WO2024084520A1 - Atténuation du syndrome de libération de cytokine en immunothérapie - Google Patents

Atténuation du syndrome de libération de cytokine en immunothérapie Download PDF

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WO2024084520A1
WO2024084520A1 PCT/IN2023/050973 IN2023050973W WO2024084520A1 WO 2024084520 A1 WO2024084520 A1 WO 2024084520A1 IN 2023050973 W IN2023050973 W IN 2023050973W WO 2024084520 A1 WO2024084520 A1 WO 2024084520A1
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nucleic acid
seq
recombinant nucleic
acid molecule
encoded
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Aaman Anjum Bilakhia
Nilay Mohanlal LAD
Dhaval Ashvinbhai Kedaria
Urvi Hrishiraj PANWAR
Jyotirmoi AICH
Jitendra Devendra VYAS
Areej AKHTAR
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Microcrispr Pvt Ltd.
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    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
    • C12N5/0636—T lymphocytes
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1136—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against growth factors, growth regulators, cytokines, lymphokines or hormones
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid
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    • C12N2510/00—Genetically modified cells
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    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the present disclosure relates to an artificially modified immune effector cell to reduce cytokine release syndrome. More specifically, the present disclosure relates to an artificially modified immune effector cell that reduces level of interleukin 6 (IL6) and granulocyte monocyte colony stimulating factor (GMCSF) released during immunotherapy for cancer.
  • IL6 interleukin 6
  • GMCSF granulocyte monocyte colony stimulating factor
  • Cancer is a disease in which abnormal cells divide uncontrollably and destroy body tissue.
  • the natural immune cells of the body recognize an advanced tumor as either “hot” or “cold” depending on whether immune cells are present or absent at the tumor site respectively.
  • the immune cells including cytotoxic T lymphocytes or T- cells
  • the chemotactic signaling of T-cells that is inhibited.
  • CAR T-cell based immunotherapy is an adoptive cell therapy (ACT) in which immune cells are engineered (genetically manipulated) to specifically target and kill cancer cells.
  • ACT adoptive cell therapy
  • the CAR constructs of the CAR T-cells are designed to target specific Tumor-associated antigens (TAAs).
  • CAR T-cell immunotherapy Although most adverse events of CAR T-cell immunotherapy are tolerable and acceptable, CAR T-cell immunotherapy is not without significant side effects.
  • Conventionally available latest CAR T-cell based immunotherapy (based on second generation CAR design) often displays serious systemic toxicities that include release of a high amount of cytokines.
  • Cytokines are signaling molecules that regulate immune system function. The release of high amount of cytokines termed as cytokine release syndrome (CRS), causes immune-related complications, and/or neurotoxicity.
  • Neurotoxicity includes symptoms such as confusion, delirium, and seizures which further leads to rapid release of cytokines into the central nervous system.
  • CRS Creactive cytokines
  • IL6 Interleukin 6
  • GMCSF Granulocyte monocyte colony stimulating factor
  • Fig. 1 depicts an immune response of conventional CAR T-cell.
  • the conventional CAR T-cell induces release of high levels of cytokines like GMCSF, IL6, etc.
  • the released GMCSF recruits pro-inflammatory immune cells like monocytes, neutrophils, basophils and macrophages.
  • pro-inflammatory immune cells induce (up-regulation) release of high levels of pro-inflammatory cytokines like IL6, Interleukin 1 (111), Nitric oxide (NO), etc.
  • These high levels of pro-inflammatory cytokines eventually lead to CRS.
  • the engineered CAR T- cells may transform into cancerous cells due to uncontrolled proliferation of the CAR T-cells.
  • CRS along with inability to control proliferation of the engineered CAR T-cells constitute a major challenge in the treatment of cancer patients with CAR T-cell based immunotherapies.
  • patients infused with conventional CAR T-cells have been diagnosed with relapse (i.e., reoccurrence of cancerous cells) as the conventional CAR T-cells do not persist for a long period of time.
  • the present disclosure relates to a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the recombinant nucleic acid molecule includes at least one first hairpin loop structure, at least one second hairpin loop structure and a first promoter.
  • the first hairpin loop structure is formed by one or more first short hairpin RNA sequences.
  • the first hairpin loop structure regulates an amount of Interleukin 6 (IL6) cytokine during immunotherapy.
  • the second hairpin loop structure is formed by one or more second short hairpin RNA sequences.
  • the second hairpin loop structure regulates an amount of granulocyte monocyte colony stimulating factor (GMCSF) cytokine during immunotherapy.
  • the second hairpin loop structure is disposed either upstream or downstream of the first hairpin loop structure.
  • the first promoter is disposed upstream of the first hairpin loop structure and the second hairpin loop structure.
  • the present disclosure relates to a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the recombinant nucleic acid molecule includes at least one first hairpin loop structure, at least one second hairpin loop structure, a first promoter, one or more chimeric antigen receptor genes, a second promoter, and one or more long terminal repeats.
  • the first hairpin loop structure is formed by one or more first short hairpin RNA sequences.
  • the first hairpin loop structure regulates an amount of Interleukin 6 (IL6) cytokine during immunotherapy.
  • the second hairpin loop structure formed by one or more second short hairpin RNA sequences.
  • the second hairpin loop structure regulates an amount of granulocyte monocyte colony stimulating factor (GMCSF) cytokine during immunotherapy.
  • the second hairpin loop structure is disposed either upstream or downstream of the first hairpin loop structure.
  • the first promoter is disposed upstream of the first hairpin loop structure and the second hairpin loop structure.
  • the chimeric antigen receptor genes include one or more single-chain variable fragment domains, one or more hinge domains, one or more co-stimulatory domains, one or more signaling domains, one or more safety switch domains, and one or more transmembrane domains.
  • the single-chain variable fragment domain is configured to bind one or more tumor associated antigens (TAAs).
  • TAAs tumor associated antigens
  • the hinge domain is coupled to the single-chain variable fragment domain.
  • the signaling domain is coupled to the co-stimulatory domain.
  • the safety switch domain is coupled to the signaling domain.
  • the transmembrane domain operationally couples the hinge domain to the co-stimulatory domain.
  • the second promoter is disposed upstream of the chimeric antigen receptor genes.
  • the long terminal repeat is disposed upstream of the first promoter and downstream of the chimeric antigen receptor genes.
  • the present disclosure relates to a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the recombinant nucleic acid molecule includes at least one first hairpin loop structure, at least one second hairpin loop structure, a first promoter, a poly-A-tail sequence, one or more chimeric antigen receptor genes, a second promoter, and one or more long terminal repeats.
  • the first hairpin loop structure is formed by one or more first short hairpin RNA sequences.
  • the first hairpin loop structure regulates an amount of Interleukin 6 (IL6) cytokine during immunotherapy.
  • the second hairpin loop structure formed by one or more second short hairpin RNA sequences.
  • the second hairpin loop structure regulates an amount of granulocyte monocyte colony stimulating factor (GMCSF) cytokine during immunotherapy.
  • the second hairpin loop structure is disposed either upstream or downstream of the first hairpin loop structure.
  • the first promoter is disposed upstream of the first hairpin loop structure and the second hairpin loop structure.
  • the poly-A-tail sequence is disposed downstream of the first hairpin loop structure and the second hairpin loop structure.
  • the chimeric antigen receptor genes include one or more single-chain variable fragment domains, one or more hinge domains, one or more co-stimulatory domains, one or more signaling domains, one or more safety switch domains, and one or more transmembrane domains.
  • the single-chain variable fragment domain is configured to bind one or more tumor associated antigens (TAAs).
  • TAAs tumor associated antigens
  • the hinge domain is coupled to the single-chain variable fragment domain.
  • the signaling domain is coupled to the co-stimulatory domain.
  • the safety switch domain is coupled to the signaling domain.
  • the transmembrane domain operationally couples the hinge domain to the co- stimulatory domain.
  • the second promoter is disposed upstream of the chimeric antigen receptor genes.
  • the long terminal repeat is disposed upstream of the first promoter and downstream of the chimeric antigen receptor genes.
  • the present disclosure relates to a transcript of a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the transcript includes a messenger RNA of a first hairpin loop structure or a second hairpin loop structure transcribed from the recombinant nucleic acid molecule.
  • the messenger RNA of the first hairpin loop structure or the second hairpin loop structure is configured to bind with a messenger RNA of a cytokine.
  • the present disclosure relates to a vector including at least one of a recombinant nucleic acid molecule ligated to at least one of a plasmid, a cosmid, a viral vector and a phage.
  • the recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the present disclosure relates to an engineered immune cell including at least one of a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the present disclosure relates to a composition including an engineered immune cell suspended in a nutrient medium.
  • the engineered immune cell including at least one of a recombinant nucleic acid molecule encoded at least by an ORF to lower a cytokine storm during immunotherapy.
  • the present disclosure relates to a method to prepare an engineered immune cell.
  • the method includes isolating a plurality of T-cells from a population of Peripheral Blood Mononuclear Cells. Replicating at least one recombinant nucleic acid molecule, encoded at least by an ORF to lower a cytokine storm during immunotherapy, in a vector. And, delivering the vector within the plurality of T-cells.
  • FIG. 1 depicts an illustration of CRS induction (Prior art), in accordance with one or more exemplary embodiments of the present disclosure.
  • Fig. 2 depicts an ORF 100 in accordance with one or more exemplary embodiments of the present disclosure.
  • FIG. 2a depicts an ORF 100a in accordance with one or more exemplary embodiments of the present disclosure.
  • FIG. 3 depicts a CAR construct 200 in accordance with one or more exemplary embodiments of the present disclosure.
  • Fig. 3a depicts a CAR construct 300 in accordance with one or more exemplary embodiments of the present disclosure.
  • FIG. 4 depicts an illustration of CRS reduction in accordance with one or more exemplary embodiments of the present disclosure.
  • Fig. 5 depicts a method 400 to make CAR T-cell in accordance with one or more exemplary embodiments of the present disclosure.
  • FIG. 6 - 8 depicts experimental observations in accordance with one or more exemplary embodiments of the present disclosure.
  • activation refers to the state of a cell that has been sufficiently stimulated to induce detectable cellular proliferation and/or differentiation into effector T-cells (or activated T-cells). Activation can also be associated with induced cytokine production and detectable effector functions.
  • activated T cells refers to, among other things, T cells (or CAR T-cells) that express the chimeric antigen receptor (CAR) construct and/or are able to bind to tumor associated antigens (TAAs).
  • CAR chimeric antigen receptor
  • antibody is used in the broadest sense and refers to monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multi-specific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity or function.
  • the antibodies in the present disclosure may exist in a variety of forms including, for example, polyclonal antibodies; monoclonal antibodies; Fv, Fab, Fab', and F(ab')2 fragments; as well as single chain antibodies and humanized antibodies.
  • antibody fragments refers to a portion of a full-length antibody, for example, the antigen binding or variable region of the antibody.
  • Other examples of antibody fragments include Fab, Fab', Ffab' , and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.
  • Fv refers to the minimum antibody fragment which contains a complete antigen-recognition and -binding site. This fragment consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. From the folding of these two domains emanates six hypervariable loops (3 loops each from the H and L chain) that contribute amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv including only three complementarity determining regions (CDRs) specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site (the dimer).
  • CDRs complementarity determining regions
  • an “antibody heavy chain,” as used herein, refers to the larger of the two types of polypeptide chains present in all antibody molecules in their naturally-occurring conformations.
  • An “antibody light chain,” as used herein, refers to the smaller of the two types of polypeptide chains present in all antibody molecules in their naturally-occurring conformations.
  • K and A light chains refer to the two major antibody light chain isotypes.
  • synthetic antibody refers to an antibody which is generated using recombinant DNA technology, such as, for example, an antibody expressed by a bacteriophage.
  • the term also includes an antibody which has been generated by the synthesis of a DNA molecule encoding the antibody and the expression of the DNA molecule to obtain the antibody or to obtain an amino acid encoding the antibody.
  • the synthetic DNA is obtained using technology that is available and well known in the art.
  • antigen refers to a molecule that provokes an immune response, which may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
  • Antigens include any macromolecule, including all proteins or peptides, or molecules derived from recombinant or genomic DNA. For example, DNA including a nucleotide sequence or a partial nucleotide sequence encoding a protein or peptide that elicits an immune response, and therefore, encodes an "antigen" as the term is used herein.
  • An antigen need not be encoded solely by a full-length nucleotide sequence of a gene.
  • an antigen can be generated, synthesized or derived from a biological sample including a tissue sample, a tumor sample, a cell, or a biological fluid.
  • the term "anti-tumor effect” as used herein, refers to a biological effect associated with a decrease in tumor volume, a decrease in the number of tumor cells, a decrease in the number of metastases, decrease in tumor cell proliferation, decrease in tumor cell survival, an increase in life expectancy of a subject having tumor cells, or amelioration of various physiological symptoms associated with the cancerous condition.
  • An “anti-tumor effect” can also be manifested by the ability of the peptides, polynucleotides, cells, and antibodies in the prevention of the occurrence of tumor in the first place.
  • auto-antigen refers to an endogenous antigen mistakenly recognized by the immune system as being foreign. Auto-antigens include cellular proteins, phosphoproteins, cellular surface proteins, cellular lipids, nucleic acids, glycoproteins, including cell surface receptors.
  • autologous is used to describe a material derived from a subject which is subsequently re-introduced into the same subject.
  • allogeneic is used to describe a graft derived from a different subject of the same species.
  • a donor subject may be a related or unrelated to the recipient subject, but the donor subject has immune system markers which are similar to the recipient subject.
  • xenogeneic is used to describe a graft derived from a subject of a different species.
  • the donor subject is from a different species than a recipient subject, and the donor subject and the recipient subject can be genetically and immunologically incompatible.
  • cancer is used to refer to a disease characterized by the rapid and uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers include breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer, and the like.
  • complementarity refers to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules.
  • sequence "A-G-T” is complementary to the sequence "T-C-A.”
  • Complementarity may be "partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules, or there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
  • the term “corresponds to” or “corresponding to” refers to (a) a polynucleotide having a nucleotide sequence that is substantially identical or complementary to all or a portion of a reference polynucleotide sequence or encoding an amino acid sequence identical to an amino acid sequence in a peptide or protein; or (b) a peptide or polypeptide having an amino acid sequence that is substantially identical to a sequence of amino acids in a reference peptide or protein.
  • co-stimulatory ligand refers to a molecule on an antigen presenting cell (e.g., an APC, dendritic cell, B cell, and the like) that specifically binds a cognate co-stimulatory molecule on a T cell, thereby providing a signal which, in addition to the primary signal provided by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, mediates a T cell response, including at least one of proliferation, activation, differentiation, and other cellular responses.
  • an antigen presenting cell e.g., an APC, dendritic cell, B cell, and the like
  • a co-stimulatory ligand also includes, inter alia, an agonist or an antibody that specifically binds with a co-stimulatory molecule present on a T cell, such as CD27, CD28, 4-1BB, 0X40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds CD83.
  • an agonist or an antibody that specifically binds with a co-stimulatory molecule present on a T cell such as CD27, CD28, 4-1BB, 0X40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds CD83.
  • LFA-1 lymphocyte function-associated antigen-1
  • co-stimulatory molecule refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T cell, such as proliferation.
  • Co-stimulatory molecules include an MHC class I molecule, BTLA, and a Toll-like receptor.
  • co-stimulatory signal refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell proliferation and/or upregulation or downregulation of key molecules.
  • the term "encoding" refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as a template for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.
  • a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system.
  • Both the coding strand the nucleotide sequence of which is identical to the mRNA sequence (except that a "T” is replaced by a "U") and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
  • exogenous refers to a molecule that does not naturally occur in a wildtype cell or organism but is typically introduced into the cell by molecular biological techniques.
  • exogenous polynucleotides include vectors, plasmids, and/or man-made nucleic acid constructs encoding the desired protein.
  • endogenous or “native” refers to naturally occurring polynucleotide or amino acid sequences that may be found in a given wild-type cell or organism.
  • polynucleotide sequences that is isolated from a first organism and transferred to a second organism by molecular biological techniques is typically considered an "exogenous" polynucleotide or amino acid sequence with respect to the second organism.
  • polynucleotide sequences can be "introduced" by molecular biological techniques into a microorganism that already contains such a polynucleotide sequence, for instance, to create one or more additional copies of an otherwise naturally occurring polynucleotide sequence, and thereby facilitate overexpression of the encoded polypeptide.
  • expression refers to the transcription and/or translation of a particular nucleotide sequence driven by its promoter.
  • expression vector refers to a vector including a recombinant polynucleotide including expression control (regulatory) sequences operably linked to a nucleotide sequence to be expressed.
  • An expression vector includes sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system.
  • Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
  • nucleic acid bases In the context of the present disclosure, the following abbreviations for the commonly occurring nucleic acid bases are used. "A” refers to adenine, “C” refers to cytosine, “G” refers to guanine, “T” refers to thymine, and “U” refers to uracil.
  • nucleotide sequence encoding an amino acid sequence includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence.
  • the phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).
  • lentivirus refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. Moreover, the use of lentiviruses enables integration of the genetic information into the host chromosome resulting in stably transduced genetic information. HIV, SIV, and FIV are all examples of lentiviruses. Vectors derived from lentiviruses offer the means to achieve significant levels of gene transfer in vivo.
  • modulating refers to mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject.
  • the term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • under transcriptional control refers to a promoter being operably linked to and in the correct location and orientation in relation to a polynucleotide to control (regulate) the initiation of transcription by RNA polymerase and expression of the polynucleotide.
  • the term “overexpressed” tumor antigen or “overexpression” of the tumor antigen is intended to indicate an abnormal level of expression of the tumor antigen in a cell from a disease area such as a solid tumor within a specific tissue or organ of the patient relative to the level of expression in a normal cell from that tissue or organ. Patients having solid tumor or a hematological malignancy characterized by overexpression of the tumor antigen can be determined by standard assays known in the art.
  • the terms “patient,” “subject,” and “individual,” and the like are used interchangeably herein and refer to any human, or animal, amenable to the methods described herein.
  • the patient, subject, or individual is a human or animal.
  • the term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). Examples of subjects include humans, and animals, such as dogs, cats, mice, rats, and transgenic species thereof.
  • a subject in need of treatment or in need thereof includes a subject having a disease, condition, or disorder that needs to be treated.
  • a subject in need thereof also includes a subject that needs treatment for prevention of a disease, condition, or disorder.
  • polynucleotide or “nucleic acid” refers to mRNA, RNA, cRNA, rRNA, cDNA or DNA.
  • the term typically refers to a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
  • the term includes all forms of nucleic acids including single and double-stranded forms of nucleic acids.
  • polynucleotide variant and “variant” and the like refer to polynucleotides displaying substantial sequence identity with a reference polynucleotide sequence or polynucleotides that hybridize with a reference sequence under stringent conditions that are defined hereinafter. These terms also encompass polynucleotides that are distinguished from a reference polynucleotide by the addition, deletion or substitution of at least one nucleotide. Accordingly, the terms “polynucleotide variant” and “variant” include polynucleotides in which one or more nucleotides have been added or deleted or replaced with different nucleotides.
  • polynucleotide variants include, for example, polynucleotides having at least 50% (and at least 51% to at least 99% and all integer percentages in between, e.g., 90%, 95%, or 98%) sequence identity with a reference polynucleotide sequence described herein.
  • polynucleotide variant and variant also include naturally occurring allelic variants and orthologs.
  • polypeptide polypeptide
  • polypeptide fragment polypeptide
  • protein protein
  • amino acid polymers in which one or more amino acid residues are synthetic non-naturally occurring amino acids, such as a chemical analogue of a corresponding naturally-occurring amino acid, as well as to naturally occurring amino acid polymers.
  • polypeptides may include enzymatic polypeptides, or "enzymes,” which typically catalyze (i.e., increase the rate of) various chemical reactions.
  • polypeptide variant refers to polypeptides that are distinguished from a reference polypeptide sequence by the addition, deletion, or substitution of at least one amino acid residue.
  • a polypeptide variant is distinguished from a reference polypeptide by one or more substitutions, which may be conservative or non-conservative.
  • the polypeptide variant comprises conservative substitutions and, in this regard, it is well understood in the art that some amino acids may be changed to others with broadly similar properties without changing the nature of the activity of the polypeptide.
  • Polypeptide variants also encompass polypeptides in which one or more amino acids have been added or deleted or replaced with different amino acid residues.
  • promoter refers to a DNA sequence recognized by the synthetic machinery of the cell or introduced synthetic machinery, required to initiate the specific transcription of a polynucleotide sequence.
  • expression control (regulatory) sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • bind refers to a molecule recognizing and adhering to a second molecule in a sample or organism but does not substantially recognize or adhere to other structurally unrelated molecules in the sample.
  • specifically binds refers to an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample.
  • an antibody that specifically binds an antigen from one species may also bind that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific.
  • an antibody that specifically binds an antigen may also bind different allelic forms of the antigen.
  • the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds a specific protein structure rather than to any protein. If an antibody is specific for epitope "A,” the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled "A” and the antibody, will reduce the amount of labeled A bound to the antibody.
  • a particular structure e.g., an antigenic determinant or epitope
  • stimulation refers to a primary response induced by binding of a stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand thereby mediating a signal transduction event, such as signal transduction via the TCR/CD3 complex.
  • a stimulatory molecule e.g., a TCR/CD3 complex
  • Stimulation can mediate altered expression of certain molecules, such as downregulation of TGF- , and/or reorganization of cytoskeletal structures.
  • stimulation molecule refers to a cognate stimulatory ligand present on an antigen presenting cell that specifically binds to a molecule on a T cell.
  • the term "stimulatory ligand” refers to a ligand that when present on an antigen presenting cell (e.g., an APC, a dendritic cell, a B-cell, and the like.) can specifically bind with a cognate binding partner (referred to herein as a "stimulatory molecule") on a cell, for example a T cell, thereby mediating a primary response by the T cell, including activation, initiation of an immune response, proliferation, and similar processes.
  • an antigen presenting cell e.g., an APC, a dendritic cell, a B-cell, and the like.
  • a cognate binding partner referred to herein as a "stimulatory molecule”
  • transfected or “transformed” or “transduced” refers to a process by which an exogenous nucleic acid is transferred or introduced into the host cell.
  • a “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed, or transduced with exogenous nucleic acid.
  • the cell includes the primary subject cell and its progeny.
  • a "chimeric antigen receptor” (CAR) molecule is a recombinant polypeptide including at least an extracellular domain, a transmembrane domain and a cytoplasmic domain or intracellular domain.
  • the present disclosure discloses a Chimeric Antigen Receptor T-cell(s) (CAR T-cell).
  • the CAR T-cell is artificially engineered by genetic manipulation.
  • the CAR T-cells may be derived from either an autologous or an allogeneic source.
  • the CAR T-cell may be used to target different cellular disorders including but not limited to B cell malignancy (blood cancer), solid tumors, etc.
  • the CAR T-cells are directed towards relapsed or refractory B- cell acute lymphoblastic leukemia (ALL) or non-Hodgkin Lymphoma (NHL).
  • ALL acute lymphoblastic leukemia
  • NHS non-Hodgkin Lymphoma
  • the CAR T-cells may be genetically engineered to include one or more sequences that express one or more chimeric antigen receptors (CARs or CAR constructs).
  • the CARs have predefined specificity towards one or more tumor associated antigens (TAAs) including but not limited to Cluster of Differentiation 19 (CD19), Cluster of Differentiation 7 (CD7), Cluster of Differentiation 20 (CD20), Cluster of Differentiation 22 (CD22), Cluster of Differentiation 123 (CD123), Cluster of Differentiation 133 (CD133), Cluster of Differentiation 30 (CD30), Cluster of Differentiation 138 (CD138), Epidermal Growth Factor Receptor (EGFR), Epidermal Growth Factor Receptor Variant III (EGFRvlll), Fibroblast Activation Protein a (FAP), Mucin 1 (MUC1), Disialoganglioside GD2 (GD2), Carcinoembryonic Antigen (CEA), Prostate-specific Membrane Antigen (PSMA), Human Epidermal
  • the CAR T-cells include CARs specific to CD19.
  • the CAR T-cells includes at least two short hairpin RNA (shRNA) sequence to lower a cytokine storm called cytokine release syndrome (CRS) during immunotherapy.
  • CRS cytokine release syndrome
  • IL6 Interleukin 6
  • GMCSF Granulocyte Macrophage Colony Stimulating Factor
  • the shRNA sequences may inhibit cytokine production and/or cytokine signaling via RNA interference (RNAi).
  • a transcript of the shRNA sequence binds with an mRNA for the cytokine to functionally inactivate the mRNA and/or degrade the mRNA.
  • the transcript of the shRNA sequence binds with the mRNA of the cytokine to prevent its translation.
  • the shRNA binds with one or more receptors of the cytokine, thus blocking the downstream signaling pathway of the said cytokine.
  • the shRNA sequence expresses a nti-l L6 (alL6) that binds with and neutralizes IL6 (an exemplary cytokine), thus at least partially blocking the activity of IL6.
  • the CAR T-cells of the present disclosure includes IL-6 receptor (IL6-R) conjugated with synthetic notch (syn-notch) receptor and GAL-VP64 domain.
  • IL6-R IL-6 receptor
  • synthetic notch syn-notch
  • GAL-VP64 domain migrates to the nucleus of the CAR T-cells and induces the expression of one of the thirty-six shRNA sequences specific to Interleukin 6 (or IL6).
  • the said expression of the shRNA sequence(s) leads to production alL6.
  • the alL6 binds with and neutralizes IL6.
  • IL6 is a critical molecule involved in eliciting CRS and leading to premature CAR T-cell apoptosis. By neutralizing the IL6, the CAR T- cells as disclosed herein have lower risk of CRS thereby, having ability to remove the cancerous cells safely and effectively.
  • the CAR T-cells of the present disclosure produce a transcript of at least one of twenty shRNAs specific to Granulocyte Monocyte Colony Stimulating Factor (or GMCSF) that contributes to cytokine release syndrome (CRS) at the time of immunotherapy.
  • GMCSF Granulocyte Monocyte Colony Stimulating Factor
  • the shRNA sequence regulates (i.e., reduces) the amount of GMCSF produced by selectively binding to the GMCSF mRNA and rendering it non-functional.
  • GMCSF is a critical molecule involved in eliciting CRS and leading to premature CAR T-cell apoptosis. By regulating the amount of GM-CSF produced, the CAR T-cells as disclosed herein have lower risk of CRS and persist longer thereby, having the ability to remove the cancerous cells safely and effectively.
  • the CAR T-cells of the present disclosure may produce at least one of shRNAs specific to each of GMCSF mRNA and IL6 mRNA thereby reducing the concentration levels of GMCSF and IL6 molecules thereby reducing the CRS burden.
  • the CARs include a safety switch (SS) domain for regulating proliferation of the CAR T-cells thereby inhibiting transformation of the CAR T-cells into cancerous cells (for example, during manufacturing or post-infusion of the CAR T-cells in the patient).
  • the SS domain may include but not limited to inducible caspase 9 (iCaspase 9), truncated Epidermal growth factor receptor (EGFRt), RQR8 or a combination thereof.
  • CAR T-cells as disclosed herein are programmed to elicit an artificial immune response against the cancerous cells without any undesirable side effects of CRS. Further, based on the conditions and requirements of a patient (or subject), the CAR T- cells of the present disclosure may be selectively depleted to prevent malignant transformation of the CAR T-cells.
  • Fig. 2 depicts an anti-sense (or template) strand of an open reading frame (ORF) 100 of a CAR T-cell (not shown).
  • the ORF 100 may include a sense (or coding) strand (not shown) complementary to the anti-sense strand.
  • the anti-sense strand of the ORF 100 extends from a 3'end to a 5' end. Hence, in terms of direction, the 3' end of the anti-sense strand of the ORF 100 is upstream and 5' end is downstream.
  • a recombinant nucleotide sequence molecule is at least encoded by the ORF 100.
  • At least a portion of the ORF 100 may be introduced into one or more natural immune cells via genetic manipulation to produce an engineered immune cell.
  • the ORF 100 (or a portion thereof) expresses one or more CARs (i.e., a protein and/or a polypeptide) and/or one or more shRNA transcripts (described below).
  • the natural immune cells may include but not limited to T-lymphocyte (T-cells), Natural Killer (NK) cells, Gamma Delta (y6) T-cells, etc.
  • the ORF 100 is introduced in a natural T-cell via Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR associated protein (CRISPR-Cas) based gene editing techniques. Additionally or alternatively, the ORF 100 is introduced in a natural T-cell using lentiviral vectors, Adeno-associated viruses (AAVs), etc.
  • the vector including the ORF 100 can be selected from plasmid, cosmid, viral vector or phage.
  • the plasmid may be a eukrayotic expression plasmid.
  • the viral vector can be derived from a lentivirus, a retrovirus, an adenovirus, an adeno-associated virus, and/or a sendai virus.
  • a lentivirus is employed for introduction of the ORF 100 into the T-cell.
  • Lentiviral (LV) vectors provide an effective means for modifying eukaryotic cells, stable transfer, and expression of gene in host cells with lower immunogenicity. LV vectors have larger gene accommodation capacity and can transduce proliferating as well as nonproliferating cells. Further, LV vectors-based gene delivery system is the most efficient method of transducing the hard-to-transfect T cells.
  • the clinical grade viral vectors were commercially obtained from Lentigen and Sirion-Biotech.
  • the ORF 100 may include one or more regions including one or more long terminal repeats (LTR) 110, one or more promoters, at least two hairpin loop structure formed by one or more first short hairpin RNA (shRNA) 130a sequences, and/or one or more second shRNA 130b sequences, one or more genes, etc.
  • the one or more promoters may include a first promoter 120 and a second promoter 140.
  • the one or more genes may include but not limited to a plurality of CAR genes 150.
  • the ORF 100 includes a first hairpin loop structure formed by the first shRNA 130a sequence and a second hairpin loop structure formed by at least one second shRNA 130b sequence.
  • the ORF 100 may include one or more nucleotide sequences such as genes for fluorescent protein, c-myc, HA, V5 etc.
  • the first and second hairpin loop structure regulates an amount of IL6 and GMCSF cytokines, respectively, during immunotherapy.
  • a transcript i.e., a messenger RNA
  • mRNA messenger RNA
  • the transcript of the first and second hairpin loop structures bind with mRNAs of IL6 and GMCSF respectively.
  • the LTR 110 may flank the ORF 100, i.e., the LTR 110 may be disposed at the 5'end and the 3'end of the ORF 100. In other words, the LTR 110 mays disposed upstream of the first promoter 120 and downstream of the CAR genes 150.
  • the LTR 110 at the 5' end of the ORF 100 is encoded by SEQ ID NO. 1.
  • the LTR 110 helps in integration of the ORF 100 in the native DNA of the T-cells while genetically manipulating the T-cells. Integration of the ORF 100 in the native DNA transforms the native T-cells into CAR T-cells (i.e., an exemplary engineered immune cell.
  • the transcription of the ORF 100 within the CAR-T cell may be controlled by the one or more promoters, i.e., the production of the transcripts of the one or more genes are controller by the one or more promoters.
  • the promoters may be disposed upstream of the one or more genes of the ORF 100.
  • One or more RNA polymerase may bind to the promoters for transcription of the ORF 100.
  • the RNA polymerase may include but not limited to eukaryotic RNA polymerase II (Pol II), eukaryotic RNA polymerase III (Pol III), etc.
  • the RNA polymerase after binding with the promoters may partially or completely transcribe the ORF 100 to one or more messenger RNAs (mRNAs) (or transcripts).
  • mRNAs messenger RNAs
  • the mRNAs may be further processed to provide one or more CARs (protein structure) and first and second shRNA 130a, 130b transcripts (and protein/polypeptide thereof).
  • Processing of mRNA may include at least one of splicing, translation of the mRNA to one or more amino acid sequences (i.e., a polypeptide) and post- translational modifications, etc.
  • Post-translational modification may include but not limited to folding of the amino acid sequence (into a protein) and/or glycosylation, etc.
  • the first promoter 120 may be disposed upstream of the first shRNA 130a (i.e., the first hairpin loop structure(s)), if the first shRNA 130a is disposed upstream of the second shRNA 130b.
  • the first promoter 120 may be disposed upstream of the second shRNA 130b (i.e., the second hairpin loop structure(s)), if the first shRNA 130a is disposed downstream of the second shRNA 130b.
  • the first promoter 120 may be selected from full-length cytomegalovirus (CMV) promoter (encoded by SEQ ID NO. 2), attenuated CMV promoter (encoded by SEQ ID NO.
  • the first promoter 120 includes a GAL-VP64 recognition domain which activates the first promoter 120 when a GAL-VP64 domain binds with the GAL-VP64 recognition domain.
  • the first promoter 120 transcribes the first shRNA 130a and second shRNA 130b to produce one or more short RNA transcripts having a hairpin loop structure each.
  • the first shRNA 130a may be encoded by at least one of the SEQ ID NO. 5 - SEQ ID NO. 40 (SEQ ID NO. 30 - SEQ ID NO. 40 are sequences of sense strand).
  • the second shRNA 130b may be encoded by at least one of the SEQ ID NO. 41 - SEQ ID NO. 60. Expression of the first shRNA 130a and the second shRNA 130b may be regulated by the first promoter 120.
  • the transcripts of first shRNA 130a and the second shRNA 130b may include a specific binding affinity towards one or more molecules.
  • the CAR T-cell includes a plurality of IL6 receptors (IL6-R) conjugated with synthetic notch (syn-notch) receptor and GAL-VP64 domain.
  • IL6-R IL6 receptors
  • synthetic notch syn-notch
  • GAL-VP64 domain migrates to the nucleus of the CAR T-cells and induces the expression of one of the thirty-six first shRNA 130a sequences.
  • the said expression of the first shRNA 130a sequence(s) leads to production alL6.
  • the alL6 binds with and neutralizes IL6, thus reducing the burden of CRS.
  • the CAR T-cell includes a plurality of GMCSF gene sequences (not shown) that produce pro-inflammatory cytokines (like GMCSF) which contribute to CRS.
  • the second shRNA 130b may inhibit cytokine production and/or cytokine signaling via RNA interference (RNAi).
  • RNAi RNA interference
  • the transcript of the second shRNA 130b binds with an mRNA corresponding to the cytokine (i.e., the GMCSF), to functionally inactivate the mRNA and/or degrade the mRNA.
  • the first shRNA 130a expressed by the CAR T-cell selectively binds with the IL6 mRNA thereby regulating the IL6 cytokine levels (via RNAi).
  • the transcript of the first shRNA 130a selectively binds with the IL6 mRNA thereby regulating the IL6 cytokine levels (via RNAi).
  • the second shRNA 130b expressed by the CAR T-cell selectively binds with the GMCSF mRNA thereby regulating the GMCSF cytokine levels (via RNAi).
  • the transcript of the second shRNA 130b selectively binds with the GMCSF mRNA thereby regulating the GMCSF cytokine levels (via RNAi).
  • Fig. 2a depicts an ORF 100a of the present disclosure.
  • the ORF 100a is structurally same as ORF 100 with addition of an optional poly-A-tail 160 sequence, i.e., the ORF 100a includes the one or more LTRs 110, at least two hairpin loop structure formed by one or more first shRNA sequence 130a and/or one or more second shRNA sequence 130b, the first promoter 120, the second promoter 140, the plurality of CAR genes 150, the poly-A-tail 160 sequence, etc.
  • the ORF 100a includes a first hairpin loop structure formed by the first shRNA 130a sequence and a second hairpin loop structure formed by at least one second shRNA 130b sequence.
  • a recombinant nucleotide sequence molecule is at least encoded by the ORF 100a.
  • the first and second hairpin loop structure regulates an amount of IL6 and GMCSF cytokines, respectively, during immunotherapy.
  • a transcript i.e., a messenger RNA
  • mRNA messenger RNA
  • the transcript of the first and second hairpin loop structures bind with mRNAs of IL6 and GMCSF respectively.
  • the poly-A-tail sequence 160 may be downstream of the first and second shRNA 130a, 130b sequences. Expression of the poly-A-tail sequence 160 may be regulated by the first promoter 120. In an exemplary embodiment, as shown in Fig. 2a, the poly-A-tail 160 sequence is downstream of the hairpin loop structures formed by the second shRNA 130b sequences. A transcript of the poly-A-tail 160 sequence may include a plurality of adenosine nucleotides. In an exemplary embodiment, the poly-A-tail 160 sequence is from either Simian virus 40 (SV40) or bovine growth hormone (bGH). The SV40 poly-A-tail 160 sequence is encoded by SEQ ID NO. 61.
  • SV40 Simian virus 40
  • bGH bovine growth hormone
  • the poly-A-tail 160 helps in mRNA stability by offering protection against enzymatic cleavage, which is a process that could lead to mRNA degradation. It further ensures that the intended regulatory effects of the IL6, and GMCSF components are maintained over time, without undue degradation or interference.
  • the second promoter 140 may be disposed upstream of the CAR genes 150.
  • the CAR genes 150 may be disposed downstream of the second promoter 140.
  • the second promoter 140 may be selected from Elongation Factor 1 (EFl) full length promoter (encoded by SEQ ID NO. 62), EFl alpha core promoter (encoded by SEQ ID NO. 63), etc. Accordingly, expression of the CAR genes 150 may be regulated by the second promoter 140.
  • EFl Elongation Factor 1
  • the CAR genes 150 include sequences encoding one or more domains of a CAR 200, as shown in Fig. 3.
  • the one or more domains of the CAR 200 include but not limited to one or more single-chain variable fragment (scFV) domains 210, one or more hinge domains 220, one or more transmembrane domains 230, one or more co-stimulatory (CSTM) domains 240, one or more signaling domains 250, one or more safety switch (SS) domains 260, etc.
  • scFV single-chain variable fragment
  • CSTM co-stimulatory domains 240
  • signaling domains 250 one or more safety switch (SS) domains 260, etc.
  • SS safety switch
  • the CAR 200 includes one scFV domain 210, one hinge domain 220, one transmembrane domain 230, one CSTM domain 240, one signaling domain 250 and one SS domain 260. Additionally or optionally, the CAR 200 may include one or more peptide sequences disposed between the domains of the CAR 200 such as a signal peptide, a linker peptide, etc.
  • the scFV domain 210 of the CAR 200 may include a light chain 210a and a heavy chain 210b.
  • the scFV domain 210 for the CD19 antigen (TAA) may be encoded by SEQ ID NO.
  • the scFV domain 210 includes a polypeptide sequence defined by SEQ ID NO. 65.
  • the scFV domain 210 for the CD19 antigen (TAA) may be encoded by SEQ ID NO. 66 such that the scFV domain 210 includes a polypeptide sequence defined by SEQ ID NO. 67.
  • the light chain 210a and the heavy chain 210b of the scFV domain 210 may be coupled to each other via a linker protein 210c.
  • the scFV domain 210 may have a binding specificity (or affinity) towards one or more TAAs including but not limited to CD19, CD7, CD20, CD22, CD123, CD133, CD30, CD138, EGFR, EGFRvlll, FAP, MUC1, GD2, CEA, PSMA, HER2, NY-ESO-1, MAGEA-A3, hTERT, etc.
  • the CAR 200 includes one scFV domain 210 specific to CD19 antigens of B- lymphocytes (B-cells).
  • the CAR 200 may include two or three scFV domains (not shown) for the same TAA or different TAAs.
  • the hinge domain 220 operationally couples the scFV domain 210 to the transmembrane domain 230.
  • the hinge domain 220 includes Cluster of Differentiation 8 (CD8) domain.
  • CD8 Cluster of Differentiation 8
  • the hinge domain 220 helps to provide flexibility to the scFV domain 210 with respect to the transmembrane domain 230.
  • the hinge domain 220 is encoded by SEQ ID NO. 68 such that the hinge domain 220 includes a polypeptide sequence defined by SEQ ID NO. 69.
  • the transmembrane domain 230 may be disposed across a bi-lipid cell membrane (or membrane) 270.
  • the membrane 270 separates an extracellular region 270a from an intracellular region 270b.
  • the transmembrane domain 230 includes a CD8 domain encoded by SEQ ID NO. 70 such that the transmembrane domain 230 includes a polypeptide sequence defined by SEQ ID NO. 71.
  • the transmembrane domain 230 helps to operationally couple the domains of the CAR 200 present in the extracellular region 270a to the domains of the CAR 200 present in the intracellular region 270b.
  • the scFV domain 210 and the hinge domain 220 are the only domains present in the extracellular region 270a.
  • the CSTM domain 240 may be coupled to the transmembrane domain 230.
  • the CSTM domain 240 may be selected from Cluster of Differentiation 28 (CD28), Inducible T-cell CO-Stimulator (ICOS), 0X40, 4-1BB, DAP10, DAP12, 2B4, etc.
  • the CD28 CSTM domain 240 may be encoded by SEQ ID NO. 72 such that the CD28 CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 73.
  • the ICOS CSTM domain 240 may be encoded by SEQ ID NO. 74 such that the ICOS CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 75.
  • the 0X40 CSTM domain 240 may be encoded by SEQ ID NO. 76 such that the 0X40 CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 77.
  • the 4-1BB CSTM domain 240 may be encoded by SEQ ID NO. 78 such that the 4-1BB CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 79.
  • the DAP10 CSTM domain 240 may be encoded by SEQ ID NO. 80 such that the DAP10 CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 81.
  • the DAP12 CSTM domain 240 may be encoded by SEQ ID NO.
  • the 2B4 CSTM domain 240 may be encoded by SEQ ID NO. 84 such that the 2B4 CSTM domain 240 includes a polypeptide sequence defined by SEQ ID NO. 85.
  • the CSTM domain 240 includes 4-IBB. The CSTM domain 240 helps to enhance cell-mediated immune response.
  • the CAR T-cells are activated by subjecting the CAR T-cells to co-stimulatory molecules (for example, CD3 and/or CD28).
  • co-stimulatory molecules for example, CD3 and/or CD28.
  • the co-stimulatory molecules stimulate the CSTM domain 240, which in turn leads to activation, proliferation, and/or differentiation of the CAR T-cells into effector T cells (thus enabling the CAR T-cells to express the CAR construct).
  • CD3/CD28 activation mimics the signals T cells receive during natural antigen recognition, thus, providing a safe and effective way to synthetically activate the CAR T-cells in vitro as well as in vivo.
  • the CD3/CD28-activated CAR T-cells (or effector T cells) are then used to target and kill cancerous cells.
  • the signaling domain 250 may be coupled to the CSTM domain 240.
  • the signaling domain 250 is a Cluster of differentiation 3 zeta (CD3Q domain encoded by SEQ ID NO. 86 such that the CD3 ⁇ signaling domain 250 includes a polypeptide sequence defined by SEQ ID NO. 87.
  • the signaling domain 250 helps to transmit an activation signal to the CAR T-cell after a TAA binds with the scFV domain 210.
  • the SS domain 260 may be coupled to the signaling domain 250.
  • the SS domain 260 may be selected from iCaspase 9, EGFRt, RQR8, etc.
  • the SS domain 260 includes iCaspase 9 encoded by SEQ ID NO. 88 such that the iCaspase 9 SS domain 260 includes a polypeptide sequence defined by SEQ ID NO. 89.
  • the SS domain 260 includes RQR8 encoded by SEQ ID NO. 90 such that the RQR8 SS domain 260 includes a polypeptide sequence defined by SEQ ID NO. 91.
  • the SS domain 260 may control the cell proliferation of the CAR T-cell thereby preventing transformation of the CAR T-cells into cancerous cells.
  • the SS domain 260 allows selective depletion of CAR T-cells.
  • the inducible caspase 9 (iCaspase9) SS domain 260 encodes a caspase recruitment domain (CARD; GenBank NM001 229) linked to 2 12-kDa human FK506 binding proteins (FKBP12; GenBank AH002 818) that contain an F36V mutation.
  • Administration of a chemical inducer of dimerization (CID) results in the dimerization of the inducible caspase 9 molecules, leading to their activation.
  • the caspase 9 dimer will subsequently activate downstream effector caspases, such as caspase 3, and ultimately induce cell apoptosis.
  • the RQR8 SS domain 260 encodes a multiepitope molecule harboring a CD34 epitope and two CD20 mimotopes.
  • the CD20 mimotopes when bound to the FDA-approved CD20 antibody rituximab, the host cell undergoes cell apoptosis.
  • Fig. 3a depicts another embodiment of a CAR 300. Similar to the CAR 200, the CAR 300 includes one or more scFV domains 310, one or more hinge domains 320, one or more transmembrane domains 330, one or more CSTM domains 340, one or more signaling domains 350, one or more SS domains 360, etc.
  • the transmembrane domain 330 may be disposed across a membrane 370 such that the scFV domain 310 and the hinge domain 320 are disposed outside the CAR T-cell i.e., in an extracellular region 370a.
  • the remaining domains of the CAR 300 may be disposed within the CAR T-cell i.e., in an intracellular region 370b.
  • the CAR 300 includes one scFV domain 310, one hinge domain 320, one transmembrane domain 330, a first CSTM domain 340a and a second CSTM domain 340b, one signaling domain 350, and one SS domain 360.
  • the scFV domain 310 of the CAR 300 may include a light chain 310a and a heavy chain 310b.
  • the light chain 310a and the heavy chain 310b of the scFV domain 310 may be coupled to each other via a linker protein 310c.
  • the first CSTM domain 340a of the CAR 300 may be selected from CD28, ICOS and/or 0X40.
  • the second CSTM domain 340b may be coupled to the first CSTM domain 340a.
  • the second CSTM domain 340b may be selected from 4-1 BB, DAP10, DAP12 and/or 2B4.
  • the first CSTM domain 340a and the second CSTM domain 340b are CD28 and 4-1 BB respectively.
  • the first CSTM domain 340a and the second CSTM domain 340b of CAR 300 help to enhance the persistence of the CAR T-cells.
  • the above-described CAR T-cell produces negligible amount of cytokines like GMCSF and IL6 as shown in Fig. 4. Therefore, the said CAR T-cell does not recruit any pro- inflammatory cells thereby down-regulating pro-inflammatory cytokines. Attenuation in levels of pro-inflammatory cytokines mitigate CRS.
  • first and second shRNAs 130a, 130b are described with the examples of CAR 200/300 in the present disclosure, the first and second shRNAs 130a, 130b may be used with any functionally equivalent CAR construct and the same is within the scope of the teachings of the present disclosure.
  • the CAR T-cells of the present invention may be prepared for each cancer patient by following a method 400 depicted in Fig. 5. Alternatively, the CAR T-cells may be prepared from an allogenic T-cell line for all cancer patients.
  • the method 400 begins at step 401 by isolating Peripheral Blood Mononuclear Cells (PBMCs) by either a ficoll-based method or an automated PBMC isolation instrument (as in case of Leukapheresis).
  • PBMCs Peripheral Blood Mononuclear Cells
  • the PBMCs are isolated by drawing blood from a cancer patient requiring CAR T-cell based immunotherapy.
  • a plurality of T-cells may be isolated from the PBMCs.
  • the isolated T- cell population may include a plurality of CD4 + and CD8 + T-cells.
  • the isolated T-cell population may include at least 40% CD4 + T-cells.
  • the isolated T-cell population include 40% CD4 + T-cells and 60% CD8 + T-cells.
  • the T-cells are activated by subjecting the T-cells to costimulatory molecules (for example, CD3 and/or CD28).
  • costimulatory molecules for example, CD3 and/or CD28.
  • the costimulatory molecules help the T-cells to become competent to receive the ORF 100 via the lentiviral vectors (described below).
  • the ORF 100 of the present invention is prepared for delivery within the isolated T-cell population.
  • the ORF 100 may be litigated and replicated in a predefined vector (or plasmid) including but not limited to pHR, pTRPE lentiviral vectors, etc.
  • the ORF 100 is replicated and packaged within lentiviral particles.
  • the ORF 100 is delivered within the isolated T-cell population via a predefined gene delivery method.
  • the pre-defined gene delivery method may be one of transformation, transfection or transduction.
  • the isolated T-cell population is transduced by Lentiviral based gene delivery system such as the third-generation self-inactivating (SIN) lentiviral system.
  • the ORF 100 is delivered to the T-cells via third generation lentiviral particles, i.e., the T-cells are transduced with third generation lentivirus.
  • the resultant CAR T-cells target and bind to specific cancer cells, thereby allowing the CAR T-cells to recognize and attack the CD19 expressing B cells (i.e., the cancerous cells).
  • the CAR T-cells are expanded in a pre-defined nutrient medium for a pre-defined time to increase the number of CAR T-cells.
  • the CAR T-cells were expanded for 7 to 9 days to increase the number of CAR T-cells by 20-40 times.
  • the engineered immune cells suspended in the predefined nutrient medium may define a composition.
  • the nutrient medium includes AIM V media with or without antibiotic, human serum albumin, phenol red and L glutamine.
  • the nutrient medium includes CTS AIM V media without antibiotics, phenol red and serum.
  • the nutrient medium may be periodically replaced with fresh nutrient medium after a pre-defined time. In an exemplary embodiment, the nutrient medium is replaced every 48 hours.
  • the transduced T-cells expressing the CAR 200, 300 are selected and isolated by subjecting the transduced T-cells to in vitro and/or in vivo testing techniques. Additionally or alternatively, the transduced T-cells expressing the CAR 200,300 are selected by immunoassay-based selection or by cell sorting techniques.
  • the selected transduced T-cells expressing the CAR 200, 300 are refrigerated for storage and transportation.
  • the frozen CAR T-cells are thawed prior to infusion into the patient.
  • the selected T-cells i.e., the CAR T-cells
  • the selected T-cells may be directly infused into the patient as decided by the physician.
  • the method 400 is described with an exemplary sequence of steps, the steps of the method 400 may be rearranged while practicing the method 400 and the same is within the scope of the teachings of present disclosure.
  • Lentiviral packaging HEK293T cells obtained from American Type Culture Collection (ATCC) were seeded at approximately 3.8xl0 6 cells per plate in Dulbecco's Modified Eagle Medium (DMEM) complete in 10 cm tissue culture plates. The tissue culture plates including the HEK293T cells were then incubated at 37°C, 5% CO2 for about 24 hours. After about 24 hours, the old medium was aspirated out and replaced with 10 mL fresh DMEM complete and 25 pM cloroquine diphosphate. The tissue culture plates including the HEK293T cells were further incubated at 37°C, 5% CO2 for about 6 hours.
  • DMEM Dulbecco's Modified Eagle Medium
  • a mixture of lenti-plasmids and CAR plasmid (including the ORF 100 of the present disclosure) were inserted into the HEK293T cells using Polyethylenimine (PEI, a non- viral vector) as the transfection reagent.
  • PEI Polyethylenimine
  • the HEK293T cells were incubated at 37°C, 5% CO2 for about another 36 hours before harvesting the medium containing the viral particles at different intervals, upto 72 hours.
  • the harvested medium was centrifuged at 1000 rpm for 5 minutes to pellet any remaining HEK293T cells.
  • the supernatant was then filtered using a 0.45 pm PES filter.
  • the filtrate (supernatant) containing the viral particles were collected and refrigerated to avoid loss of titer.
  • the viral particles had the lenti-plasmid integrated with the CAR plasmid (including the ORF 100 of the present disclosure).
  • PBMCs peripheral blood mononuclear cells
  • T-cells were then isolated from the collected PBMCs using RosetteSe Human CD4+ T Cell Enrichment assay and RosetteSe Human CD8+ T Cell Enrichment assay.
  • the isolated T-cell population had 40% CD4+ T-cells and 60% CD8+ T-cells.
  • the isolated T cells were cryopreserved in RPMI-1640 with 20% human AB serum and 10% DMSO.
  • the isolated T cells are cultured in human T cell medium consisting of X-VIVO 15 (Lonza), 5% Human AB serum, and 10 mM neutralized N-acetyl L-Cysteine (Sigma-Aldrich). Further, IL-2 were used for cell proliferation and used at 30 units/mL IL-2.
  • the isolated T-cells were stimulated (activated) with Human T-Activator CD3/CD28 Dynabeads (Life Technologies) at a 1:3 celkbead ratio.
  • the primary T cells were exposed to the supernatant (containing the viral particles) for transduction.
  • the Dynabeads were removed, and the T cells were expanded until day 9.
  • the T-cells were sorted with FACs ARIA II. Thus, the T-cells exhibiting basal CAR expression (i.e., the CAR T-cells) were isolated.
  • the isolated CAR T-cells were expanded in the nutrient medium including CTS AIM V media without antibiotics, phenol red and serum at 37°C, 5% CO2.
  • the nutrient medium was replaced every 48 hours with fresh nutrient medium. It was observed that after expanding the CAR T-cells for about 7-9 days, the number of CAR T-cells increased by 20-40 times.
  • the CAR T-cells were frozen for storage and transportation.
  • the CAR T cells (as obtained in Example 1) were thawed. About 1 x 106 CAR T- cells per kilogram weight of a patient's weight were then intravenously infused into the patient in an outpatient setting. The CAR T-cells quickly migrated to the bone marrow and lymphoid tissues. After migration, the CAR T-cells had selectively bound to the cancer cells expressing CD19. The binding between the CAR T-cell and the cancerous cell triggered activation and proliferation of the CAR T-cells, after which the cancer cells were killed via mechanisms such as cytokine release and cytotoxicity.
  • the CAR T-cells persisted in the patient and continued to attack CD19-expressing cancerous cells, providing long-term therapeutic effect to the patient. It was observed that the CAR T-cells of the present disclosure provided response rates of up to 90% in patients with acute lymphoblastic leukemia and up to 50-60% in patients with non-Hodgkin lymphoma. The CAR T-cells specifically targeted cancer cells expressing CD19, reducing the risk of harm to healthy cells and reducing the risk of false-positive interactions. Unlike traditional chemotherapy and radiation therapy, CAR T cell therapy has minimal toxicity to healthy cells.
  • EXAMPLE 3 IL6 and GMCSF knockdown (Present invention): [00140] The best performing first shRNA 130a sequences and second shRNA 130b sequences as described in the present disclosure were evaluated for their effect on regulation of the IL6 and GMCSF levels. The screening was done in T cells. The bar graph, as shown in Fig.
  • Non-targeting shRNA Scram
  • said IL6 targeting first shRNAs 130a and GMCSF targeting second shRNAs 130b were evaluated in activated T cells for their effect in knocking down of the IL6 gene and the GMCSF gene.
  • T cells were transfected with respective first and second shRNAs 130a, 130b and mRNA was extracted after 24 hours of transfection. The assay was performed by RT-qPCR using IL6 and GMCSF mRNA specific primers.
  • the protein fraction was collected from the respective T-cells as described in example 3.
  • the collected protein fractions were subjected to enzyme linked immunosorbent assay (ELISA) to determine the amount of IL6 and GMCSF cytokines present in each of the protein fractions.
  • the bar graph, as shown in Fig. 7, depicts IL6 and GMCSF cytokines present in respective protein fractions.
  • the statistical analysis was done using the non-parametric t test revealing significance levels of **** (P ⁇ 0.0001), ** (P ⁇ 0.01), and ns (not significant) when comparing GMCSF/IL6 shRNA-expressing T cells to those expressing Scram (see Fig. 7).
  • the first and second shRNA 130a, 130b sequences as described in examples 3 and 4 were evaluated for its effect on regulation of the IL6 and GMCSF levels.
  • the screening was done in CAR T-cells.
  • Non-targeting shRNA (CART Scram ) and the said IL6 and GMCSF targeting first and second shRNAs 130a, 130b (CART shGMCSF/shlL6 ) were evaluated in activated CAR T-cells for their effect in knocking down of the IL6 and GMCSF genes.
  • a conventional CAR T- cell (CART con ) was also evaluated after its activation.
  • the assay and analysis were similar to as described in example 4 above.
  • the bar graph, as shown in Fig. 8, depicts IL6 and GMCSF cytokine present in respective protein fractions.
  • the statistical analysis was done using the non- parametric t test revealing significance levels of **** (P ⁇ 0.0001), when comparing IL6 shRNA- expressing T cells to those expressing Scram (see Fig. 8).

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Abstract

La présente invention divulgue une molécule d'acide nucléique recombinante codée au moins par un ORF (100, 100a) pour abaisser une tempête de cytokines pendant l'immunothérapie. La molécule d'acide nucléique recombinant comprend au moins une première structure en boucle en épingle à cheveux, au moins une seconde structure en boucle en épingle à cheveux et un premier promoteur (120). La première structure de boucle en épingle à cheveux est formée par une ou plusieurs premières séquences d'ARN court en épingle à cheveux (130a). La première structure en boucle en épingle à cheveux régule une quantité de cytokine interleukine 6 (IL6) pendant l'immunothérapie. La seconde structure de boucle en épingle à cheveux est formée par une ou plusieurs secondes séquences d'ARN court en épingle à cheveux (130b). La seconde structure en boucle en épingle à cheveux régule une quantité de cytokine du facteur de stimulation des colonies de monocytes granulocytes (GMCSF, « granulocyte monocyte colony stimulating factor ») pendant l'immunothérapie et est agencée soit en amont soit en aval de la première structure en boucle en épingle à cheveux. Le premier promoteur (120) est agencé en amont de la première et de la seconde structure en boucle en épingle à cheveux.
PCT/IN2023/050973 2022-10-20 2023-10-20 Atténuation du syndrome de libération de cytokine en immunothérapie WO2024084520A1 (fr)

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Publication number Priority date Publication date Assignee Title
WO2019232425A1 (fr) * 2018-06-01 2019-12-05 Washington University Suppression du syndrome de libération des cytokines lors d'une thérapie cellulaire par récepteur antigénique chimérique

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* Cited by examiner, † Cited by third party
Title
HUIHUI ZHANG: "IL-6/IFN-γ double knockdown CAR-T cells reduce the release of multiple cytokines from PBMCs in vitro", HUMAN VACCINES & IMMUNOTHERAPEUTICS, TAYLOR & FRANCIS, US, vol. 18, no. 1, 31 January 2022 (2022-01-31), US , pages 1 - 14, XP093165099, ISSN: 2164-5515, DOI: 10.1080/21645515.2021.2016005 *

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