EP2190870A1 - Cell marker of melanocyte cell lineage and uses thereof - Google Patents
Cell marker of melanocyte cell lineage and uses thereofInfo
- Publication number
- EP2190870A1 EP2190870A1 EP08828507A EP08828507A EP2190870A1 EP 2190870 A1 EP2190870 A1 EP 2190870A1 EP 08828507 A EP08828507 A EP 08828507A EP 08828507 A EP08828507 A EP 08828507A EP 2190870 A1 EP2190870 A1 EP 2190870A1
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- EP
- European Patent Office
- Prior art keywords
- seq
- nucleic acid
- acid molecule
- cell
- peptide
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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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
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
- G01N33/5751—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the skin, e.g. melanoma
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K38/00—Medicinal preparations containing peptides
Definitions
- the present invention relates to cell markers and in particular to cell markers of melanocyte lineage and cancer cells.
- the invention also relates to novel targets for treatment of disorders of cells of the melanocyte lineage, and to compositions and methods for treatment of such disorders.
- the invention has been developed primarily for the diagnosis and/or treatment of melanocyte disorders such as cancer, and more specifically melanoma. However, it will be appreciated that the invention is not limited to this particular field of use. BACKGROUND OF THE INVENTION
- Melanoma is the most serious and aggressive form of skin cancer. However, if recognized and treated early, it is nearly 100 percent curable. If not captured early, the cancer can advance and spread to other parts of the body, where it becomes hard to treat and can be fatal. While it is not the most common skin cancer, it causes the most deaths.
- Melanoma is a malignant tumor that originates in melanocytes.
- Melanocytes manufacture the pigment melanin within melanosomes, which are transferred to keratinocytes to pigment the skin. All melanocyte specific genes identified to date are in some way involved in the melanosome production pathway.
- Well known melanocyte- specific genes include melcmA, tyrosinase, trp-1, trp-2 and gp 100.
- MelanA, gplOO and tyrosinase are genes that are currently used as targets for immunotherapy.
- DTIC dacarbazine
- BCNU carmustin
- tamoxifen tamoxifen
- cisplatin and vinblastine a drug that is administered orally.
- temozolomide Another drug, temozolomide, can be given orally.
- the present invention is concerned with a novel gene and its products that appear to be expressed primarily in melanocytes.
- the present invention is also concerned with methods of modulating the expression or function of the gene and/or its products.
- an isolated nucleic acid molecule that encodes a melanocyte-specific protein comprising a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or functional fragments thereof.
- the nucleic acid molecule that encodes a protein having SEQ. ID. No.3, or a functional fragment thereof.
- an isolated nucleic acid molecule that encodes a melanocyte-specific protein, wherein the nucleic acid molecule has at least 75% sequence identity with SEQ. ID. No. 1.
- the nucleic acid molecule has from 80% to 95% sequence identity with SEQ. ID. No. 1.
- Nucleic acid molecules that have higher sequence identities with SEQ. ID. NO. 1, for example 80%, 85%, 90% or 95% are even more preferred.
- nucleic acid sequence of the present invention may vary from that provided in SEQ. ID. No.l as a result of codon degeneracy (i.e. alternative codons for the same amino acid residue) or preferential codon usage if the sequence is to be expressed in different expression systems (e.g. prokaryotic, eukaryotic systems etc.).
- a nucleic acid molecule that is complementary to a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or fragments thereof.
- a protein comprising a polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two.
- a cell marker comprising a peptide or polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two, or part thereof.
- a cell marker comprising a peptide or polypeptide sequence comprising SEQ ID No. 3.
- the cell marker is a skin cell marker such as, for example, a melanocyte cell marker.
- the skin cell is a melanocyte.
- the cell marker is a cell marker for skin-related neoplastic conditions such as skin cancer. More preferably the neoplastic condition is melanoma.
- the condition may also be a disorder of pigmentation resulting from, for example, abnormal localisation, growth, or function of melanocytes.
- an antibody that binds to the peptide or polypeptide sequence encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or to a protein comprising SEQ ID No. 3, or part thereof.
- the antibody is a monoclonal antibody or a functional fragment thereof.
- the antibody is a polyclonal antibody or a functional fragment thereof.
- antibody includes functional fragments of antibodies, derived by enzymatic means or recombinant expression.
- a pharmaceutical composition comprising an antibody according to the seventh aspect, optionally in combination with a pharmaceutically acceptable carrier.
- a vector comprising a nucleic acid sequence set forth in any one of aspects one to three, or a part thereof, operatively linked to a promoter.
- the vector can be selected from an expression vector commonly used for in vitro protein expression in prokaryotic or eukaryotic cells, or vectors for introducing nucleic acid sequences into mammalian cells or vectors for mammalian gene therapy or vaccination.
- a prokaryotic or eukaryotic cell comprising the expression vector according to the ninth aspect.
- the prokaryotic cell is a bacterial cell or a fungal cell.
- the eukaryotic cell is selected from a mammalian cell, an avian cell, an amphibian cell, a reptilian cell or an insect cell.
- nucleic acid molecule of aspect one or aspect two a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, as a marker of a melanocyte cell lineage.
- an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, for identifying melanocyte cell lineage.
- the identification of cell lineage can be conducted by a number of well known techniques, including for example FACS, ELISA, RIA, Western blot, cytometric bead array, SISCARPA , and the like.
- nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or part thereof, or a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ ID No.3, or part thereof, or an antibody that specifically binds to said peptide or polypeptide and/or said protein, in the diagnosis and/or detection of a skin cancer.
- nucleic acid molecule of aspect one or aspect two or part thereof or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a polypeptide encoded by a nucleic acid of aspect one or aspect two, or part thereof, or a protein comprising said polypeptide in the preparation or manufacture of a medicament for the treatment of a skin cancer or disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
- a method of diagnosing and/or treating a skin cancer comprising the step of administering to a subject in need of said treatment an effective amount of an inhibitory or interfering RNA or DNA sense or antisense sequence capable of blocking or inhibiting expression of a nucleic acid molecule of aspect one or aspect two, or part thereof, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ. ID No.3.
- the skin cancer is melanoma.
- a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample comprising: a) contacting a biological sample with a nucleic acid having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) determining whether the nucleic acid binds to a nucleic acid molecule in the sample.
- a method of screening for the presence of a peptide or polypeptide or part thereof, encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample comprising: a) contacting a biological sample with an antibody that specifically binds to the peptide or polypeptide, or part thereof; and b) determining whether the antibody binds to the peptide or polypeptide, or part thereof, in the sample.
- a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other nucleic acid molecule which codes for a cell marker commonly used to identify cells of melanocyte lineage in a sample comprising: a) contacting a biological sample with i) a nucleic acid molecule having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No.
- nucleic acid molecules having a sequence that is complementary to the at least one other nucleic acid molecule or part thereof; and b) determining whether the nucleic acid molecules bind to the nucleic acid molecules in the sample.
- a method of screening for the presence of a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other polypeptide which is a cell marker commonly used to identify cells of melanocyte lineage in a sample comprising: a) contacting a biological sample with i) an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and ii) an antibody that specifically binds to the at least one other polypeptide; and b) determining whether the antibodies bind to their corresponding polypeptides in the sample.
- the cell marker commonly used to identify cells of melanocyte lineage may be selected from for example, melanA, gplOO, tyrosinase, trp-1 and trp-2. It will be understood however, that any other markers that identify melanocyte cell origin can also be used in conjunction with the present invention.
- the use of the cell marker encoded by any one of SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8 in a panel of other markers is advantageous since not all cancerous cells express traditional markers such as gplOO or melanA, and the like, which are typically used in methods for screening for melanoma. Inclusion of an additional marker such as that of the present invention significantly enhances the diagnostic power of the diagnostic methods used.
- a method of diagnosing and/or detecting skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) detecting localisation of the nucleic acid as an indicator of the presence (and/or type) of skin cancer or skin condition.
- a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) detecting localisation of the antibody as an indicator of the presence (and/or type) of skin cancer or skin condition.
- a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ.
- nucleic acid molecules selected from the group comprising, but not limited to melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof; and b) determining localisation of the nucleic acids as an indicator of the presence (and/or type) of skin cancer or skin condition.
- a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other antibody that binds to a polypeptide encoded by melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof, and b) determining localisation of the antibodies as an indicator of the presence (and/or type) of skin cancer or skin condition.
- a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of nucleic acid molecules or parts thereof, comprising melanA, gplOO, tyrosinase, trp-1 and trp-2 and a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the nucleic acid molecules as an indicator of the presence (and/or type) of skin cancer or skin condition.
- a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of antibodies that bind specifically to melanA, gplOO, tyrosinase, trp-1 and trp-2 and a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the antibodies as indicator of the presence (and/or type) of skin cancer or skin condition.
- the biological sample used in the method of diagnosing skin cancer is selected from the group consisting of a tissue biopsy, a biological fluid and a surgical specimen. It will be understood, however, that the diagnosis and/or detection of skin cancer with nucleic acid molecules and antibodies of the present invention may also be conducted in vivo or ex vivo.
- the nucleic acid molecules or antibodies used in the method of screening or diagnosis are tagged with a visible or detectable marker to permit visual inspection or measurement/detection.
- the tag is preferably selected from a group consisting of a fluorescent dye, an isotope, an enzyme (e.g. peroxidase or alkaline phosphatase), a chemical moiety (e.g. biotin) that binds another labelled ligand (e.g. avidin) with high affinity.
- the skin cancer to be screened, diagnosed or treated is melanoma.
- the melanoma can be in the form of a cutaneous melanoma, a melanoma of the nail bed, a melanoma of the eye or a mucosal melanoma.
- the skin cancer to be screened, diagnosed or treated may be of metastatic origin.
- the skin condition may be a disorder of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
- a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting a cell with a short interfering nucleic acid molecule directed against a nucleic acid sequence selected from
- SEQ. ID. No. 1 SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ.
- the short interfering nucleic acid molecule is selected from a group consisting of short interfering RNA (siRNA), double stranded RNA, micro RNA and short hairpin DNA.
- siRNA short interfering RNA
- double stranded RNA double stranded RNA
- micro RNA micro RNA
- short hairpin DNA short interfering RNA
- a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting the cells with an antisense nucleic acid molecule directed against a nucleic acid sequence selected from
- SEQ. ID. No. 1 SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof.
- the skin cancer is melanoma.
- nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or a protein comprising said peptide or polypeptide, in the treatment of disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
- the disorders of pigmentation include hyperpigmentation disorders such as melasma, cafe au lait macules, drug-induced hyper-pigmentation and phototoxic reactions or hypo- pigmentation disorders such as vitiligo.
- hyperpigmentation disorders such as melasma, cafe au lait macules, drug-induced hyper-pigmentation and phototoxic reactions or hypo- pigmentation disorders such as vitiligo.
- autoimmune vitiligo Ogg GS, Dunbar PR, Romero P, Chen JL, Cerundolo V (1998) High frequency of skin-homing melanocyte-specific cytotoxic T lymphocytes in autoimmune vitiligo. Journal of Experimental Medicine 188:1203-8). More preferably, the disorders of pigmentation is selected from hypo- pigmentation and/or hyper-pigmentation.
- a method of modulating expression of genes associated with changes in skin pigmentation or cosmetic lightening or darkening of skin tone comprising contacting a cell with an inhibitory or interfering RNA or DNA, sense or antisense, sequence directed against a nucleic acid molecule of aspect one or aspect two.
- the nucleic acid molecules and antibodies of present invention may be formulated into pharmaceutical preparations by any number of processes well known in the art and may include injectable, topical, oral, slow release and other suitable dosage forms and preparations.
- the present invention is suitable for the diagnosis and/or treatment of skin cancers, in particular melanoma.
- LOCI 46481 is used for convenience to describe the genomic locus LOC 146481.
- Novel nucleic acid sequences of the present invention in addition to being allocated SEQ ID Nos. may also be referred to as "SHML” sequences (Specific for Human Melanocyte Lineage). It will be understood that the acronym is merely a convenient designation and should not be construed to limit the nucleic acid or the protein to human origin only.
- the present invention encompasses both mammalian and non-mammalian species SHML.
- SHML mRNA “SHML gene”, “SHML transcript” and “SHML protein” may be used interchangeably with specific SEQ ID nos. and are intended to describe the nucleic acid, mRNA and protein sequences of the present invention.
- nucleotide As used in the context of the present invention, are intended to encompass a gene, DNA, ssDNA, cDNA, synthetic DNA, RNA, genomic sequences and derivatives thereof.
- peptide and “polypeptide” as used in the context of the present invention are intended to encompass peptides and fragments of polypeptides or proteins which comprise an amino acid sequence encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or parts thereof. Such sequences may be detectable by an antibody raised against a peptide encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, such as for example SEQ ID No. 3 or part thereof.
- treatment covers any treatment of a disease and/or condition in an animal, particularly a human, and includes:
- an “antibody” or “antibodies” includes reference to all the various forms of antibodies, including but not limited to: full antibodies (e.g. having an intact Fc region), including, for example, monoclonal antibodies; antigen-binding antibody fragments, including, for example, Fv, Fab, Fab' and F(ab') 2 fragments; humanized antibodies; human antibodies (e.g., produced in transgenic animals or through phage display); single domain antibodies and immunoglobulin-derived polypeptides produced through genetic engineering techniques. Unless otherwise specified, the terms "antibody” or “antibodies” and as used herein encompasses both full antibodies and antigen-binding fragments thereof.
- the treatments described herein can be administered by oral or parenteral routes, including intravenous, intramuscular, intraperitoneal, subcutaneous, rectal and topical administration, and inhalation.
- oral administration the treatments will generally be provided in the form of tablets or capsules or as an aqueous solution or suspension.
- Tablets for oral use may include the active ingredient mixed with pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavouring agents, colouring agents and preservatives.
- pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavouring agents, colouring agents and preservatives.
- “pharmaceutically acceptable carrier” includes any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and is non-reactive with the subject's immune system. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, water, emulsions such as oil/water emulsion, and various types of wetting agents. Preferred diluents for aerosol or parenteral administration are phosphate buffered saline or normal (0. 9%) saline.
- Figure 1 The PCR products derived from human melanocyte cDNA encoding SHML Sequence 1. AU sequences are shown 5'- 3'.
- B PCR product 2 - SEQ ID No.
- 10 - shows 546bp of the sequence of the PCR product generated from human melanocyte cDNA with forward primer 527F (5'- TGGTCAGGATGGAGGGGAAG-3') and reverse primer 1145R (5'- GCACCCAGCTCAAGCCTCAT-3 '); C) Alignment of two PCR products in A) and B), which overlap by lObp, to make
- SEQ. ID. No. 3 is the protein sequence encoded by the underlined portion of SEQ. ID. No. 2.
- Figure 2 Excerpt of the GenBank entry for the human FRG2 gene sequence
- Figure 3 Alignment of SHML protein sequence (SEQ. ID. No. 3) with FRG2 protein sequence (by Needleman-Wunsch global alignment, Geneious software, www.geneious.com). Potential nuclear localisation signals are boxed, and a potential protein kinase C phosphoryation site is underlined.
- FIG. 4 Expression of SHML, tyrosinase & melanA relative to the house-keeping gene HPRT in cDNA from human tissues, cell lines, and primary cell cultures. Expression of these three genes was quantified with quantitative RT-PCR relative to the housekeeping gene HPRT, which was expressed in all samples. SHML expression was detected in human skin, which contain melanocytes, and also in cultured human melanocytes, but not cultured human dermal fiboblasts. The melanocyte-associated gene tyrosinase and melanA were also expressed in human skin and melanocytes, but not dermal fibroblasts.
- siRNAs targeting SHML mRNA achieved approximately 70% knockdown of SHML expression, similar to the level of knockdown seen with previously- validated siRNAs targeting tyrosinase mRNA.
- 5OnM siRNA had similar effects, but InM siRNAs were less effective. These data indicate the siRNAs used were capable of significantly knocking down SHML mRNA expression at both the 1OnM and 5OnM doses. Data shown are the average of triplicate measurements, with error bars representing the standard error of the mean.
- Figure 6 siRNAs targeting SHML gene expression
- FIG. 6 The two siRNA sequences used to knock down SHML expression in Figure 6 are shown, along with the positions of the sequences they target in the SHML sequence (bold and underlined in SEQ. ID. No. 1 as shown)
- Figure 7 Alternate transcripts coding for SHML.
- A)-D) Four predicted alternate transcripts are shown that are capable of encoding SHML protein (SEQ. ID. No. 3), each full length from transcription initiation site (TCATTCTT, nucleotides 1-8 in each transcript) to poly- A tail start. The coding sequence is underlined in each sequence. Three polymorphic sites are highlighted in each sequence by use of a bold capitalised A or G.
- the first 360bp of each sequence, and the sequences 3' to the regions shown here, have been omitted, since they are identical between the transcripts.
- Figure 8 Features of the SHML promoter region.
- TTATGTAA 115..122 cAMP Response Element
- TGAGGTTA cAMP Response Element
- CACATG Putative Mitf binding site
- the present invention is based on a surprising observation that an uncharacterised gene in the human genome encodes a protein that is present in cells of melanocy e lineage, but not other cells.
- an uncharacterised gene in the human genome encodes a protein that is present in cells of melanocy e lineage, but not other cells.
- novel nucleic acid sequence that encodes the novel, cell-specific protein, provided herein is designated
- the protein-encoding open reading frame (ORF) from SEQ. ID. No. 1 mRNA is the nucleotide sequence shown below (SEQ. ID. No. 2): SEQ. ID. No. 2
- SEQ. ID. No. 3 This ORF is one of several possible ORFs in SEQ. ID. No. 1, but based on the present findings of the encoded protein's high homology to another human protein, as described below, SEQ. ID. No. 2 was identified as the protein coding sequence.
- the protein encoded by SEQ. ID. No. 2 has the following amino acid sequence (SEQ. ID. No. 3):
- SEQ. ID. No. 3 has significant homology to another known protein, called FRG2 (FSHD region gene 2), the sequence of which is given in Figure 2, along with other information on the gene encoding FRG2 protein.
- FRG2 is a gene implicated in facioscapulohumeral muscular dystrophy (T. Rijkers et al, FRG2, an FSHD candidate gene, is transcriptionally up-regulated in differentiating primary myoblast cultures of FSHD patients. J. MedGenet. 2004;41; 826-836).
- Alignment of the SEQ. ID. No. 3 with FRG2 protein sequence is shown in Figure 3. In this alignment, 50 of 113 amino acids in SEQ. ID. No. 3 protein are identical to those in FRG2, for 44% overall homology.
- SEQ. ID. No. 3 has a homologous protein sequence for only the second sequence at amino acids 70-73 (sequence KQHR).
- SEQ. ID. No. 3 does have a potential nuclear localisation signal (sequence LKKKLKS) that is not present in FRG2 (using PredictNLS online http://cubic.bioc.columbia.edu/cgi/var/nair/resonline.pl). Based on these findings it is therefore likely that the SEQ. ID. No. 3 protein will localise to the nucleus of the cell after translation, as does FRG2.
- the sequence SNKL at amino acids 47-50 in the SEQ. ID. No. 3 protein is a potential protein kinase C (PKC) phosphorylation site, implicating PKC as a regulator of the protein's function.
- PKC protein kinase C
- the SEQ. ID. No. 3 protein is thus potentially capable of post- translational modification by phosphorylation at this site.
- MITF microophthalmia-associated transcription factor
- CREB cAMP-responsive element binding protein
- the genomic locus LOC146481 had been predicted by NCBI to encode mRNAs (XR_017714.1, XR_017753.1, and XR_041323.1), different from that identified herein as SEQ. ID. No. 1. These predicted mRNAs (XR_017714.1, XRJH7753.1, and XR_041323.1), had been predicted to encode a protein different from SEQ. ID. No. 3 described herein (predicted hypothetical protein XPJ)01723191.1).
- GenBank National Institutes of Health Mammalian Gene Collection project (NIH MGC) also differs from SEQ. ID. No. 1, and has several reading frames.
- SEQ. ID. No. 1 of the present invention In analysing SEQ. ID. No. 1 of the present invention, it was found that one of several open-reading frames encoded a protein with strong homology to another human protein, FRG2. Based on analytical and comparative studies described above, particularly the recognition that the sequence was restricted to cells of the melanocytic lineage and, on the basis of strong homology to another protein, (that only one of the open-reading frames present in SEQ. ID. No. 1 was likely to encode protein) the present invention provides a novel nucleotide sequence, SEQ. ID. No.l, the mRNA sequence included therein, SEQ. ID. No. 2, and the corresponding protein sequence, SEQ. ID. No. 3. The restriction of the sequences to cells of the melanocytic lineage, indicates a function related to the specialised properties of such cells, as described below. Expression of SHML transcripts in human tissues and cells
- the gene and its corresponding protein will therefore have value as a diagnostic marker for confirmation of diagnosis of cancers such as melanoma, a marker of a melanocyte cell lineage, as a therapeutic drug target, for example as a target for immunotherapy of melanoma or a drug target for melanoma or disorders of pigmentation. Its corresponding antibody will also have value as a diagnostic tool or as a treatment/therapy for melanoma in its various forms and for disorders associated with melanoma and/or disorders of pigmentation. Functional roles of SHML protein
- DAGI melanoma cell line
- siRNAs targeting SHML mRNA both siRNAs shown in Fig 6
- control siRNAs targeting the melanocyte marker tyrosinase were exposed to siRNAs targeting SHML mRNA.
- DAGI melanoma cell line
- siRNAs targeting SHML mRNA both siRNAs shown in Fig 6
- control siRNAs targeting the melanocyte marker tyrosinase was exposed to siRNAs targeting SHML mRNA (both siRNAs shown in Fig 6), as well as control siRNAs targeting the melanocyte marker tyrosinase.
- Fig 5 This was equivalent to the knock down in tyrosinase mRNA concentrations in the same experiment, carried out with siRNAs that had been previously validated.
- DAGI cells with and without SHML mRNA knockdown were subjected to whole genome microarray analysis, to detect gene modulated by SHML.
- Wnt proteins interact with a cell surface receptor complex consisting of Frizzled and LRP5/6, resulting in stabilisation of cytoplasmic ⁇ -catenin.
- ⁇ -catenin accumulates in the cytoplasm and moves to the nucleus. Once in the nucleus ⁇ -catenin interacts with the LEF/TCF family of transcription factors to activate transcription of TCF/LEF target genes.
- DKKl is able to inhibit Wnt signalling at the cell surface by binding to LRP5/6 component of the Wnt receptor complex. The complex is endocytosed upon DKKl binding, thereby blocking the ability of Frizzled to send the Wnt signal upon binding of Wnt.
- Wnt signalling is crucial in development, differentiation, and pigmentation. Wnt signalling is required to maintain melanocyte precursor cells in a stem cell like state during development. Wnt signalling has been shown to control pigmentation by activation of Mitf-M transcription via the TCF/LEF1 binding site in the Mitf-M promoter. Wnt signalling in melanocytes results in the ⁇ -catenin/TCF/LEF complex increasing transcription of Mitf-M. Downstream of Mitf-M the pigmentation pathway is activated and melanosomes are produced. (2-4)
- SHML protein therefore appears to be a negative regulator of DKKl expression. Reduction in SHML mRNA levels resulted in increased DKKl mRNA expression levels, as demonstrated herein.
- SHML protein is a putative transcription factor and may regulate DKKl mRNA levels via interaction with the DKKl promoter.
- SHML protein is a melanocyte-specific regulator of the Wnt signalling pathway, which has been shown to be required for melanocyte development, differentiation and pigmentation.
- the tissue specificity of SHML protein expression enables systemic drug treatment with a tissue specific effect on Wnt signalling.
- siRNAs were used to successfully knock down expression of SHML mRNA in melanoma cells by at least 60%, with subsequent effects on the transcription of other genes, notably DKKl.
- the location of the sequences successfully targeted by siRNAs are shown in Fig 6, along with the siRNA sequences. These sequences are located at residues 552-570, and 637-655 of the SEQ. ID. No. I 5 and were targeted by siRNAs 293438 and 293439 (provided by Applied Biosystems/Ambion, Austin, TX, USA).
- the siRNAs have similar efficacy when used individually as when combined.
- transcripts include the lOObp additional sequence shown in transcripts 2 and 4 (SEQ. ID. No. 5 and SEQ. ID. No. 7) because RT-PCR of cDNA from cells of melanocytic origin using primers that span this region of cDNA occasionally produce two bands that differ in size by lOObp (data not shown).
- SNPs Single Nucleotide Polymorphisms
- allelic variants of all 4 alternate transcripts are possible, though none of these affect the encoded protein, because they are located in the untranslated regions of each mRNA.
- SNP # 11647911 is a C/T polymorphism transcript start site, as shown at position 4018. This is not predicted to be a site involved in transcription factor binding or transcription initiation, but it is still possible that it will affect the transcription of the gene in different individuals, potentially affecting melanocyte structure or function.
- novel SHML protein described herein, or parts thereof, represents a new and useful target for diagnosis and treatment of skin and other conditions that are caused or mediated by abnormal melanocyte function, growth, proliferation and/or localisation.
- the active agents described herein including anti-sense and sense nucleic acid approaches, and antibodies, to manipulating expression of the SHML protein can be applied to both diagnostic and therapeutic uses in the treatment of melanocyte-mediated disorders, the most important of which is skin cancer such as melanoma.
- cosmetic applications are also contemplated such as alteration of skin and hair pigmentation, masking or removal of skin blemishes and the like.
- Manipulation of regulatory processes within melanocytes has been clearly demonstrated herein using siRNAs that modulate expression of SHML.
- the structure of the gene and its regulatory regions, and the protein sequence, provided herein enable other known therapeutic and diagnostic approaches to be adopted for manipulating the expression and/or function of
- Seed Cascade melanocytes (catalogue # C-024-5C, Cascade Biologies Inc. 1341 SW Custer Drive, Portland OR 97219, USA, ph 503 292 9521) at a density of 5x10 3 cells/cm 2 in a 25 cm 2 flask with Cascade medium 254 (cat # M254-500) with PMA free melanocyte supplement (cat # S-015-5C).
- DAGI Cell Culture Thaw vial of 0.5 million cells in a 37°C water bath. Open vial in a laminar flow hood and resuspend cell pellet using a ImL pipette. Transfer cells to a 15mL tube then add 1OmL RPMIl 640/10% FBS/lxPSGCpenicillin/streptomycin/glutamate). Mix cells then centrifuge for 5min at 18Og. Remove supernatant, add 5mL RPMI1640/10% FBS/lxPSG, resuspend cells and transfer to a 25 cm 2 flask. Incubate at 37°C/5%CO 2 for 24 hours then replace the media and remove dead cells. Change media every 2-3 days and passage 1:2 whenever flask becomes confluent. Passage using 2x trypsin.
- RNAniix l ⁇ L l Ox RT buffer
- siRNA & LF2000 mixes & incubate at room temperature for 20min.
- Microarray Information Chips used - Affymetrix Human Genome Ul 33 Plus 2.0 Array Genechip Users protocol - http://www.affymetrix.com/support/technical/manual/expression_manual.affx Used as protocol for Genechip use from RNA to producing expression data
- EXAMPLE 2 Determination of tissue expression specificity of the nucleic acid encoding SHML in humans using quantitative real time PCR.
- SHML mRNA levels were measured by quantitative real time PCR (qPCR) using the Taqman specific assay ID # HsO139O151_ml. Since SHML was suspected to be a melanocyte specific gene, expression of two known melanocyte specific genes, tyrosinase and melan ⁇ , were also measured using Applied Biosystems Taqman assays, ID # HsOOl 65976_ml & HsOO924233_ml respectively. All qPCR reactions were 45 cycles, triplicates with IOng of each tissue cDNA.
- SHML mRNA was also tested in normal human melanocytes (Cascade Biologies), samples of normal human skin and melanoma tumor-infiltrated lymph nodes (TILNs) (obtained from consenting patients), and a number of melanoma cell lines, obtained from collaborating research groups.
- TILNs tumor-infiltrated lymph nodes
- SHML mJRNA was shown to be expressed in skin and at a higher level in normal human melanocytes. SHML mRNA was also expressed in most melanoma cell lines including MZ2 where no other markers of melanocytic origin were expressed.
- EXAMPLE 3 Sequencing of the nucleic acid encoding SHML in normal human melanocytes
- PCR fragments of the nucleic acid sequence encoding SHML were generated from cDNA synthesized using RNA extracted from normal human melanocytes
- the resulting PCR product was gel purified using the Qiagen Qiaex II Gel
- PCR product was sequenced using the PCR primers, at 5 ⁇ M, with approximately 50ng of PCR product per reaction, on a
- siRNAs specific for SHML can be used to knockdown SHML mRNA levels as in the melanoma cell line DAGI.
- RNA from the siRNA knockdown can be used for microarray experiments. RNA is extracted using the Qiagen Rneasy Mini kit (Qiagen catalogue #74104). Microarray analysis of the RNA generated from these knockdowns can be done using the Affymetrix Ul 33 plus
- SHML mRNA was found to be expressed in many melanoma cell lines and tumour samples, but was absent from nearly all normal human tissues.
- Commercial cDNA libraries were sourced from volunteers by the respective companies and information on these donors and tissue processing is available on the company websites; normal human skin and melanoma tumor-infiltrated lymph nodes were sourced from consenting volunteers undergoing plastic surgery and lymph node resection respectively, under appropriate ethics committee oversight, and part of each sample was snap frozen in liquid nitrogen as soon as practicable and stored at -80°C until RNA extraction.
- SHML mRNA was also switched on in skin and some neural samples.
- SHML mRNA was found to be expressed in melanocytes, the normal cells that melanoma develops from, and which are found in skin and some neural tissue. Indeed, the expression pattern of SHML mRNA in human cell lines and tissues mirrors other genes that are only switched on in melanocytes. This finding made it highly likely that the gene is specific to cells of the melanocyte lineage, and may even play a role in some of the unique functions of these cells, such as pigmentation.
- EXAMPLE 4 Expression of SHML protein
- the nucleic acid sequence encoding SHML is amplified from a cDNA template using PCR and cloned into expression vectors for protein expression in E. coli, yeast and mammalian cells. The confirmed plasmid is then transfected into the appropriate cell line/cells and expression of the protein can be induced.
- Recombinant SHML protein is purified from these cellular sources by the use of tags attached to the protein, that are encoded in the expression vector.
- peptide Approximately lOmg of peptide is synthesized for the antibody production. The peptide is analyzed by mass spectral and HPLC analyses to ensure sequence integrity and purity prior to conjugation. The peptide is then conjugated to KLH or BSA (2-3mg). The peptide-protein conjugate is purified by gel filtration and freeze dried. The remaining unconjugated peptide is supplied. Immunization and Sera Collection:
- the conjugated peptide is injected subcutaneously at multiple sites.
- the initial immunization is given in Complete Freund's Adjuvant with all subsequent immunizations given in Incomplete Freund's Adjuvant.
- the animals are bled at intervals to ascertain the titer of the antiserum. Antisera are used unpurified.
- Immunization/Bleed Protocol A detailed immunization and bleeding schedule is provided below:
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| EP1218538A2 (en) * | 1999-06-30 | 2002-07-03 | Ludwig Institute For Cancer Research | Cancer associated antigens and uses therefor |
| AU2001251613A1 (en) * | 2000-04-14 | 2001-10-30 | Millennum Pharmaceuticals, Inc. | Novel genes, compositions and methods for the identification, assessment, prevention, and therapy of human cancers |
| CA2427112A1 (en) * | 2000-10-27 | 2002-08-22 | Pe Corporation (Ny) | Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof |
| US20040142325A1 (en) * | 2001-09-14 | 2004-07-22 | Liat Mintz | Methods and systems for annotating biomolecular sequences |
| DE10238298A1 (en) * | 2002-08-21 | 2004-03-04 | Beiersdorf Ag | Use of antisense oligonucleotides for the treatment of degenerative skin symptoms |
| SI1530636T1 (en) * | 2002-08-21 | 2010-12-31 | Stry Liaison Ofiice The University Of British Columbia Umiversity Indu | Treatment of melanoma by reduction in clusterin levels |
| WO2004093804A2 (en) * | 2003-04-18 | 2004-11-04 | Five Prime Therapeutics, Inc. | Human polypeptides encoded by polynucleotides and methods of their use |
| EP1815021A2 (en) * | 2004-11-03 | 2007-08-08 | Almac Diagnostics Limited | Transcriptome microarray technology and methods of using the same |
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