more preferably up to 2000 Da, even more preferably up to about 1000 Da, e.g., up to about 900, 800, 700, 600 or up to about 500 Da.
The term“soluble receptor” generally refers to the soluble (i.e., circulating, not bound to a cell) form of a cell-surface molecule, e.g., a cell-surface receptor, or a fragment or derivative thereof. For example, a cell-surface molecule can be made soluble by attaching a soluble fusion partner, e.g., an immunoglobulin (Ig) moiety, or a portion thereof, to the extracellular domain, or by removing its transmembrane domain.
Targeted genome modification is a powerful tool for genetic manipulation of cells and organisms, including mammals. Genome modification or gene editing, including insertion, deletion or replacement of DNA in the genome, can be carried out using a variety of known gene editing systems. The term“gene editing system” or“genome editing system” as used herein refers to a tool to induce one or more nucleic acid modifications, such as DNA or RNA modifications, into a specific DNA or RNA sequence within a cell. Gene editing systems typically make use of an agent capable of inducing a nucleic acid modification. In certain embodiments, the agent capable of inducing a nucleic acid modification may be a (endo)nuclease or a variant thereof having altered or modified activity. (endo)Nucleases typically comprise programmable, sequence-specific DNA- or RNA-binding modules linked to a nonspecific DNA or RNA cleavage domain. In DNA, these nucleases create site-specific double-strand breaks at desired locations in the genome. The induced double-stranded breaks are repaired through nonhomologous end-joining or homologous recombination, resulting in targeted mutations. In certain embodiments, said (endo)nuclease may be RNA-guided. In certain embodiments, said (endo)nuclease can be engineered nuclease such as a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated (Cas) (endo)nuclease, such as Cas9, Cpfl, or C2c2, a (zinc finger nuclease (ZFN),a transcription factor like effector nuclease (TALEN), a meganuclease, or modifications thereof. Methods for using TALEN technology, Zinc Finger technology and CRISPR/Cas technology are known by the skilled person.
In certain embodiments, the nucleic acid SRSF2-modulating agent is an oligonucleotide. The term “oligonucleotide” as used herein refers to a nucleic acid (including nucleic acid analogues and mimetics) oligomer or polymer as defined herein. Preferably, an oligonucleotide is (substantially) single-stranded. Oligonucleotides as intended herein may be preferably between about 10 and about 100 nucleoside units (i.e., nucleotides or nucleotide analogues) in length, preferably between about 15 and about 50, more preferably between about 20 and about 40, also preferably between about 20 and about 30. Preferably, oligonucleotides as intended herein may comprise one or more or all non- naturally occurring heterocyclic bases and/or one or more or all non-naturally occurring sugar groups and/or one or more or all non-naturally occurring inter-nucleoside linkages, the inclusion of which may improve properties such as, for example, enhanced cellular uptake, increased stability in the presence of nucleases and increased hybridization affinity, increased tolerance for mismatches, etc. Further, oligonucleotides as intended herein may be configured to not activate RNAse H, accordance with known techniques (see, e.g., U.S. Pat. 5,149,797).
In certain embodiments, the oligonucleotide SRSF2-modulating agent is capable of specifically hybridising with an RNA molecule bound by the SRSF2 component, and said oligonucleotide SRSF2-modulating agent comprises one or more mr5C. The formation of such duplex of, on the one hand, the RNA molecule bound by the SRSF2 component and, on the other hand, an mr5C- containing oligonucleotide agent, can modulate, such as restore binding of the SRSF2 component (e.g., mutated SRSF2) to said RNA.
The term“antisense” generally refers to an agent (e.g., an oligonucleotide as defined elsewhere in the specification ) configured to specifically anneal with (hybridise to) a given sequence in a target nucleic acid, such as for example in a target DNA, hnRNA, pre-mRNA or mRNA, and typically comprises, consist essentially of or consist of a nucleic acid sequence that is complementary or substantially complementary to said target nucleic acid sequence. Antisense agents suitable for use herein may typically be capable of annealing with (hybridising to) the respective target nucleic acid sequences at high stringency conditions, and capable of hybridising specifically to the target under physiological conditions.
The terms“complementary” or“complementarity” as used herein with reference to nucleic acids, refer to the normal binding of single-stranded nucleic acids under permissive salt (ionic strength) and temperature conditions by base pairing, preferably Watson-Crick base pairing. By means of example, complementary Watson-Crick base pairing occurs between the bases A and T, A and U or G and C. For example, the sequence 5'-A-G-U-3' is complementary to sequence 5'-A-C-U-3'.
The sequence of an antisense agent need not be 100% complementary to that of its target sequence to bind or hybridise specifically with the latter as defined elsewhere in the specification. An antisense agent may be said to be specifically hybridisable when binding of the agent to a target nucleic acid molecule interferes with the normal function of the target nucleic acid such as to attain an intended outcome (e.g., loss of utility), and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense agent to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed. Thus,“specifically hybridisable” and“complementary” may indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between an antisense agent and a nucleic acid target.
Preferably, to ensure specificity of antisense agents towards the desired target over unrelated molecules, the sequence of said antisense agents may be at least about 80% identical, preferably at least about 90% identical, more preferably at least about 95% identical, such as, e.g., about 96%, about 97%, about 98%, about 99% and up to 100% identical to the respective target sequence.
Antisense agents as intended herein preferably comprise or denote antisense molecules such as more preferably antisense nucleic acid molecules or antisense nucleic acid analogue molecules. Preferably, antisense agents may refer to antisense oligonucleotides or antisense oligonucleotide analogues.
Antisense agents such as oligonucleotides as taught herein may be further conjugated (e.g., covalently or non-covalently, directly or via a suitable linker) to one or more moieties or conjugates that enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium l,2-di-0-hexadecyl- rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl- oxycholesterol moiety.
It is not necessary for all positions in a given agent to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single agent or even at a single nucleoside within an oligonucleotide. Further included are antisense compounds that are chimeric compounds.“Chimeric” antisense compounds or“chimeras” are antisense molecules, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the increased resistance to nuclease degradation, increased cellular uptake, and an additional region for increased binding affinity for the target nucleic acid.
The term“RNA interference agent” or“RNAi agent” refers to ribonucleic acid sequences, modified ribonucleic acid sequences, or DNA sequences encoding said ribonucleic acid sequences, which cause RNA interference and thus decrease expression of the target gene.
An RNAi (RNA interference) agent typically comprises, consists essentially of or consists of a double-stranded portion or region (notwithstanding the optional and potentially preferred presence of single-stranded overhangs) of annealed complementary strands, one of which has a sequence corresponding to a target nucleotide sequence (hence, to at least a portion of an mRNA) of the target gene to be down-regulated. The other strand of the RNAi agent is complementary to said target nucleotide sequence. Non- limiting examples of RNAi agents are shRNAs, siRNAs, miRNAs, and DNA-RNA hybrids.
Whereas the sequence of an RNAi agent need not be completely identical to a target sequence to be down-regulated, the number of mismatches between a target sequence and a nucleotide sequence of the RNAi agent is preferably no more than 1 in 5 bases, or 1 in 10 bases, or 1 in 20 bases, or 1 in 50 bases.
Preferably, to ensure specificity of RNAi agents towards the desired target over unrelated molecules, the sequence of said RNAi agents may be at least about 80% identical, preferably at least about 90% identical, more preferably at least about 95% identical, such as, e.g., about 96%, about 97%, about 98%, about 99% and up to 100% identical to the respective target sequence.
An RNAi agent may be formed by separate sense and antisense strands or, alternatively, by a common strand providing for fold-back stem-loop or hairpin design where the two annealed strands of an RNAi agent are covalently linked. An siRNA molecule may be typically produced, e.g., synthesised, as a double stranded molecule of separate, substantially complementary strands, wherein each strand is about 18 to about 35 bases long, preferably about 19 to about 30 bases, more preferably about 20 to about 25 bases and even more preferably about 21 to about 23 bases.
shRNA is in the form of a hairpin structure. shRNA can be synthesized exogenously or can be formed by transcribing from RNA polymerase III promoters in vivo. Preferably, shRNAs can be engineered in host cells or organisms to ensure continuous and stable suppression of a desired gene. It is known that siRNA can be produced by processing a hairpin RNA in cells.
RNAi agents as intended herein may include any modifications as set out herein for nucleic acids and oligonucleotides, in order to improve their therapeutic properties.
In embodiments, at least one strand of an RNAi molecules may have a 3’ overhang from about 1 to about 6 bases in length, e.g., from 2 to 4 bases, more preferably from 1 to 3 bases. For example, one strand may have a 3’ overhang and the other strand may be either blunt-ended or may also have a 3’overhang. The length of the overhangs may be the same or different for each strand. The 3’ overhangs can be stabilised against degradation. For example, the RNA may be stabilised by including purine nucleotides, such as A or G nucleotides. Alternatively, substitution of pyrimidine nucleotides by modified analogues, e.g., substitution of U 3’ overhangs by 2’-deoxythymidine is tolerated and does not affect the efficiency of RNAi.
An exemplary but non-limiting siRNA molecule may by characterized by any one or more, and preferably by all of the following criteria:
at least about 80% sequence identity, more preferably at least about 90 % or at least about 95% or at least about 97% sequence identity to target mRNA;
having a sequence which targets an area of the target gene present in mature mRNA (e.g., an exon or alternatively spliced intron);
showing a preference for targeting the 3’ end of the target gene.
The exemplary siRNA may be further characterised by one or more or all of the following criteria: having a double-stranded nucleic acid length of between 16 to 30 bases and preferably of between 18 to 23 bases, and preferably of 19 nucleotides;
having GC content between about 30 and about 50 %
having a TT(T) sequence at 3’ end;
showing no secondary structure when adopting the duplex form; having a Tm (melting temperature) of lower than 20°C
having the nucleotides indicated here below in the sequence of the nucleotides, wherein “h” is A, C, T/U but not G; wherein“d” is A, G, T/U but not C, and wherein“w” is A or T/U, but not G or C:
Figure imgf000036_0001
5 RNAi agents as intended herein may particularly comprise or denote (i.e., may be selected from a group comprising or consisting of) RNAi nucleic acid molecules or RNAi nucleic acid analogue molecules, such as preferably short interfering nucleic acids and short interfering nucleic acid analogues (siNA) such as short interfering RNA and short interfering RNA analogues (siRNA), and may further denote inter alia double-stranded RNA and double-stranded RNA analogues (dsRNA), 10 micro-RNA and micro-RNA analogues (miRNA), and short hairpin RNA and short hairpin RNA analogues (shRNA).
Production of antisense agents and RNAi agents can be carried out by any processes known in the art, such as inter alia partly or entirely by chemical synthesis (e.g., routinely known solid phase synthesis; an exemplary an non-limiting method for synthesising oligonucleotides on a modified 15 solid support is described in US 4,458,066; in another example, diethyl-phosphoramidites are used as starting materials and may be synthesised as described by Beaucage el al. 1981 (Tetrahedron Letters 22: 1859-1862)), or partly or entirely by biochemical (enzymatic) synthesis, e.g. , by in vitro transcription from a nucleic acid construct (template) using a suitable polymerase such as a T7 or SP6 RNA polymerase, or by recombinant nucleic acid techniques, e.g., expression from a vector in 20 a host cell or host organism. Nucleotide analogues can be introduced by in vitro chemical or biochemical synthesis. In an embodiment, the antisense agents of the invention are synthesised in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules.
The term“modulate” broadly denotes a qualitative and/or quantitative alteration, change or 25 variation in that which is being modulated. Where modulation can be assessed quantitatively - for example, where modulation comprises or consists of a change in a quantifiable variable such as a quantifiable property or where a quantifiable variable provides a suitable surrogate for the modulation - modulation specifically encompasses both increase (e.g., activation) or decrease (e.g., inhibition) in the measured variable. The term encompasses any extent of such modulation, e.g., any extent of such increase or decrease, and may more particularly refer to statistically significant increase or decrease in the measured variable. By means of example, modulation may encompass an increase in the value of the measured variable by at least about 10%, e.g., by at least about 20%, preferably by at least about 30%, e.g., by at least about 40%, more preferably by at least about
50%, e.g., by at least about 75%, even more preferably by at least about 100%, e.g., by at least about 150%, 200%, 250%, 300%, 400% or by at least about 500%, compared to a reference situation without said modulation; or modulation may encompass a decrease or reduction in the value of the measured variable by at least about 10%, e.g., by at least about 20%, by at least about
30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said modulation. Preferably, modulation may be specific or selective, hence, that which is being modulated may be changed or altered without modulated without substantially altering other (unintended, undesired, unrelated) targets, functions, properties or processes.
By means of an example and not limitation, an agent may modulate one or more aspects of the biological activity of the SRSF2 polypeptide or mutated SRSF2 polypeptide, such as its ability to bind to an RNA molecule comprising one or more mr5C and/or its ability to modulate splicing of an RNA molecule, particularly of a messenger RNA molecule, such as RNA or mRNA comprising one or more mr5C.
For example, determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule may typically involve measuring said binding in the presence (optionally at different concentrations of said test agent) vs. absence of said test agent and comparing said measurements to identify any difference or deviation there between.
The term“contact” or“contacting” as used herein means bringing one or more first components (such as one or more molecules, biological entities, cells, or materials) together with one or more second components (such as one or more molecules, biological entities, cells, or materials) in such a manner that the first component(s) can - if capable thereof - bind or modulate the second component(s) or that the second component(s) can - if capable thereof - bind or modulate the first component(s). Such modulation may occur either directly, i.e., by way of direct interaction between the first and second component(s); or indirectly, e.g., when the first component(s) interact with or modulate one or more further component(s), one or more of which in turn interact with or modulate the second component(s), or vice versa. The term“contacting” may depending on the context be synonymous with“exposing”,“incubating”,“mixing”,“reacting”,“treating”, or the like.
In certain embodiments, contacting may be performed in a cell-free system or in a cell lysate or in isolated or cultured cells or in an isolated or cultured tissue. Cell- free systems may be prepared, for example, by mixing the investigated components and optionally any other chemical and/or biological substances required for obtaining the investigated outcome, such as binding of the polypeptide and RNA molecule and modulation thereof by a test agent, to take place. Typically, the components are combined in a suitable aqueous environment, such as in an aqueous solution comprising a buffer system. Commonplace buffers include without limitation histidine-buffers, citrate-buffers, succinate-buffers, acetate-buffers, phosphate-buffers, formate buffers, benzoate buffers, TRIS (Tris(hydroxymethyl)-aminomethan) buffers or maleate buffers, or mixtures thereof. Typically, the experimental conditions may be selected to approximate physiological conditions, e.g., temperature 25-38°C, pH 7.0-7.5, ionic strength 100-250 mM.
Cell lysates refer to cell suspensions or fractions thereof obtained by disruption or lysing of cells. Crude cell lysates (without further treatment) or cell lysate solutions (treated for example to remove or render inactive selected molecules) may be employed. Any method can be used to lyse cells in a cell sample. For example, osmotic shock, sonication, heating, physical disruption, microwave treatment, and enzymatic and/or alkaline lysis are methods that can be used to lyse cells.
The term“isolated” as used throughout this specification with reference to a particular component generally denotes that such component exists in separation from - for example, has been separated from or prepared and/or maintained in separation from - one or more other components of its natural environment. More particularly, the term“isolated” as used herein in relation to cells or tissues denotes that such cells or tissues do not form part of an animal or human body.
Isolated cells or tissues may be suitably cultured or cultivated in vitro. The terms“culturing” or “cell culture” are common in the art and broadly refer to maintenance of cells and potentially expansion (proliferation, propagation) of cells in vitro. Typically, animal cells, such as mammalian cells, such as human cells, are cultured by exposing them to (i.e., contacting them with) a suitable cell culture medium in a vessel or container adequate for the purpose (e.g., a 96-, 24-, or 6-well plate, a T-25, T-75, T-150 or T-225 flask, or a cell factory), at art-known conditions conducive to in vitro cell culture, such as temperature of 37°C, 5% v/v CO2 and > 95% humidity.
The term“medium” as used herein broadly encompasses any cell culture medium conducive to maintenance of cells, preferably conducive to proliferation of cells. Typically, the medium will be a liquid culture medium, which facilitates easy manipulation (e.g., decantation, pipetting, centrifugation, filtration, and such) thereof.
Typically, the medium will comprise a basal medium formulation as known in the art. Many basal media formulations (available, e.g., from the American Type Culture Collection, ATCC; or from lnvitrogen, Carlsbad, California) can be used, including but not limited to Eagle’s Minimum Essential Medium (MEM), Dulbecco’s Modified Eagle's Medium (DMEM), alpha modified Minimum Essential Medium (alpha-MEM), Basal Medium Essential (BME), lscove’s Modified Dulbecco's Medium (1MDM), BGJb medium, F-12 Nutrient Mixture (Ham), Liebovitz L-15, DMEM/F-12, Essential Modified Eagle's Medium (EMEM), RPM1-1640, Medium 199, Waymouth's MB 752/1 or Williams Medium E, and modifications and/or combinations thereof. Compositions of basal media are generally known in the art and it is within the skill of one in the art to modify or modulate concentrations of media and/or media supplements as necessary for the cells cultured.
Such basal media formulations contain ingredients necessary for mammalian cell development, which are known per se. By means of illustration and not limitation, these ingredients may include inorganic salts (in particular salts containing Na, K, Mg, Ca, Cl, P and possibly Cu, Fe, Se and Zn), physiological buffers (e.g., HEPES, bicarbonate), nucleotides, nucleosides and/or nucleic acid bases, ribose, deoxyribose, amino acids, vitamins, antioxidants (e.g., glutathione) and sources of carbon (e.g., glucose, sodium pyruvate, sodium acetate), etc.
For use in culture, basal media can be supplied with one or more further components. For example, additional supplements can be used to supply the cells with the necessary trace elements and substances for optimal growth and expansion. Furthermore, antioxidant supplements may be added, e.g., b-mercaptoethanol. While many basal media already contain amino acids, some amino acids may be supplemented later, e.g., L-glutamine, which is known to be less stable when in solution. A medium may be further supplied with antibiotic and/or antimycotic compounds, such as, typically, mixtures of penicillin and streptomycin, and/or other compounds, exemplified but not limited to, amphotericin, ampicillin, gentamicin, bleomycin, hygromycin, kanamycin, mitomycin, mycophenolic acid, nalidixic acid, neomycin, nystatin, paromomycin, polymyxin, puromycin, rifampicin, spectinomycin, tetracycline, tylosin, and zeocin.
Lipids and lipid carriers can also be used to supplement cell culture media. Such lipids and carriers can include, but are not limited to cyclodextrin, cholesterol, linoleic acid conjugated to albumin, linoleic acid and oleic acid conjugated to albumin, unconjugated linoleic acid, linoleic-oleic- arachidonic acid conjugated to albumin, oleic acid unconjugated and conjugated to albumin, among others. Albumin can similarly be used in fatty-acid free formulations. Also contemplated is supplementation of cell culture media with mammalian plasma or sera. Plasma or sera often contain cellular factors and components that facilitate cell viability and expansion. Optionally, plasma or serum may be heat inactivated. Heat inactivation is used in the art mainly to remove the complement. Heat inactivation typically involves incubating the plasma or serum at 56°C for 30 to 60min, e.g., 30min, with steady mixing, after which the plasma or serum is allowed to gradually cool to ambient temperature. A skilled person will be aware of any common modifications and requirements of the above procedure. Optionally, plasma or serum may be sterilised prior to storage or use. Usual means of sterilisation may involve, e.g., filtration through one or more filters with pore size smaller than 1 pm, preferably smaller than 0.5 pm, e.g., smaller than 0.45pm, 0.40pm, 0.35pm, 0.30pm or 0.25pm, more preferably 0.2pm or smaller, e.g., 0.15pm or smaller, 0.10pm or smaller. Suitable sera or plasmas for use in media as taught herein may include human serum or plasma, or serum or plasma from non-human animals, preferably non human mammals, such as, e.g., non-human primates (e.g., lemurs, monkeys, apes), foetal or adult bovine, horse, porcine, lamb, goat, dog, rabbit, mouse or rat serum or plasma, etc., or any combination of such. In certain preferred embodiments, a medium as taught herein may comprise bovine serum or plasma, preferably foetal bovine (calf) serum or plasma, more preferably foetal bovine (calf) serum (FCS or FBS). When culturing human cells, media may preferably comprise human serum or plasma, such as autologous or allogeneic human serum or plasma, preferably human serum, such as autologous or allogeneic human serum, more preferably autologous human serum or plasma, even more preferably autologous human serum.
ln certain preferred embodiments, serum or plasma can be substituted in media by serum replacements, such as to provide for serum-free media (i.e., chemically defined media). The provision of serum- free media may be advantageous particularly with view to administration of the media or fraction(s) thereof to subjects, especially to human subjects (e.g., improved bio-safety). By the term“serum replacement” it is broadly meant any a composition that may be used to replace the functions (e.g., cell maintenance and growth supportive function) of animal serum in a cell culture medium. A conventional serum replacement may typically comprise vitamins, albumin, lipids, amino acids, transferrin, antioxidants, insulin and trace elements. Many commercialized serum replacement additives, such as KnockOut Serum Replacement (KOSR), N2, B27, lnsulin- Transferrin-Selenium Supplement (1TS), and G5 are well known and are readily available to those skilled in the art.
Plasma or serum or serum replacement may be comprised in media as taught herein at a proportion (volume of plasma or serum or serum replacement /volume of medium) between about 0.5% v/v and about 40.0% v/v, preferably between about 5.0% v/v and about 20.0% v/v, e.g., between about 5.0% v/v and about 15.0 % v/v, more preferably between about 8.0% v/v and about 12.0% v/v, e.g., about 10.0% v/v.
Suitable isolated or cultured cells may be without limitation bacterial cells, fungal cells, including yeast cells, plant cells, animal cells, mammalian cells, human cells, or non-human mammalian cells. Animal cells, such as mammalian cells, human cells, or non-human mammalian cells may be preferred. Cells may include primary cells, secondary, tertiary etc. cells, or may include immortalised cell lines, including clonal cell lines. Non-limiting examples of bacterial cells include Escherichia coli, Yersinia enterocolitica, Brucella sp., Salmonella tymphimurium, Serratia marcescens, or Bacillus subtilis. Non-limiting examples of firngal cells include Yarrowia lipolytica, Arxula adeninivorans, Pichia pastoris, Hansenula polymorpha, Saccharomyces cerevisiae, or Schizosaccharomyces pombe. Non-limiting examples of insect cells include cells derived from Drosophila melanogaster, such as Schneider 2 cells, cell lines derived from the army worm Spodoptera frugiperda, such as Sf9 and Sf2l cells, or cells derived from the cabbage looper Trichoplusia ni, such as High Five cells. Non-limiting example of human cells include the human HeLa (cervical cancer) cell line. Other human cell lines common in tissue culture practice include inter alia human embryonic kidney 293 cells (HEK cells), DU145 (prostate cancer), Lncap (prostate cancer), MCF-7 (breast cancer), MDA-MB-438 (breast cancer), PC3 (prostate cancer), T47D (breast cancer), THP-l (acute myeloid leukemia), U87 (glioblastoma), SHSY5Y (neuroblastoma), or Saos-2 cells (bone cancer). A non-limiting example of primate cells are Vero (African green monkey Chlorocebus kidney epithelial cell line) cells, and COS cells. Non-limiting examples of rodent cells are rat GH3 (pituitary tumor), CHO (Chinese hamster ovary), PC12 (pheochromocytoma) cell lines, or mouse MC3T3 (embryonic calvarium) cell line. Such cells can be obtained from a variety of commercial sources and research resource facilities, such as, for example, the American Type Culture Collection (Rockville, MD).
ln certain embodiments, the cells may have an intact cell membrane ln other embodiments, the cell membrane may be permeabilised (transiently or permanently) to allow diffusion of components across the cell membrane which are not transported or are transported less effectively across an intact cell membrane. Suitable detergents for cell membrane permeabilisation include without limitation saponins (e.g., digitonin), Triton™ X-100, or Polysorbate 20. The cells may be live or viable, or may be non- viable.
The polypeptide and RNA molecule, the interaction of which is investigated in isolated or cultured cells or tissues, may be endogenous, i.e., endogenously produced by the cell; or the polypeptide may be endogenous and the RNA molecule or an expressible nucleic acid molecule encoding said RNA molecule may be introduced into the cell; or the polypeptide or an expressible nucleic acid molecule encoding said polypeptide may be introduced into the cell and the RNA molecule may be endogenous; or the polypeptide or an expressible nucleic acid molecule encoding said polypeptide and the RNA molecule or an expressible nucleic acid molecule encoding said RNA molecule may both be introduced into the cell.
Methods for introducing polypeptides and/or nucleic acids into viable cells are known to the person skilled in the art, and may include calcium phosphate co-precipitation, electroporation, micro injection, protoplast fusion, lipofection, exosome-mediated transfection, transfection employing polyamine transfection reagents, bombardment of cells by nucleic acid-coated tungsten micro projectiles, viral particle delivery, etc. Such introduction may also be referred to as delivery, transfection or transformation. Cell penetrating peptides (CPPs) may also be employed for delivering polypeptides or nucleic acids into cells. CPP translocation may be classified into three main entry mechanisms: direct penetration in the membrane, endocytosis-mediated entry, and translocation through the formation of a transitory structure. CPPs typically have an amino acid composition that either contains a high relative abundance of positively charged amino acids such as lysine or arginine or has sequences that contain an alternating pattern of polar/charged amino acids and non-polar, hydrophobic amino acids. These two types of structures are referred to as polycationic or amphipathic, respectively. A third class of CPPs are the hydrophobic peptides, containing only apolar residues, with low net charge or have hydrophobic amino acid groups that are crucial for cellular uptake. One of the initial CPPs discovered was the trans-activating transcriptional activator (Tat) from Human lmmunodeficiency Virus 1 (H1V-1) which was found to be efficiently taken up from the surrounding media by numerous cell types in culture. Since then, the number of known CPPs has expanded considerably and small molecule synthetic analogues with more effective protein transduction properties have been generated. CPPs include but are not limited to Penetratin, Tat (48-60), Transportan, and (R-AhX-R4) (Ahx=aminohexanoyl). US 8,372,951, provides a CPP derived from eosinophil cationic protein (ECP) which exhibits highly cell-penetrating efficiency and low toxicity. Aspects of delivering the CPP with its cargo into a vertebrate subject are also provided. Further aspects of CPPs and their delivery are described in US 8,575,305; US 8;614,194 and US 8,044,019. CPPs can be conjugated or complex with the cargo as known in the art, e.g., via a thioether bond or via formation of particles.
Expressible nucleic acid molecules, such as for example expression cassettes or expression vectors, encoding polypeptides or RNAs of interest can be provided as generally known in the art. An expressible nucleic acid molecule may typically comprise a nucleic acid molecule encoding the polypeptide of interest and/or a nucleic acid molecule encoding the RNA molecule of interest and a promoter(s) operably linked to said nucleic acid molecule(s). The promoter may be selected or configured to effect expression of the polypeptide and/or RNA of interest in a cell of interest, such as a bacterial cell, fungal cell, yeast cell, plant cell, animal cell, mammalian cell, human cell, or non-human mammalian cell.
The terms“expression vector” or“vector” as used herein refers to nucleic acid molecules, typically DNA, to which nucleic acid fragments, preferably the recombinant nucleic acid molecule as defined herein, may be inserted and cloned, i.e., propagated. Hence, a vector will typically contain one or more unique restriction sites, and may be capable of autonomous replication in a defined cell or vehicle organism such that the cloned sequence is reproducible. A vector may also preferably contain a selection marker, such as, e.g., an antibiotic resistance gene, to allow selection of recipient cells that contain the vector. Vectors may include, without limitation, plasmids, phagemids, bacteriophages, bacteriophage-derived vectors, PAC, BAC, linear nucleic acids, e.g., linear DNA, transposons, viral vectors, etc., as appropriate (see, e.g., Sambrook et al., 1989; Ausubel 1992). Viral vectors may include inter alia retroviral vectors, lentiviral vectors, adenoviral vectors, or adeno-associated viral vectors, for example, vectors based on H1V, SV40, EBV, HSV or BPV. Expression vectors are generally configured to allow for and/or effect the expression of nucleic acids or open reading frames introduced thereto in a desired expression system, e.g., in vitro, in a cell, organ and/or organism. For example, expression vectors may advantageously comprise suitable regulatory sequences.
Factors of importance in selecting a particular vector include inter alia: choice of recipient cell, ease with which recipient cells that contain the vector may be recognised and selected from those recipient cells which do not contain the vector; the number of copies of the vector which are desired in particular recipient cells; whether it is desired for the vector to integrate into the chromosome or to remain extra-chromosomal in the recipient cells; and whether it is desirable to be able to“shuttle” the vector between recipient cells of different species.
Expression vectors can be autonomous or integrative. A nucleic acid can be in introduced into a cell in the form of an expression vector such as a plasmid, phage, transposon, cosmid or virus particle. The recombinant nucleic acid can be maintained extrachromosomally or it can be integrated into the cell chromosomal DNA. Expression vectors can contain selection marker genes encoding proteins required for cell viability under selected conditions (e.g., URA3, which encodes an enzyme necessary for uracil biosynthesis, or LEU2, which encodes an enzyme required for leucine biosynthesis, or TRP1, which encodes an enzyme required for tryptophan biosynthesis) to permit detection and/or selection of those cells transformed with the desired nucleic acids. Expression vectors can also include an autonomous replication sequence (ARS). The ARS may comprise a centromere (CEN) and an origin of replication (OR1). For example, the ARS may be ARS18 or ARS68. Integrative vectors generally include a serially arranged sequence of at least a first insertable DNA fragment, a selectable marker gene, and a second insertable DNA fragment. The first and second insertable DNA fragments are each about 200 (e.g., about 250, about 300, about 350, about 400, about 450, about 500, or about 1000 or more) nucleotides in length and have nucleotide sequences which are homologous to portions of the genomic DNA of the cell species to be transformed. A nucleotide sequence containing a nucleic acid of interest for expression is inserted in this vector between the first and second insertable DNA fragments, whether before or after the marker gene. Integrative vectors can be linearized prior to transformation to facilitate the integration of the nucleotide sequence of interest into the cell genome.
As used herein, the term“promoter” refers to a DNA sequence that enables a gene to be transcribed. A promoter is recognized by RNA polymerase, which then initiates transcription. Thus, a promoter contains a DNA sequence that is either bound directly by, or is involved in the recruitment, of RNA polymerase. A promoter sequence can also include“enhancer regions”, which are one or more regions of DNA that can be bound with proteins (namely the trans-acting factors) to enhance transcription levels of genes in a gene-cluster. The enhancer, while typically at the 5’ end of a coding region, can also be separate from a promoter sequence, e.g., can be within an intronic region of a gene or 3’ to the coding region of the gene.
An“operable linkage” is a linkage in which regulatory sequences and sequences sought to be expressed are connected in such a way as to permit said expression. For example, sequences, such as, e.g., a promoter and an open reading frame (ORF), may be said to be operably linked if the nature of the linkage between said sequences does not: (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter to direct the transcription of the ORF, (3) interfere with the ability of the ORF to be transcribed from the promoter sequence. Hence, “operably linked” may mean incorporated into a genetic construct so that expression control sequences, such as a promoter, effectively control transcription / expression of a sequence of interest.
The promotor may be a constitutive or inducible (conditional) promoter. A constitutive promoter is understood to be a promoter whose expression is constant under the standard culturing conditions. Inducible promoters are promoters that are responsive to one or more induction cues. For example, an inducible promoter can be chemically regulated (e.g., a promoter whose transcriptional activity is regulated by the presence or absence of a chemical inducing agent such as an alcohol, tetracycline, a steroid, a metal, or other small molecule) or physically regulated (e.g., a promoter whose transcriptional activity is regulated by the presence or absence of a physical inducer such as light or high or low temperatures). An inducible promoter can also be indirectly regulated by one or more transcription factors that are themselves directly regulated by chemical or physical cues. Non- limiting examples of promoters include T7, U6, Hl, retroviral Rous sarcoma virus (RSV) LTR promoter, the cytomegalovirus (CMV) promoter, the SV40 promoter, the dihydrofolate reductase promoter, the b-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EFla promoter.
Prior to introducing the vectors into a cell of interest, the vectors can be grown (e.g., amplified) in bacterial cells such as Escherichia coli ( E . coli). The vector DNA can be isolated from bacterial cells by any of the methods known in the art which result in the purification of vector DNA from the bacterial milieu. The purified vector DNA can be extracted extensively with phenol, chloroform, and ether, to ensure that no E. coli proteins are present in the plasmid DNA preparation, since these proteins can be toxic to mammalian cells.
The evaluation of the binding of the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof with the RNA molecule comprising one or more mr5C (for reasons of brevity, SRSF2 component and RNA component, respectively) may in certain embodiments involve measuring either the so-bound SRSF2 component or the so-bound RNA component or both, after said components have been contacted to allow for their binding to take place.“Measuring” as used throughout the present specification broadly refers to any means of detecting or determining the presence or absence and/or quantity of that which is“measured”, such as a marker, peptide, polypeptide, protein, or nucleic acid, or such as binding, activity, function, etc.
Any existing, available or conventional separation, detection and/or quantification methods may be used to measure the presence or absence and/or quantity of any marker, peptide, polypeptide, protein, or nucleic acid, as discussed herein, such as of the SRSF2 and/or RNA components.
ln certain examples, such methods may include biochemical assay methods, including inter alia assays of enzymatic activity, membrane channel activity, substance-binding activity, gene regulatory activity, or cell signaling activity of a marker, peptide, polypeptide, protein, or nucleic acid.
ln other examples, such methods may include affinity-based assay methods, wherein the ability of an assay to separate, detect and/or quantify a marker, peptide, polypeptide, protein, or nucleic acid is conferred by specific binding between a separable, detectable and/or quantifiable binding agent and i) the marker peptide, polypeptide, protein, or nucleic acid, or ii) a label or tag comprised by (e.g., covalently bound to or conjugated with) the marker peptide, polypeptide, protein, or nucleic acid. The binding agent may be an immunological binding agent (antibody) or a non- immunological binding agent. Examples of antibodies capable of binding to human SRSF2 include without limitation those available from the following vendors (“#” stands for catalogue number): OriGene (#APl2450PU-N, #APl8l94PU-N, rabbit polyclonals); Invitrogen (#RA5-12402, #PA5- 62086, rabbit polyclonals); GeneTex (#GTXl l826, mouse monoclonal); ProteoGenix (#PTGX-SC- 4F11, mouse monoclonal); and Santa Cruz (#sc-535l8, mouse monoclonal). Further example of i) include anti-myc antibodies, which specifically bind to a myc tag (EQKLISEEDL), or anti-FLAG antibodies, which specifically bind to a FLAG tag (DYKDDDDK). Non-limiting examples of ii) include streptavidin, which specifically binds to biotin; metal ion (e.g., Ni2+), which specifically binds to his-tag; and maltose binding protein (MBP), which specifically binds maltose. Affinity- based assay methods, such immunological assay methods, include without limitation immunohistochemistry, immunocytochemistry, flow cytometry, mass cytometry, fluorescence activated cell sorting (FACS), fluorescence microscopy, fluorescence based cell sorting using microfluidic systems, (immuno)affinity adsorption based techniques such as affinity chromatography, magnetic particle separation, magnetic activated cell sorting or bead based cell sorting using microfluidic systems, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA) and ELISPOT based techniques, radioimmunoassay (RIA), Western blot, etc.
In further examples, such methods may include mass spectrometry analysis methods. Generally, any mass spectrometric (MS) techniques that are capable of obtaining precise information on the mass of peptides, and preferably also on fragmentation and/or (partial) amino acid sequence of selected peptides (e.g., in tandem mass spectrometry, MS/MS; or in post source decay, TOF MS), may be useful herein for separation, detection and/or quantification of markers, peptides, polypeptides, or proteins, or nucleic acid (such as, preferably, peptides, polypeptides, or proteins). Suitable peptide MS and MS/MS techniques and systems are well-known per se (see, e.g., Methods in Molecular Biology, vol. 146:“Mass Spectrometry of Proteins and Peptides”, by Chapman, ed., Humana Press 2000, 1SBN 089603609x; Biemann 1990. Methods Enzymol 193: 455-79; or Methods in Enzymology, vol. 402:“Biological Mass Spectrometry”, by Burlingame, ed., Academic Press 2005, 1SBN 9780121828073) and may be used herein. MS arrangements, instruments and systems suitable for peptide analysis may include, without limitation, matrix-assisted laser desorption/ionisation time- of- flight (MALD1-TOF) MS; MALD1-TOF post-source-decay (PSD); MALD1-TOF/TOF; surface- enhanced laser desorption/ionization time-of-flight mass spectrometry (SELD1-TOF) MS; electrospray ionization mass spectrometry (ES1-MS); ES1-MS/MS; ES1- MS/(MS)n (n is an integer greater than zero); ES1 3D or linear (2D) ion trap MS; ES1 triple quadrupole MS; ES1 quadrupole orthogonal TOF (Q-TOF); ES1 Fourier transform MS systems; desorption/ionization on silicon (DlOS); secondary ion mass spectrometry (S1MS); atmospheric pressure chemical ionization mass spectrometry (APC1-MS); APC1-MS/MS; APC1- (MS)n; atmospheric pressure photoionization mass spectrometry (APP1-MS); APP1-MS/MS; and APP1- (MS)n. Peptide ion fragmentation in tandem MS (MS/MS) arrangements may be achieved using manners established in the art, such as, e.g., collision induced dissociation (CID). Detection and quantification of markers by mass spectrometry may involve multiple reaction monitoring (MRM), such as described among others by Kuhn et al. 2004 (Proteomics 4: 1175-86). MS peptide analysis methods may be advantageously combined with upstream peptide or protein separation or fractionation methods, such as for example with the chromatographic and other methods.
In other examples, such methods may include chromatography methods. The term “chromatography” encompasses methods for separating substances, such as chemical or biological substances, e.g., peptides, polypeptides, proteins, or nucleic acids, referred to as such and vastly available in the art. In a preferred approach, chromatography refers to a process in which a mixture of substances (analytes) carried by a moving stream of liquid or gas (“mobile phase”) is separated into components as a result of differential distribution of the analytes, as they flow around or over a stationary liquid or solid phase (“stationary phase”), between said mobile phase and said stationary phase. The stationary phase may be usually a finely divided solid, a sheet of filter material, or a thin film of a liquid on the surface of a solid, or the like. Chromatography is also widely applicable for the separation of chemical compounds of biological origin.
Chromatography may be preferably columnar (i.e., wherein the stationary phase is deposited or packed in a column), preferably liquid chromatography, and yet more preferably HPLC. While particulars of chromatography are well known in the art, for further guidance see, e.g., Meyer M., 1998, ISBN: 047198373X, and“Practical HPLC Methodology and Applications”, Bidlingmeyer, B. A., John Wiley & Sons Inc., 1993. Exemplary types of chromatography include, without limitation, high-performance liquid chromatography (HPLC), normal phase HPLC (NP-HPLC), reversed phase HPLC (RP-HPLC), ion exchange chromatography (IEC), such as cation or anion exchange chromatography, hydrophilic interaction chromatography (HILIC), hydrophobic interaction chromatography (HIC), size exclusion chromatography (SEC) including gel filtration chromatography or gel permeation chromatography, chromatofocusing, affinity chromatography such as immunoaffinity, immobilised metal affinity chromatography, and the like.
Further techniques for separating, detecting and/or quantifying markers, peptides, polypeptides, proteins, or nucleic acids, may be used, optionally in conjunction with any of the above described analysis methods. Such methods include, without limitation, chemical extraction partitioning, isoelectric focusing (IEF) including capillary isoelectric focusing (CIEF), capillary isotachophoresis (CITP), capillary electrochromatography (CEC), and the like, one-dimensional polyacrylamide gel electrophoresis (PAGE), two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), capillary gel electrophoresis (CGE), capillary zone electrophoresis (CZE), micellar electrokinetic chromatography (MEKC), free flow electrophoresis (FFE), etc. Further, standard quantitative nucleic acid measurement tools known in the art may be used. Non limiting examples include hybridisation-based analysis, microarray analysis, RNA-in-situ hybridisation (RISH), Northern-blot analysis and the like; PCR, RT-PCR, RT-qPCR, end-point PCR, digital PCR or the like; supported oligonucleotide detection, pyrosequencing, polony cyclic sequencing by synthesis, simultaneous bi-directional sequencing, single-molecule sequencing, single molecule real time sequencing, true single molecule sequencing, hybridization-assisted nanopore sequencing, sequencing by synthesis, single-cell RNA sequencing (sc-RNA seq), or the like.
In further examples, any combinations of methods such as discussed herein may be employed.
Non-limiting examples employing techniques such as discussed above include without limitation the following. An embodiment employs RNA pull-down assay. For example, endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line. For example, endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line. The RNA component is produced synthetically and conjugated with a tag configured for specific binding to a binding agent. For example, the tag is biotin and the binding agent is streptavidin. The so-tagged RNA component is captured onto streptavidin-conjugated (magnetic) beads, and a known quantity of the beads having the RNA component displayed thereon are contacted with a known quantity of the SRSF2 component, under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, the unbound SRSF2 component is washed away. The beads are collected (such as magnetically or by centrifugation), and the RNA-beads-bound SRSF2 component is optionally eluted and is suitably detected / quantified, such as by Western blotting, dot blotting, EL1SA, or MS.
Another embodiment employs protein pull-down assay. For example, SRSF2 component is recombinantly produced in and isolated from a cell line. For example, human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line. The SRSF2 component is recombinantly fused to a tag configured for specific binding to a binding agent. For example, the tag is a FLAG tag, such as N-terminal or C-terminal FLAG tag, and the binding agent is anti-FLAG antibody. The RNA component is produced synthetically. The RNA component is unlabelled or labelled (e.g., radioactive ly labelled, such as 32P- or 33P-labelled, or fluorescently- or chemiluminescently-labelled). The so-tagged SRSF2 component is captured onto anti-FLAG antibody-conjugated (magnetic) beads, and a known quantity of the beads having the SRSF2 component displayed thereon are contacted with a known quantity of the RNA component, under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, the unbound RNA component is washed away. The beads are collected (such as magnetically or by centrifugation), and the SRSF2-beads-bound RNA component is optionally eluted and suitably detected / quantified, such as by Northern blotting, dot blotting, scintillation counting, fluorescent signal detection, chemiluminiscence signal detection, or sequencing.
A yet another embodiment employs RNA electrophoretic mobility shift assay (RNA EMSA). For example, endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line. For example, endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line. The RNA component is produced synthetically and is labelled (e.g., radioactively labelled, such as 32P- or 33P-labelled, or fluorescently- or chemiluminescently-labelled). Known quantities of the SRSF2 and RNA components are contacted under conditions conducive to the binding of the SRSF2 and RNA components. The binding reaction is then separated by non- denaturing polyacrylamide gel electrophoresis (PAGE), or the SRSF2-RNA complex is crosslinked and the binding reaction is separated by denaturing PAGE. The SRSF2-bound RNA component displays a migration shift relative to the unbound RNA component. The SRSF2-bound RNA is quantified, typically following transfer onto a nylon membrane, by quantification of the label provided on the RNA component.
The evaluation of the binding of the SRSF2 component with the RNA component may in further embodiments rely on the detection of spatial proximity of moieties conjugated to the SRSF2 and RNA components, such as moieties configured to provide for fluorescence resonance energy transfer (FRET) or bioluminescence resonance energy transfer (BRET).
An embodiment employs FRET. For example, endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line. For example, endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line. The RNA component is produced synthetically. The SRSF2 component is labelled with a donor fluorophore and the RNA component is labelled with an acceptor fluorophore, wherein when the donor and acceptor fluorophores are in spatial proximity (typically in the range of 1-10 nm), the donor fluorophore in its excited state non-radiatively transfers its excitation energy to the neighbouring acceptor fluorophore, thereby causing the acceptor fluorophore to emit its characteristic fluorescence, which can be detected. Alternatively, the SRSF2 component is labelled with the acceptor fluorophore and the RNA component is labelled with the donor fluorophore. When one of the fluorophores is a fluorescent protein (FP), the SRSF2 component may be recombinantly fused to the FP. Suitable FRET pairs (donor-acceptor) include without limitation Alexa Fluor 405 - Alexa Fluor 430, Cy2 - Cy3, Cy3 - Cy5, FITC (fluorescein isothiocyanate) - TRITC (tetramethylrhodamine), PE (phycoerythrin) - APC (allophycocyanin), Alexa Fluor 488 - Alexa Fluor 514/532/546/610, Alexa Fluor 647 - Alexa Fluor 680/700/750. Suitable FRET FP pairs (donor-acceptor) include without limitation CFP (cyan FP) - YFP (yellow FP), cerulean FP - YFP, GFP (green FP)- YFP, GFP - mRFP (monomeric red FP). Known quantities of the SRSF2 and RNA components are contacted (e.g., in solution or in permeabilised cells) under conditions conducive to the binding of the SRSF2 and RNA components. The binding reaction is illuminated at a frequency configured to excite the donor fluorophore, and the light emitted by the acceptor fluorophore is suitably detected / quantified, such as using a fluorescent microscope or reader. Detailed guidance to performing FRET can be found inter alia in Bajar et al. (Sensors (Basel). 2016, vol. 16(9), 1488).
Another embodiment employs BRET ln BRET bioluminescence provides the light source (donor) for the excitation of the acceptor fluorophore, thus avoiding external illumination. For example, a bioluminescent luciferase, such as a bioluminescent luciferase from Renilla reniformis or from Oplophorus gracilirostris, may be used. Typically, the bioluminescent luciferase is recombinantly fused to one of the interaction partners ln an example, luciferase from Renilla reniformis may be used in conjunction with YFP as acceptor ln another example, luciferase from Oplophorus gracilirostris may be used in conjunction with a chloroalkane derivative of nonchloro TOM (NCT) dye with peak light emission at 635 nm as acceptor (see Machleidt et al. ACS Chem Biol. 2015, vol. 10(8), 1797-804). A BRET system based on luciferase from Oplophorus gracilirostris (NanoLuc®) and a HaloTag® protein- fluorophore conjugate has been described in Machleidt et al. {supra) and is commercialised by Promega Corp under the designation NanoBRET™ (see also Fig. 6). Hence, for example, endogenous SRSF2 component is isolated from a cell line, or SRSF2 component is recombinantly produced in and isolated from a cell line. For example, endogenous SRSF2 component is isolated from a human cell line, or human SRSF2 component is recombinantly produced in and isolated from an animal cell line, such as a human or non-human mammalian cell line. The RNA component is produced synthetically. The SRSF2 component is recombinantly fused to a bioluminescent luciferase, such as Renilla reniformis luciferase or NanoLuc® luciferase. The RNA component is conjugated with YFP or with Alexa-594, respectively. Known quantities of the SRSF2 and RNA components are contacted (e.g., in solution or in permeabilised cells) under conditions conducive to the binding of the SRSF2 and RNA components. Subsequently, a suitable luciferase substrate is added and the light emitted by the acceptor fluorophore is suitably detected / quantified, such as using a fluorescent microscope or reader. In certain embodiments, the SRSF2-modulating agent may be capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof to said one or more mr5C on the RNA molecule. Without limitation, the binding between the SRSF2 and RNA components may be reduced or decreased by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said SRSF2-modulating agent. Said percentage may refer to the value of a quantifiable variable representative of said binding, such as without limitation the quantitative a signal or read-out in an RNA pull-down, EMSA, FRET, BRET, or similar experiment. For example, inclusion of such SRSF2-modulating agent at a given concentration in a binding reaction may lead to apparent decrease in KA / increase in KD of binding between the SRSF2 and RNA components by > 1 order of magnitude (lOx), such as > 2 (100c), > 3 (IOOOc), > 4 (lxlO4), or > 5 (lxl 05) orders of magnitude.
ln certain embodiments, the lC5o of the SRSF2-modulating agent for modulating such as reducing the binding between the SRSF2 and RNA components may be 0.1 nM and 10 mM, preferably between 0.1 nM and 5 mM, more preferably between 0.1 nM and 1 mM, even more preferably between 0.1 nM and 100 nM, e.g., between 10-100 nM, preferably between 1.0-10 nM, more preferably between 0.1-5.0 nM, even more preferably between 0.1-1.0 nM.
ln certain embodiments, the present methods may further comprise determining whether the SRSF2-modulating agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant. For example, the effect of the SRSF2-modulating agent on said quantity and/or activity may be determined in a cell-free system, in cell lysates, in isolated or cultured cells or tissues, or in non-human animal model organisms. Without limitation, where the SRSF2-modulating agent reduces said quantity and/or activity, such may be reduced or decreased by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said SRSF2-modulating agent. Said percentage may refer to the value of a quantifiable variable representative of said quantity and/or activity, such as without limitation the quantitative a signal or read-out in a Western blot, EL1SA, MS, or similar experiment.
ln certain embodiments, the present methods may further comprise determining whether the SRSF2-modulating agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant, such as specifically bind to the mr5C- binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant. Specific binding particularly denotes that the SRSF2-modulating agent binds to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant substantially to the exclusion of other molecules which are random or unrelated. Specificity of binding may be determined, for example, in a cell- free system (e.g., including a suitable control protein, such as bovine serum albumin or casein), in cell lysates, or in isolated or cultured cells or tissues, such as cell lysates, cells and tissues of human origin. As an example, SRSF2-modulating agent displaying such specific binding may have affinity for the SRSF2 target under the conditions of binding at least about 100-fold, or at least about 1000-fold, or at least about 104-fold, or at least about 105-fold, or at least about 106-fold or more greater, than its affinity for a non-target molecule. An exemplary, non- limiting way for evaluating the specificity of binding of a SRSF2-modulating agent to the SRSF2 component may be pull-down of proteins from a cell lysate, such as human cell lysate, using the agent conjugated to (magnetic) beads, and identifying the pulled-down proteins by for example MS, to determine the abundance / enrichment of SRSF2 and the presence of other ‘contaminating’ proteins. An exemplary, non- limiting way for evaluating the specificity of binding of a SRSF2-modulating agent to the mr5C-binding site of the SRSF2 component may involve a computational protein modelling analysis modelling the agent into said site.
ln certain embodiments, the RNA molecule may be susceptible to splicing and the present methods may further comprise determining whether the SRSF2-modulating agent can alter the splicing of said RNA molecule.
The terms“splicing”,“splicing of a gene”,“splicing of a pre-mRNA” and similar as used herein are synonymous and have their art-established meaning. By means of additional explanation, splicing denotes the process and means of removing intervening sequences (introns) from pre- mRNA in the process of producing mature mRNA. The reference to splicing particularly aims at native splicing such as occurs under normal physiological conditions. The terms“pre-mRNA” and “transcript” are used herein to denote RNA species that precede mature mRNA, such as in particular a primary RNA transcript and any partially processed forms thereof. Sequence elements required for splicing refer particularly to cis elements in the sequence of pre-mRNA which direct the cellular splicing machinery (spliceosome) towards correct and precise removal of introns from the pre-mRNA. Sequence elements involved in splicing are generally known per se and can be further determined by known techniques including inter alia mutation or deletion analysis. By means of further explanation,“splice donor site” or“5' splice site” generally refer to a conserved sequence immediately adjacent to an exon-intron boundary at the 5’ end of an intron. Commonly, a splice donor site may contain a dinucleotide GU, and may involve a consensus sequence of about 8 bases at about positions +2 to -6.“Splice acceptor site” or“3' splice site” generally refers to a conserved sequence immediately adjacent to an intron-exon boundary at the 3’ end of an intron. Commonly, a splice acceptor site may contain a dinucleotide AG, and may involve a consensus sequence of about 16 bases at about positions -14 to +2.
An exemplary, non-limiting way for evaluating the impact of an SRSF2-modulating agent on the splicing of an RNA molecule may comprise i) providing or being provided with cells expressing SRSF2 (endogenously or recombinantly) and expressing an RNA molecule (endogenously or recombinantly), wherein said RNA molecule is susceptible to splicing and SRSF2 plays a role in said splicing, ii) contacting said cells with said SRSF2-modulating agent, and iii) determining whether the splicing of said RNA molecule has been altered. Altered splicing may manifest as, for example, diminished quantity of the RNA molecule or of a protein encoded by said RNA molecule and/or as production of alternatively-spliced species of said RNA molecule. Such alteration can be detected by conventional techniques, such as Northern blotting or RNA sequencing.
In certain embodiments, the present methods may further comprise determining whether the SRSF2-modulating agent displays anti-neoplastic property, such as anti-cancer property. This broadly refers to any the agent’s ability to act to prevent, inhibit or halt the emergence or development of a neoplasm. By means of an example, anti-neoplastic properties may particularly include, cytostatic effects on neoplastic cells or tissues.
A further aspect provides an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
A related aspect provides a method of treating a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation in a subject, comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule.
A further related aspect provides the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
A further related aspect provides the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
Features, characteristics or embodiments discussed elsewhere in the present specification in connection with the elements of these aspects, such as inter alia in connection with the agent, SRSF2-modulating agent, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof, the RNA molecule comprising one or more mr5C, the binding of the SRSF2 and RNA components and modulation thereof by the SRSF2-modulating agent, apply mutatis mutandis to these aspects.
Hence, in certain embodiments:
the agent is capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to the one or more mr5C on the RNA molecule;
the agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant;
the agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant; and/or
the RNA molecule is susceptible to splicing and the agent can alter the splicing of said RNA molecule.
The terms “subject”, “individual” or “patient” are used interchangeably throughout this specification, and typically and preferably denote humans, but may also encompass reference to non-human animals, preferably warm-blooded animals, even more preferably mammals, such as, e.g., non-human primates, rodents, canines, felines, equines, ovines, porcines, and the like. The term“non-human animals” includes all vertebrates, e.g., mammals, such as non-human primates, (particularly higher primates), sheep, dog, rodent (e.g. mouse or rat), guinea pig, goat, pig, cat, rabbits, cows, and non-mammals such as chickens, amphibians, reptiles etc. In certain embodiments, the subject is a non-human mammal. In certain preferred embodiments, the subject is human. In other embodiments, the subject is an experimental animal or animal substitute as a disease model. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. Examples of subjects include humans, dogs, cats, cows, goats, and mice. The term subject is further intended to include transgenic species. In certain embodiments, the subject may be a human subject, and said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of human origin.
As used throughout this specification, the terms“therapy” or“treatment” refer to the alleviation or measurable lessening of one or more symptoms or measurable markers of a pathological condition such as a disease or disorder. The terms encompass primary treatments as well as neo-adjuvant treatments, adjuvant treatments and adjunctive therapies.
The term“prophylactically effective amount” refers to an amount of an active compound or pharmaceutical agent that inhibits or delays in a subject the onset of a disorder as being sought by a researcher, veterinarian, medical doctor or other clinician. The term“therapeutically effective amount” as used herein, refers to an amount of active compound or pharmaceutical agent that elicits the biological or medicinal response in a subject that is being sought by a researcher, veterinarian, medical doctor or other clinician, which may include inter alia alleviation of the symptoms of the disease or condition being treated. Methods are known in the art for determining therapeutically and prophylactically effective doses for the pharmaceutical formulation as taught herein.
The term“dysregulation” as used herein refers to an abnormality, deviation, or alteration in the value or quantity of a variable that is said to be dysregulated in one or more cells or tissues of a subject from the value or quantity of said variable in corresponding one or more cells or tissues of a healthy subject. The term may particularly denote a statistically significant deviation or alteration. For example, values representing dysregulation may fall outside of error margins of reference values in a healthy population (as expressed, for example, by standard deviation or standard error, or by a predetermined multiple thereof, e.g., ±lxSD or ±2xSD or ±3xSD, or ±lxSE or ±2xSE or ±3xSE). For example, values representing dysregulation may fall outside of a reference range defined by reference values in a healthy population (for example, outside of a range which comprises >40%, > 50%, >60%, >70%, >75% or >80% or >85% or >90% or >95% or even >100% of values in said population). Dysregulation specifically encompasses both increase (e.g., increased expression and/or activity) or decrease (e.g., decreased expression and/or activity) in the variable that is said to be dysregulated. The term encompasses any extent of such increase or decrease.
Any one or more of the several successive molecular mechanisms involved in the expression of SRSF2 may be dysregulated and may lead to dysregulation of the quantity of SRSF2 produced by one or more cells or tissues of a subject. Without limitation, these may include alterations in the gene sequence (e.g., the polypeptide-encoding, non-coding and/or regulatory portions of the gene sequence), the transcription of the gene into RNA, the polyadenylation and where applicable splicing and/or other post-transcriptional modifications of the RNA into mRNA, the localisation of the mRNA into cell cytoplasm, where applicable other post-transcriptional modifications of the mRNA, the translation of the mRNA into a polypeptide chain, where applicable post-translational modifications of the polypeptide, and/or folding of the polypeptide chain into the mature conformation of the polypeptide. For compartmentalised polypeptides, such as secreted polypeptides and transmembrane polypeptides, this may further include targeting trafficking of the polypeptides, i.e., the cellular mechanism by which polypeptides are transported to the appropriate sub-cellular compartment or organelle, membrane, e.g. the plasma membrane, or outside the cell.
Any one or more aspects of SRSF2 activity or function may be dysregulated in one or more cells or tissues of a subject. For example, the binding of SRSF2 to RNAs comprising one or more mr5C may be dyregulated, or modulation of splicing of RNAs or mRNAs, particularly RNAs or mRNAs comprising one or more mr5C, by SRSF2 may be dyregulated, or both. By means of an example, dyregulated binding of SRSF2 to an RNA comprising one or more mr5C may alter the corresponding equilibrium constant for the dissociation (KD) by > 1 order of magnitude (lOx), such as > 2 (IOOc), > 3 (IOOOc), > 4 (lx lO4), or > 5 (lx l 05) orders of magnitude, compared to normal or reference binding.
ln certain embodiments, the dysregulation of SRSF2 expression and/or activity may be due to a mutation in SRSF2. Any types of mutations and particular are contemplated herein, inter alia SRSF2 mutations and mutated SRSF2 as described elsewhere in this specification.
ln certain embodiments, RNA mr5C methylation may be dysregulated in one or more cells or tissues of a subject. The extent or quantity of mr5C methylation of an RNA molecule or of a population of RNA molecules or of transcriptome may be expressed by a convenient variable, such as the ratio of 5-methylated cytosines to all cytosines, or the quantity of 5-methylated cytosines per given quantity of RNA (w/w), or the quantity of 5-methylated cytosines per given quantity of cells or tissue (w/w), or similar. Methods for measuring mr5C are available, and typically rely on either separation according to physicochemical properties, differential enzymatic turnover or differential chemical reactivity. Suitable methods and assays are reviewed for example in Motorin et al. (Nucleic Acids Research. 2010, vol. 38, 1415-1430) and Helm and Motorin (Nature Reviews Genetics. 2017, vol. 18, 275-291).
ln certain embodiments, the disease is a neoplastic disease.
Thus, also provided are the following aspects:
an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an
RNA molecule, for use in the treatment of a neoplastic disease; a method of treating a neoplastic disease in a subject, comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule; use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of a neoplastic disease;
the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the treatment of a neoplastic disease.
In certain embodiments, the disease is cancer.
Thus, also provided are the following aspects:
an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of cancer;
a method of treating cancer in a subject, comprising administering to the subject a therapeutically or prophylactically effective amount of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule;
use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the manufacture of a medicament for use in treatment of cancer;
the use of an agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule for the treatment of cancer.
The term“neoplastic disease” generally refers to any disease or disorder characterized by neoplastic cell growth and proliferation, whether benign (not invading surrounding normal tissues, not forming metastases), pre-malignant (pre-cancerous), or malignant (invading adjacent tissues and capable of producing metastases). The term neoplastic disease generally includes all transformed cells and tissues and all cancerous cells and tissues. Neoplastic diseases or disorders include, but are not limited to abnormal cell growth, benign tumors, premalignant or precancerous lesions, malignant tumors, and cancer. Examples of neoplastic diseases or disorders are benign, pre-malignant, or malignant neoplasms located in any tissue or organ, such as in the prostate, colon, abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, or urogenital tract.
In certain embodiments of the methods or uses as taught herein, the neoplastic disease may be a tumor or may be characterized by the presence of a tumor.
As used herein, the terms“tumor” or“tumor tissue” refer to an abnormal mass of tissue that results from excessive cell division. A tumor or tumor tissue comprises tumor cells which are neoplastic cells with abnormal growth properties and no useful bodily function. Tumors, tumor tissue and tumor cells may be benign, pre-malignant or malignant, or may represent a lesion without any cancerous potential. A tumor or tumor tissue may also comprise tumor-associated non-tumor cells, e.g., vascular cells which form blood vessels to supply the tumor or tumor tissue. Non-tumor cells may be induced to replicate and develop by tumor cells, for example, the induction of angiogenesis in a tumor or tumor tissue.
ln certain embodiments, the tumor, including any metastases of the tumor, may be of epithelial origin ln certain embodiments, the tumor, including any metastases of the tumor, may originate from glial cells, astrocytes, oligodendrocyte progenitor cells or neural stem cells.
Tumors of epithelial origin include any tumors originated from epithelial tissue in any of several sites, such as without limitation breast, lung, bladder, cervix, intestine, colon, skin, head and neck (including lips, oral cavity, salivary glands, nasal cavity, nasopharynx, paranasal sinuses, pharynx, throat, larynx, and associated structures), esophagus, thyroid, kidney, liver, pancreas, penis, testes, prostate, vagina, or anus.
As used herein, the term“cancer” refers to a malignant neoplasm characterized by deregulated or unregulated cell growth. The term“cancer” includes primary malignant cells or tumors (e.g., those whose cells have not migrated to sites in the subject’s body other than the site of the original malignancy or tumor) and secondary malignant cells or tumors (e.g., those arising from metastasis, the migration of malignant cells or tumor cells to secondary sites that are different from the site of the original tumor). The term“metastatic” or“metastasis” generally refers to the spread of a cancer from one organ or tissue to another non-adjacent organ or tissue. The occurrence of the neoplastic disease in the other non-adjacent organ or tissue is referred to as metastasis.
Examples of cancer include but are not limited to carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More particular examples of such cancers include without limitation: squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung and large cell carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioma, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulvar cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as CNS cancer, melanoma, head and neck cancer, bone cancer, bone marrow cancer, duodenum cancer, esophageal cancer, thyroid cancer, or hematological cancer.
Other examples of cancers or malignancies include, but are not limited to: Acute Childhood Lymphoblastic Leukemia, Acute Lymphoblastic Leukemia, Acute Lymphocytic Leukemia, Acute Myeloid Leukemia, Adrenocortical Carcinoma, Adult (Primary) Hepatocellular Cancer, Adult (Primary) Liver Cancer, Adult Acute Lymphocytic Leukemia, Adult Acute Myeloid Leukemia, Adult Hodgkin's Disease, Adult Hodgkin's Lymphoma, Adult Lymphocytic Leukemia, Adult Non- Hodgkin's Lymphoma, Adult Primary Liver Cancer, Adult Soft Tissue Sarcoma, AIDS-Related Lymphoma, AIDS-Related Malignancies, Anal Cancer, Astrocytoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Brain Stem Glioma, Brain Tumors, Breast Cancer, Cancer of the Renal Pelvis and Urethra, Central Nervous System (Primary) Lymphoma, Central Nervous System Lymphoma, Cerebellar Astrocytoma, Cerebral Astrocytoma, Cervical Cancer, Childhood (Primary) Hepatocellular Cancer, Childhood (Primary) Liver Cancer, Childhood Acute Lymphoblastic Leukemia, Childhood Acute Myeloid Leukemia, Childhood Brain Stem Glioma, Glioblastoma, Childhood Cerebellar Astrocytoma, Childhood Cerebral Astrocytoma, Childhood Extracranial Germ Cell Tumors, Childhood Hodgkin's Disease, Childhood Hodgkin's Lymphoma, Childhood Hypothalamic and Visual Pathway Glioma, Childhood Lymphoblastic Leukemia, Childhood Medulloblastoma, Childhood Non-Hodgkin's Lymphoma, Childhood Pineal and Supratentorial Primitive Neuroectodermal Tumors, Childhood Primary Liver Cancer, Childhood Rhabdomyosarcoma, Childhood Soft Tissue Sarcoma, Childhood Visual Pathway and Hypothalamic Glioma, Chronic Lymphocytic Leukemia, Chronic Myelogenous Leukemia, Colon Cancer, Cutaneous T-Cell Lymphoma, Endocrine Pancreas Islet Cell Carcinoma, Endometrial Cancer, Ependymoma, Epithelial Cancer, Esophageal Cancer, Ewing's Sarcoma and Related Tumors, Exocrine Pancreatic Cancer, Extracranial Germ Cell Tumor, Extragonadal Germ Cell Tumor, Extrahepatic Bile Duct Cancer, Eye Cancer, Female Breast Cancer, Gallbladder Cancer, Gastric Cancer, Gastrointestinal Carcinoid Tumor, Gastrointestinal Tumors, Germ Cell Tumors, Gestational Trophoblastic Tumor, Hairy Cell Leukemia, Head and Neck Cancer, Hepatocellular Cancer, Hodgkin's Disease, Hodgkin's Lymphoma, Hypergammaglobulinemia, Hypopharyngeal Cancer, Intestinal Cancers, Intraocular Melanoma, Islet Cell Carcinoma, Islet Cell Pancreatic Cancer, Kaposi's Sarcoma, Kidney Cancer, Laryngeal Cancer, Lip and Oral Cavity Cancer, Liver Cancer, Lung Cancer, Lymphoproliferative Disorders, Macroglobulinemia, Male Breast Cancer, Malignant Mesothelioma, Malignant Thymoma, Medulloblastoma, Melanoma, Mesothelioma, Metastatic Occult Primary Squamous Neck Cancer, Metastatic Primary Squamous Neck Cancer, Metastatic Squamous Neck Cancer, Multiple Myeloma, Multiple Myeloma/Plasma Cell Neoplasm, Myelodysplastic Syndrome, Myelogenous Leukemia, Myeloid Leukemia, Myeloproliferative Disorders, Nasal Cavity and Paranasal Sinus Cancer, Nasopharyngeal Cancer, Neuroblastoma, Non-Hodgkin's Lymphoma During Pregnancy, Non-melanoma Skin Cancer, Non-Small Cell Lung Cancer, Occult Primary Metastatic Squamous Neck Cancer, Oropharyngeal Cancer, Osteo- /Malignant Fibrous Sarcoma, Osteosarcoma/Malignant Fibrous Histiocytoma, Osteosarcoma/Malignant Fibrous Histiocytoma of Bone, Ovarian Epithelial Cancer, Ovarian Germ Cell Tumour, Ovarian Low Malignant Potential Tumor, Pancreatic Cancer, Paraganglioma, Paraproteinemias, Purpura, Parathyroid Cancer, Penile Cancer, Pheochromocytoma, Pituitary Tumor, Plasma Cell Neoplasm/Multiple Myeloma, Primary Central Nervous System Lymphoma, Primary Liver Cancer, Prostate Cancer, Rectal Cancer, Renal Cell Cancer, Renal Pelvis and Urethra Cancer, Retinoblastoma, Rhabdomyosarcoma, Salivary Gland Cancer, Sarcoidosis Sarcomas, Sezary Syndrome, Skin Cancer, Small Cell Lung Cancer, Small Intestine Cancer, Soft Tissue Sarcoma, Squamous Neck Cancer, Stomach Cancer, Supratentorial Primitive Neuroectodermal and Pineal Tumors, T-Cell Lymphoma, Testicular Cancer, Thymoma, Thyroid Cancer, Transitional Cell Cancer of the Renal Pelvis and Urethra, Transitional Renal Pelvis and Urethra Cancer, Trophoblastic Tumours, Urethra and Renal Pelvis Cell Cancer, Urethral Cancer, Uterine Cancer, Uterine Sarcoma, Vaginal Cancer, Visual Pathway and Hypothalamic Glioma, Vulvar Cancer, Waldenstrom's Macroglobulinemia, or Wilms’ Tumour.
In certain embodiments, the disease may be myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML).
In certain embodiments, one or more agents as taught herein may be formulated into and administered as pharmaceutical formulations or compositions. Such pharmaceutical formulations or compositions may be comprised in a kit of parts.
The term“pharmaceutically acceptable” as used herein is consistent with the art and means compatible with the other ingredients of a pharmaceutical composition and not deleterious to the recipient thereof.
As used herein,“carrier” or“excipient” includes any and all solvents, diluents, buffers (such as, e.g., neutral buffered saline or phosphate buffered saline), solubilisers, colloids, dispersion media, vehicles, fillers, chelating agents (such as, e.g., EDTA or glutathione), amino acids (such as, e.g., glycine), proteins, disintegrants, binders, lubricants, wetting agents, emulsifiers, sweeteners, colorants, flavourings, aromatisers, thickeners, agents for achieving a depot effect, coatings, antifungal agents, preservatives, antioxidants, tonicity controlling agents, absorption delaying agents, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active substance, its use in the therapeutic compositions may be contemplated.
Illustrative, non-limiting carriers for use in formulating the pharmaceutical compositions include, for example, oil-in-water or water-in-oil emulsions, aqueous compositions with or without inclusion of organic co-solvents suitable for intravenous (IV) use, liposomes or surfactant- containing vesicles, microspheres, microbeads and microsomes, powders, tablets, capsules, suppositories, aqueous suspensions, aerosols, and other carriers apparent to one of ordinary skill in the art.
Pharmaceutical compositions as intended herein may be formulated for essentially any route of administration, such as without limitation, oral administration (such as, e.g., oral ingestion or inhalation), intranasal administration (such as, e.g., intranasal inhalation or intranasal mucosal application), parenteral administration (such as, e.g., subcutaneous, intravenous, intramuscular, intraperitoneal or intrastemal injection or infusion), transdermal or transmucosal (such as, e.g., oral, sublingual, intranasal) administration, topical administration, rectal, vaginal or intra-tracheal instillation, and the like. In this way, the therapeutic effects attainable by the methods and compositions can be, for example, systemic, local, tissue-specific, etc., depending of the specific needs of a given application.
For example, for oral administration, pharmaceutical compositions may be formulated in the form of pills, tablets, lacquered tablets, coated (e.g., sugar-coated) tablets, granules, hard and soft gelatin capsules, aqueous, alcoholic or oily solutions, syrups, emulsions or suspensions. In an example, without limitation, preparation of oral dosage forms may be is suitably accomplished by uniformly and intimately blending together a suitable amount of the active compound in the form of a powder, optionally also including finely divided one or more solid carrier, and formulating the blend in a pill, tablet or a capsule. Exemplary but non-limiting solid carriers include calcium phosphate, magnesium stearate, talc, sugars (such as, e.g., glucose, mannose, lactose or sucrose), sugar alcohols (such as, e.g., mannitol), dextrin, starch, gelatin, cellulose, polyvinylpyrrolidine, low melting waxes and ion exchange resins. Compressed tablets containing the pharmaceutical composition can be prepared by uniformly and intimately mixing the active ingredient with a solid carrier such as described above to provide a mixture having the necessary compression properties, and then compacting the mixture in a suitable machine to the shape and size desired. Moulded tablets maybe made by moulding in a suitable machine, a mixture of powdered compound moistened with an inert liquid diluent. Suitable carriers for soft gelatin capsules and suppositories are, for example, fats, waxes, semisolid and liquid polyols, natural or hardened oils, etc.
For example, for oral or nasal aerosol or inhalation administration, pharmaceutical compositions may be formulated with illustrative carriers, such as, e.g., as in solution with saline, polyethylene glycol or glycols, DPPC, methylcellulose, or in mixture with powdered dispersing agents, further employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilising or dispersing agents known in the art. Suitable pharmaceutical formulations for administration in the form of aerosols or sprays are, for example, solutions, suspensions or emulsions of the agents as taught herein or their physiologically tolerable salts in a pharmaceutically acceptable solvent, such as ethanol or water, or a mixture of such solvents. If required, the formulation can also additionally contain other pharmaceutical auxiliaries such as surfactants, emulsifiers and stabilizers as well as a propellant. Illustratively, delivery may be by use of a single-use delivery device, a mist nebuliser, a breath-activated powder inhaler, an aerosol metered-dose inhaler (MDI) or any other of the numerous nebuliser delivery devices available in the art. Additionally, mist tents or direct administration through endotracheal tubes may also be used.
Examples of carriers for administration via mucosal surfaces depend upon the particular route, e.g., oral, sublingual, intranasal, etc. When administered orally, illustrative examples include pharmaceutical grades of mannitol, starch, lactose, magnesium stearate, sodium saccharide, cellulose, magnesium carbonate and the like, with mannitol being preferred. When administered intranasally, illustrative examples include polyethylene glycol, phospholipids, glycols and glycolipids, sucrose, and/or methylcellulose, powder suspensions with or without bulking agents such as lactose and preservatives such as benzalkonium chloride, EDTA. In a particularly illustrative embodiment, the phospholipid 1,2 dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) is used as an isotonic aqueous carrier at about 0.01-0.2% for intranasal administration of the compound of the subject invention at a concentration of about 0.1 to 3.0 mg/ml.
For example, for parenteral administration, pharmaceutical compositions may be advantageously formulated as solutions, suspensions or emulsions with suitable solvents, diluents, solubilisers or emulsifiers, etc. Suitable solvents are, without limitation, water, physiological saline solution or alcohols, e.g. ethanol, propanol, glycerol, in addition also sugar solutions such as glucose, invert sugar, sucrose or mannitol solutions, or alternatively mixtures of the various solvents mentioned. The injectable solutions or suspensions may be formulated according to known art, using suitable non-toxic, parenterally-acceptable diluents or solvents, such as mannitol, l,3-butanediol, water, Ringer's solution or isotonic sodium chloride solution, or suitable dispersing or wetting and suspending agents, such as sterile, bland, fixed oils, including synthetic mono- or diglycerides, and fatty acids, including oleic acid. The agents and pharmaceutically acceptable salts thereof of the invention can also be lyophilised and the lyophilisates obtained used, for example, for the production of injection or infusion preparations. For example, one illustrative example of a carrier for intravenous use includes a mixture of 10% USP ethanol, 40% USP propylene glycol or polyethylene glycol 600 and the balance USP Water for Injection (WFI). Other illustrative carriers for intravenous use include 10% USP ethanol and USP WFI; 0.01-0.1% triethanolamine in USP WFI; or 0.01-0.2% dipalmitoyl diphosphatidylcholine in USP WFI; and 1-10% squalene or parenteral vegetable oil-in-water emulsion. Illustrative examples of carriers for subcutaneous or intramuscular use include phosphate buffered saline (PBS) solution, 5% dextrose in WFI and 0.01- 0.1% triethanolamine in 5% dextrose or 0.9% sodium chloride in USP WFI, or a 1 to 2 or 1 to 4 mixture of 10% USP ethanol, 40% propylene glycol and the balance an acceptable isotonic solution such as 5% dextrose or 0.9% sodium chloride; or 0.01-0.2% dipalmitoyl diphosphatidylcholine in USP WFI and 1 to 10% squalene or parenteral vegetable oil- in- water emulsions.
Where aqueous formulations are preferred, such may comprise one or more surfactants. For example, the composition can be in the form of a micellar dispersion comprising at least one suitable surfactant, e.g., a phospholipid surfactant. Illustrative examples of phospholipids include diacyl phosphatidyl glycerols, such as dimyristoyl phosphatidyl glycerol (DPMG), dipalmitoyl phosphatidyl glycerol (DPPG), and distearoyl phosphatidyl glycerol (DSPG), diacyl phosphatidyl cholines, such as dimyristoyl phosphatidylcholine (DPMC), dipalmitoyl phosphatidylcholine (DPPC), and distearoyl phosphatidylcholine (DSPC); diacyl phosphatidic acids, such as dimyristoyl phosphatidic acid (DPMA), dipahnitoyl phosphatidic acid (DPPA), and distearoyl phosphatidic acid (DSPA); and diacyl phosphatidyl ethanolamines such as dimyristoyl phosphatidyl ethanolamine (DPME), dipalmitoyl phosphatidyl ethanolamine (DPPE) and distearoyl phosphatidyl ethanolamine (DSPE). Typically, a surfactant: active substance molar ratio in an aqueous formulation will be from about 10:1 to about 1 :10, more typically from about 5:1 to about 1 :5, however any effective amount of surfactant may be used in an aqueous formulation to best suit the specific objectives of interest.
When rectally administered in the form of suppositories, these formulations may be prepared by mixing the compounds according to the invention with a suitable non-irritating excipient, such as cocoa butter, synthetic glyceride esters or polyethylene glycols, which are solid at ordinary temperatures, but liquidify and/or dissolve in the rectal cavity to release the drug.
Suitable carriers for microcapsules, implants or rods are, for example, copolymers of glycolic acid and lactic acid. One skilled in this art will recognize that the above description is illustrative rather than exhaustive. Indeed, many additional formulations techniques and pharmaceutically-acceptable excipients and carrier solutions are well-known to those skilled in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens.
The dosage or amount of the present active agents used, optionally in combination with one or more other active compound to be administered, depends on the individual case and is, as is customary, to be adapted to the individual circumstances to achieve an optimum effect. Thus, it depends on the nature and the severity of the disorder to be treated, and also on the sex, age, body weight, general health, diet, mode and time of administration, and individual responsiveness of the human or animal to be treated, on the route of administration, efficacy, metabolic stability and duration of action of the compounds used, on whether the therapy is acute or chronic or prophylactic, or on whether other active compounds are administered in addition to the agent(s) as taught herein.
Without limitation, depending on the type and severity of the disease, a typical daily dosage of an agent as disclosed herein, or combinations of two or more such agents, might range from about 1 pg/kg to 1 g/kg of body weight or more, depending on the factors mentioned above. For instance, a daily dosage of the agent(s) may range from about 1 mg/kg to 1 g/kg of body weight. For repeated administrations over several days or longer, depending on the condition, the treatment is sustained until a desired suppression of disease symptoms occurs. A preferred dosage of the agent(s) may be in the range from about 10.0 mg/kg to about 500 mg/kg of body weight. Thus, one or more doses of about 10.0 mg/kg, 20.0 mg/kg, 50.0 mg/kg, 100 mg/kg, 200 mg/kg, 300 mg/kg, 400 mg/kg, or 500 mg/kg (or any combination thereof) may be administered to the patient. Such doses may be administered intermittently, e.g., every day, every week or every two or three weeks.
In certain embodiments, the agent(s) may be administered daily during the treatment. In certain embodiments, the agent(s) may be administered at least once a day during the treatment, for example the agent(s) may be administered at least twice a day during the treatment, for example the agent(s) may be administered at least three times a day during the treatment. In certain embodiments, the agent(s) may be administered continuously during the treatment for instance in an aqueous drinking solution.
In certain embodiments, the agent(s) or pharmaceutical formulation as taught herein may be used alone or in combination with one or more active compounds that are suitable in the treatment of diseases as disclosed herein, such as neoplastic diseases, such as cancer (i.e., combination therapy). The latter can be administered before, after, or simultaneously with the administration of the agent(s) or pharmaceutical formulation as taught herein.
Non-limiting examples of anti-cancer therapies include surgery, radiotherapy, chemotherapy, biological therapy, and combinations thereof, as generally known in the art.
The present realisation that SRSF2 is a reader capable of recognising the mr5C modification also allows the detection and/or quantification of mr5C on RNA or RNA comprising mr5C, using a SRSF2 reagent as a‘detection tool’.
Hence, an aspect provides an in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
Features, characteristics or embodiments discussed elsewhere in the present specification in connection with the elements of this aspects, such as inter alia in connection with the RNA molecule comprising one or more mr5C, the SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant thereof, the binding of the SRSF2 and RNA components and the methods for detection and/or quantification thereof, apply mutatis mutandis to this aspects.
The terms“sample” or“biological sample” as used throughout this specification include any biological specimen obtained (isolated, removed) from a subject. Samples may include without limitation organ tissue (e.g., primary or metastatic tumor tissue), whole blood, plasma, serum, whole blood cells, red blood cells, white blood cells (e.g., peripheral blood mononuclear cells), saliva, urine, stool (feces), tears, sweat, sebum, nipple aspirate, ductal lavage, tumor exudates, synovial fluid, cerebrospinal fluid, lymph, fine needle aspirate, amniotic fluid, any other bodily fluid, exudate or secretory fluid, cell lysates, cellular secretion products, inflammation fluid, semen and vaginal secretions. Preferably, a sample may be readily obtainable by non-invasive or minimally invasive methods, such as blood collection (‘liquid biopsy’), urine collection, feces collection, tissue (e.g., tumor tissue) biopsy or fine-needle aspiration, allowing the provision / removal / isolation of the sample from a subject. The term“tissue” as used herein encompasses all types of cells of the body including cells of organs but also including blood and other body fluids recited above. The tissue may be healthy or affected by pathological alterations, e.g., tumor tissue. The tissue may be from a living subject or may be cadaveric tissue.
Particularly useful samples may be those known to comprise, or expected or predicted to comprise, or known to potentially comprise, or expected or predicted to potentially comprise cells having dysregulation of RNA mr5C methylation, or tumor or cancer cells. Any suitable weight or volume of a sample may be removed from a subject for analysis. Without limitation, a liquid sample may have a volume between 1 ml and 20 ml, such as 5 ml, 7.5 ml, 10 ml, 15 ml or 20 ml. A solid sample may have a weight of between 1 g and 20 g, such as 5 g, 7.5 g, 10 g, 15 g or 20 g.
The biological sample may be any sample in which the quantity, activity and/or methylation level of a relevant marker can be determined. Preferably, the biological sample is a neoplastic tissue sample, such as a tumor sample, e.g., a primary or metastatic tumor sample. The biological sample may also be derived from a biological fluid or bodily fluid, for example, whole blood, blood, urine, lymph fluid, serum, plasma, nipple aspirate, ductal fluid, and tumor exudate ft has been shown in the literature that cancer or tumor cells often release genomic DNA in circulating or other bodily fluids. Since said genomic DNA has the same methylation profile of the DNA inside the tumor or cancer cell, said methylation profile can be detected in the circulating or other bodily fluid sample. This has for example been reviewed by Qureshi et al., 2010 (lnt. J. Surgery 2010, 8:194-198), hereby incorporated by reference in its entirety. A skilled person will appreciate that the same may apply to RNA. ln certain embodiments, the sample is a bodily fluid comprising neoplastic cells.
The present realisation that SRSF2 is a reader capable of recognising the mr5C modification also allows to predict or evaluate whether a given mutation in SRSF2 may be causative of or may contribute to a neoplastic disease. For example, such SRSF2 mutation may be a mutation discovered or identified in a subject having a neoplastic disease. For example, such SRSF2 mutation may be a germline mutation discovered or identified in a subject having a neoplastic disease. For example, such SRSF2 mutation may be a somatic mutation discovered or identified in a subject having a neoplastic disease, particularly in one or more neoplastic cells of said subject. This prediction or evaluation is based on the premise that mutations which affect the binding of SRSF2 to mr5C on RNA are likely or probable to be causative of or contributory to neoplastic diseases, such as likely or probable to facilitate the emergence and/or maintenance of the neoplastic phenotype of cells.
Hence, an aspect provides an in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
(a) measuring the binding of SRSF2 polypeptide or biologically active fragment thereof comprising said mutation to an RNA molecule comprising one or more mr5C;
(b) determining that the mutation causes or contributes to the neoplastic disease when the binding as measured in (a) differs from binding of an SRSF2 polypeptide or a biologically active fragment thereof not comprising said mutation to the RNA molecule. Features, characteristics or embodiments discussed elsewhere in the present specification in connection with the elements of this aspects, such as inter alia in connection with mutations, SRSF2 mutations, neoplastic diseases, the SRSF2 polypeptide or biologically active fragment thereof, the RNA molecule comprising one or more mr5C, the binding of the SRSF2 and RNA components and the methods for detection and/or quantification thereof, apply mutatis mutandis to this aspects.
The present realisation that SRSF2 is a reader capable of recognising the mr5C modification, and that mutations which affect the binding of SRSF2 to mr5C on RNA may cause or contribute to neoplastic diseases, also allows to diagnose neoplastic diseases in subjects.
Hence, an aspect provides a method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
Features, characteristics or embodiments discussed elsewhere in the present specification in connection with the elements of this aspects, such as inter alia in connection with mutations, SRSF2 mutations, neoplastic diseases, the SRSF2 polypeptide, the RNA molecule comprising one or more mr5C, the binding of the SRSF2 and RNA components and the methods for detection and/or quantification thereof, apply mutatis mutandis to this aspects.
The terms“diagnosis” are commonplace and well-understood in medical practice. By means of further explanation and without limitation the term“diagnosis” generally refers to the process or act of recognizing, deciding on or concluding on a disease or condition in a subject on the basis of symptoms and signs and/or from results of various diagnostic procedures (such as, for example, from knowing the presence, absence and/or quantity of one or more biomarkers characteristic of the diagnosed disease or condition).
The present application also provides aspects and embodiments as set forth in the following Statements:
Statement 1. An in vitro method for identifying a serine and arginine rich splicing factor 2 (SRSF2)-modulating agent, said method comprising:
contacting a SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof and a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C), wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant binds to said one or more mr5C on the RNA molecule, with a test agent; and determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
Statement 2. The method according to Statement 1, wherein the SRSF2-modulating agent can reduce the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
Statement 3. The method according to Statement 1 or 2, further comprising determining whether the SRSF2-modulating agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
Statement 4. The method according to any one of Statements 1 to 3, further comprising determining whether the SRSF2-modulating agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
Statement 5. The method according to any one of Statements 1 to 4, wherein said RNA molecule is susceptible to splicing and said method further comprises determining whether the SRSF2- modulating agent can alter the splicing of said RNA molecule.
Statement 6. The method according to any one of Statements 1 to 5, further comprising determining whether the SRSF2-modulating agent displays anti-neoplastic property, such as anti-cancer property.
Statement 7. The method according to any one of Statements 1 to 6, wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant and/or the RNA molecule is of human origin.
Statement 8. The method according to any one of Statements 1 to 7, wherein the amino acid sequence of said SRSF2 polypeptide is as set forth in GenBank accession no. NP 001182356.1.
Statement 9. The method according to any one of Statements 1 to 7, wherein the mutated SRSF2 polypeptide is mutated at:
(a) one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide; (b) amino acid position 95 relative to a wild-type SRSF2 polypeptide;
(c) one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide; and/or
(d) one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide.
Statement 10. The method according to any one of Statements 1 to 9, wherein the method is performed in a cell- free system or in a cell lysate or in isolated or cultured cells or in an isolated or cultured tissue.
Statement 11. The method according to any one of Statements 1 to 10, wherein the test agent is selected from the group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof.
Statement 12. The method according to Statement 11, wherein the chemical substance is an organic molecule, preferably a small organic molecule, or wherein the nucleic acid is an oligonucleotide.
Statement 13. The method according to Statement 12, wherein said oligonucleotide is capable of specifically hybridising with said RNA molecule and comprises one or more mr5C.
Statement 14. An agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
Statement 15. The agent for use according to Statement 14, wherein the agent is capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to the one or more mr5C on the RNA molecule.
Statement 16. The agent for use according to Statement 14 or 15, wherein the agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant.
Statement 17. The agent for use according to any one of Statements 14 to 16, wherein the agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant.
Statement 18. The agent for use according to any one of Statements 14 to 17, wherein said RNA molecule is susceptible to splicing and said agent can alter the splicing of said RNA molecule.
Statement 19. The agent for use according to any one of Statements 14 to 18, wherein the dysregulation of SRSF2 expression and/or activity is due to a mutation in SRSF2.
Statement 20. The agent for use according to any one of Statements 14 to 19, wherein the disease is a neoplastic disease, such as cancer.
Statement 21. The agent for use according to any one of Statements 14 to 20, wherein the disease is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML).
Statement 22. The agent for use according to any one of Statements 14 to 21 in a human subject, wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of human origin.
Statement 23. The agent or composition for use according to any one of Statements 14 to 22, wherein the mutated SRSF2 polypeptide is mutated at:
(a) one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide;
(b) amino acid position 95 relative to a wild-type SRSF2 polypeptide;
(c) one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide; and/or
(d) one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide.
Statement 24. The agent for use according to any one or Statements 14 to 23, wherein the agent is selected from a group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof. Statement 25. The agent for use according to Statement 24, wherein the chemical substance is an organic molecule, preferably a small organic molecule, or wherein the nucleic acid is an oligonucleotide.
Statement 26. The agent for use according to Statement 25, wherein said oligonucleotide is capable of specifically hybridising with said RNA molecule and comprises one or more mr5C.
Statement 27. An in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
Statement 28. An in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
(a) measuring the binding of SRSF2 polypeptide or biologically active fragment thereof comprising said mutation to an RNA molecule comprising one or more mr5C;
(b) determining that the mutation causes or contributes to the neoplastic disease when the binding as measured in (a) differs from binding of an SRSF2 polypeptide or a biologically active fragment thereof not comprising said mutation to the RNA molecule.
Statement 29. A method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
While the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications, and variations will be apparent to those skilled in the art in light of the foregoing description. Accordingly, it is intended to embrace all such alternatives, modifications, and variations as follows in the spirit and broad scope of the appended claims.
The herein disclosed aspects and embodiments of the invention are further supported by the following non-limiting examples.
EXAMPLES
Example 1 - Specific 5-methylcytidine (mr5C) reader discovery and validation
An RNA affinity approach involving biotinylated-RNA pull-down assay schematically illustrated in Fig. 1, using methylated and control versions of RNA baits followed by mass spectrometry (MS) or Western blotting (WB), was used to identify novel mr5C-binding proteins. The adenosine (A) and N(6)-methyladenosine (mr6A) probes as described by Dominissini et al. (Nature 2012, vol. 485, 201-6) were used as technical efficiency controls. The 5’-GACU-3’ consensus sequence-containing A and mr6A probes have been reported to be bound by the YTH family proteins (as seen for YTHDF2). The cytosine (C), 5-methylcytosine (mr5C) and 5- hydroxymethylcytosine (hmr5C) probes contain a 5’-CCGG-3’ sequence corresponding to the reported SSNG consensus sequence (where S is G or C, N is A, C, G or U). 5’-SSNG-3’ was reported as RNA-binding consensus sequence for SRSF2 and was implicated in disease where altered binding of targets was observed when SRSF2 was mutated (see Daubner et al. EMBO J. 2012, vol. 31(1), 162-74; Pandit et al. Mol Cell. 2013, vol. 50(2), 223-235; Kim et al. Cancer Cell. 2015, vol. 27(5), 617-630; Zhang et al. Proc Natl Acad Sci USA. 2015, vol. 112(34), E4726- E4734).
The probe sequences were as follows (Btn corresponds to biotin moiety):
A probe (A) (SEQ ID NO: 1):
5’ -/Btn/AU GGGC CGUU C AU CU GCU AAAAGGACUGCUUUU GGGGCUU GC - 3’
mr6A probe (m6A) (SEQ ID NO: 2):
5’ -/Btn/AU GGGC CGUU C AU CU GCU AAAAGG/m6A/CUGCUUUU GGGGCUU GC - 3’
C probe (C) (SEQ ID NO: 3):
5’ -/Btn/UUUCAGCUCCGGUC ACGCUC- 3’
mr5C probe (mC) (SEQ ID NO: 4):
5’ -/Btn/UUUCAGCUC/m5C/GGUC ACGCUC-3’
hmr5C probe (hmC) (SEQ ID NO: 5):
5’ -/Btn/UUUCAGCUC/hm5C/GGUC ACGCUC-3’
The 5’-GACU-3’ consensus sequence in A and mr6A probes and the 5’-CCGG-3’ sequence in the C, mr5C and hmr5C probes are underlined.
The RNA affinity chromatography approach involving biotinylated-RNA pull-down assay followed by MS identified SRSF2 as a specific mr5C-reader (Fig. 2). Affinity pulldown assays of biotinylated RNA for detection of protein-RNA complexes are described inter alia in Panda et al. (Bio Protoc. 2016, vol. 6(24)). In the present experiments, source of protein was endogenous SRSF2 from Hela cell extract. lOxlO6 cells were used per pulldown condition. The biotinylated- RNA pulldown assay protocol used in the present examples was as follows: 1. Hela cells were harvested at 70-80% confluence, washed with PBS and lysed in (500 ul/lOxlO6 cells) lysis buffer (lOmM NaCl, 2mM EDTA, 0.5% Triton X-100, 0.5mM DTT, lOmM Tris-HCl, pH7.5) containing complete protease inhibitor cocktail (Roche) and phosphatase inhibitor cocktail 2 (Sigma- Aldrich). 2. Lysates were separated from insoluble cell debris by centrifugation (l0,000g for 15 min at 4 °C) and pre-cleared for 1 h at 4 °C by incubation with 20 ul streptavidin-conjugated agarose beads (Sigma- Aldrich) in (+500ul/cond) binding buffer (l50mM KC1, l.5mM MgCf, 0.05% (v/v) NP- 40, 0.5mM DTT, lOmMTris-HCl pH7.5). Final volume: lml/cond. 3. Biotinylated RNA baits (2ug) were incubated with pre-cleared cell lysates supplemented with 0.4 units/ul RNasin (Promega) for 30 min at room temperature followed by lh30 incubation at 4°C. The mixture was then added to streptavidin-conjugated agarose beads pre-blocked (lh30) with BSA (1%) and tRNA (50ug/ml) fol h at 4 °C. 4. RNA-protein complexes were pulled-down and washed extensively (4-5x with Binding buffer).
While the baits retrieved several proteins, SRSF2 was the only significantly enriched protein to show specificity for the mr5C probe (n=3), even within the SRSF family of proteins.
The control RNA affinity approach involving biotinylated-RNA pull-down assay followed by MS identified known YTH family proteins as specific mr6A-readers. The A and mr6A probes from Dominissini et al. 2012 {supra) were used as technical efficiency controls. As expected the methylated bait retrieved known mr6A readers while the unmethylated control bait did not (n=3) (Fig. 3), demonstrating the efficiency and specificity of our approach.
The RNA affinity approach involving biotinylated-RNA pull-down assay followed by WB confirmed SRSF2 as a specific mr5C-reader (Fig. 4). For western blot analysis, samples were separated on 15% (w/v) polyacrylamide Bis-Tris gels (Invitrogen) and transferred onto nitrocellulose membrane. Membrane was blocked in 5% milk, 0.05% Tween-20 in PBS for 1 h, and then incubated overnight at 4 °C with anti-YTHDF2 polyclonal antibody (Abeam, ab 170118 ) diluted 1 :500 or anti-SRSF2 monoclonal antibody (Abeam, ab2049l6) diluted 1 :2000 in 5% milk. Proteins were visualized using the SuperSignal West Femto Luminol/Enhancer solution (Thermo scientific). Panel A of Fig. 4 shows technical efficiency validation of our approach through Western blotting of known YTHDF2 binding to the mr6A bait versus the unmethylated (A) bait. Panel B shows validation of the RNA affinity chromatography-mediated identification of endogenous SRSF2 as a specific mr5C reader through WB. Representative experiment of n=3.
The RNA affinity approach involving biotinylated-RNA pull-down assay followed by WB confirmed SRSF2 as a specific and direct mr5C-reader (Fig. 5). Panel A of Fig. 5, which shows Western blot after RNA affinity assay of overexpressed Myc-tagged SRSF2 in Hela cells, confirmed mr5C-specific binding. Myc-tagged SRSF2 was overexpressed in Hela cells. Vector used was pcDNA3.l-SC35-cMyc purchased from Addgene, plasmid #44721, Myc tag was C- terminal on backbone. Plasmid DNA was transfected in Hela cells using Lipofectamine 2000 transfection reagent from Invitrogen by Life technologies using provider’s protocol. Cells were collected after a 24h final incubation, pooled, counted, pelleted and kept at -80°C until proceeding with biotinylated-RNA pulldown assay (see step 1 of the above biotinylated-RNA pulldown assay protocol for Myc-tagged SRSF2 protein isolation). Cell lysate was equally divided among pulldown conditions in order to insure equiloading between the differential RNA probe submitted samples. Loading control western blot was performed for each experiment in order to verify equiloading of proteins between different RNA probe conditions of biotinylated-RNA pulldown assay. Anti-cMyc monoclonal antibody from Santa Cruz (sc-40) was used at 1 :1000 dilution in 5% milk PBS-T solution. Panels B and C, which show Biotin-RNA pulldown followed by WB of recombinant GST-tagged SRSF2 (commercial GST-tagged (N-term) SRSF2 was purchased from MyBioSource.com catalog # MBS961916; lug of GST-SRSF2 was loaded per biotinylated-RNA pulldown condition; anti-GST antibody was purchased from Abeam) or His-tagged SRSF2 (Ffis- tagged SRSF2 recombinant protein was produced and purified in-house. Vector: pET-30a(+)-His- SRSF2., His tag N-term. BL21 E.coli bacteria were transformed with plasmid using heat shock technique, grown in LB with antibiotic overnight and then induced for protein production using 1PTG during a 4h incubation. Bacteria pellet was resuspended in a TBS/triton/lOmM lmidazole/anti-proteases solution for sonication. The protein containing supernatant discarded from cellular debris by centrifugation was exposed to Ni-NTA beads and incubated for lhour. Protein- bound beads were then washed 3x with TBS/Triton/40 mM Imidazole prior to TBS/l50mM lmidazole elution of recombinant His-tagged SRSF2 proteins. Equiloading Western blot was performed. Anti-His monoclonal antibody from Abeam (abl8l84) at a 1 :1000 dilution in 5% milk was used for protein detection by WB), respectively, revealed a direct binding of SRSF2 to its preferred mr5C bait. Representative experiment of n=3.
Example 2 - Validation of SRSF2 as a specific mr5C reader in cellulo
To validate the binding of SRSF2 to mr5C in cellulo we used a modified version of the Bioluminescence Resonance Energy Transfer (BRET)-based assay to detect protein-protein interactions in live cells originally developed by Xu et al. Proc. Natl. Acad. Sci. USA 1999, vol. 96, 151-156, more particular the NanoBRET™ platform as described by Machleidt et al. ACS Chem. Biol. 2015, vol. 10, 1797-1804 (see also WO 2014/093677) and commercialised by Promega Corp.
The NanoBRET™ platform uses NanoLuc® Luciferase as a BRET energy donor, and HaloTag® protein labelled with the NanoBRET™ 618 fluorophore as the energy acceptor to measure the interaction of specific protein pairs. The NanoBRET™ technology enables sensitive, reproducible detection of protein interactions (PP1) in the natural cellular environment. The use of full-length proteins expressed at low levels enables PPI monitoring and screening studies that reflect true cellular physiology. Fig. 6 schematically illustrates the operation of the NanoBRET™ platform for detecting PPL
In the present study, the NanoBRET assay (https://be.promega.com/products/protein- interactions/live-cell-protein- interactions/nanobret-ppi-starter-systems/?catNum=N 1821) was adapted to a protein-RNA interaction assay. NanoLuc®-SRSF2 protein was expressed in mammalian cells, which were subsequently permeabilised with digitonin and exposed to Alexa- 594-labelled bait RNA. NanoBRET signal was measured only when there was a direct protein- RNA interaction. Fig. 7 schematically illustrates the operation of the modified NanoBRET™ platform for detecting protein-RNA interactions.
As shown in Fig. 8 the NanoBRET™-based proteimRNA interaction assay showed a higher affinity of SRSF2 for the methylated tracer RNA (mrC) in comparison with the unmethylated version (C) (panel A). The assay shown in panel B used corresponding‘cold’ RNA oligos and demonstrated the specificity of the detected NanoBRET signal. At equilibrium between Tracer RNA and Cold RNA, the detected NanoBRET™ signal has dropped to half of the original detected signal in absence of cold RNA. Panel C shows NanoBRET™ competition assays with cold RNA at diverse concentrations and demonstrated the specificity of the detected signal and the higher affinity of SRSF2 for the methylated RNA.

Claims

1. An in vitro method for identifying a serine and arginine rich splicing factor 2 (SRSF2)- modulating agent, said method comprising:
contacting a SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof and a ribonucleic acid (RNA) molecule comprising one or more 5-methylcytosines (mr5C), wherein said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant binds to said one or more mr5C on the RNA molecule, with a test agent; and
determining whether the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
identifying the test agent as a SRSF2-modulating agent when the test agent modulates the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule.
2. The method according to claim 1, wherein any one or more of a) to i) below apply:
a) the SRSF2-modulating agent can reduce the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to said one or more mr5C on the RNA molecule;
b) the method further comprises determining whether the SRSF2-modulating agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant;
c) the method further comprises determining whether the SRSF2-modulating agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant;
d) said RNA molecule is susceptible to splicing and said method further comprises determining whether the SRSF2-modulating agent can alter the splicing of said RNA molecule;
e) the method further comprising determining whether the SRSF2-modulating agent displays anti-neoplastic property, such as anti-cancer property; f) said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant and/or the RNA molecule is of human origin;
g) the amino acid sequence of said SRSF2 polypeptide is as set forth in GenBank accession no. NP_00l 182356.1;
h) the mutated SRSF2 polypeptide is mutated at:
- one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide;
- amino acid position 95 relative to a wild-type SRSF2 polypeptide;
- one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide; and/or
- one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide;
i) the method is performed in a cell-free system or in a cell lysate or in isolated or cultured cells or in an isolated or cultured tissue.
3. The method according to claim 1 or 2, wherein the test agent is selected from the group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof.
4. The method according to claim 3, wherein:
- the chemical substance is an organic molecule, preferably a small organic molecule, or the nucleic acid is an oligonucleotide; or
- the nucleic acid is an oligonucleotide capable of specifically hybridising with said RNA molecule and comprises one or more mr5C.
5. An agent capable of modulating the binding of an SRSF2 polypeptide or a mutated SRSF2 polypeptide or a biologically active fragment or variant thereof to one or more mr5C on an RNA molecule, for use in the treatment of a disease characterised by dysregulation of SRSF2 expression and/or activity or by dysregulation of RNA mr5C methylation.
6. The agent for use according to claim 5, wherein any one or more of a) to i) below apply:
a) the agent is capable of reducing the binding of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant to the one or more mr5C on the RNA molecule;
b) the agent can alter the quantity and/or activity of said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant;
c) the agent can specifically bind to said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant, such as specifically bind to the mr5C-binding site of said SRSF2 polypeptide or mutated SRSF2 polypeptide or a biologically active fragment or variant;
d) said RNA molecule is susceptible to splicing and said agent can alter the splicing of said RNA molecule;
e) the dysregulation of SRSF2 expression and/or activity is due to a mutation in SRSF2;
f) wherein the disease is a neoplastic disease, such as cancer.
g) the disease is myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML);
h) the agent is for use in a human subject, and said SRSF2 polypeptide or mutated SRSF2 polypeptide or biologically active fragment or variant is of human origin;
i) the mutated SRSF2 polypeptide is mutated at:
- one or more amino acid positions selected from position 2, 22, 25, 26, 52, 189, 191, 204, 206, 208, 212, and 220 relative to a wild-type SRSF2 polypeptide;
- amino acid position 95 relative to a wild-type SRSF2 polypeptide;
- one or more amino acid positions selected from position 1, 3, 13, 15, 35, 47, 48, 51, 52, 57, 59, 69, 80, 94, 96, 99, 101, 104, 107, 110, 123, 129, 131, 133, 134, 136, 139, 149, 156, 167, 168, 179, 187, 193, 195, 199, 205, 206, 207, 209, 217, and 220 relative to a wild-type SRSF2 polypeptide; and/or
- one or more amino acid positions selected from position 31, 42, 43, 44, 50, 51, 52, 82, 85, 87, 91, 95, 99, 100, 101, 102, 103, 107, 143, 144, 145, and 167 relative to a wild-type SRSF2 polypeptide.
7. The agent for use according to claim 6 or 7, wherein the agent is selected from a group consisting of a chemical substance, an antibody, an antibody fragment, an antibody-like protein scaffold, a protein or polypeptide, a peptide, a peptidomimetic, an aptamer, a photoaptamer, a spiegelmer, a nucleic acid, a gene-editing system, an antisense agent, an RNAi agent, a soluble receptor, and combinations thereof.
8. The agent for use according to claim 7, wherein:
- the chemical substance is an organic molecule, preferably a small organic molecule, or the nucleic acid is an oligonucleotide;
- the nucleic acid is an oligonucleotide capable of specifically hybridising with said RNA molecule and comprises one or more mr5C.
9. An in vitro method for detecting one or more mr5C on an RNA molecule in a sample from a subject, the method comprising measuring binding of an SRSF2 polypeptide or biologically active fragment thereof to one or more mr5C on the RNA in the sample from the subject.
10. An in vitro method for determining whether an SRSF2 mutation causes or contributes to a neoplastic disease, the method comprising:
(a) measuring the binding of SRSF2 polypeptide or biologically active fragment thereof comprising said mutation to an RNA molecule comprising one or more mr5C;
(b) determining that the mutation causes or contributes to the neoplastic disease when the binding as measured in (a) differs from binding of an SRSF2 polypeptide or a biologically active fragment thereof not comprising said mutation to the RNA molecule.
11. A method for diagnosing a neoplastic disease in a subject, the method comprising detecting in a sample from the subject an SRSF2 mutation, wherein said mutation alters binding of SRSF2 polypeptide to an RNA molecule comprising one or more mr5C compared to an SRSF2 polypeptide not comprising said mutation.
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