Patent Application
20230355762
A Sequence Listing conforming to the rules of WIPO Standard ST.26 is hereby incorporated by reference. Said Sequence Listing has been filed as an electronic document via PatentCenter in ASCII format encoded as XML. The electronic document, created on Apr. 25, 2023, is entitled “0875200290_ST26.xml”, and is 349,973 bytes in size.
Human cancers are comprised of normal cells that have undergone a genetic or conversion to become abnormal cancer cells. In doing so, cancer cells begin to express proteins and other antigens that are distinct from those expressed by normal cells. These aberrant tumor antigens can be used by the body's innate immune system to specifically target and kill cancer cells. However, cancer cells employ various mechanisms to prevent immune cells from efficiently mounting an attack to effectively kill cancer cells and eradicate cancer. Nonetheless, immune responses do occur and it is possible to isolate and detect individual T cells, for example, that recognize antigens on the cancer cells and have the ability to kill such cancer cells. Accordingly, the antigens on the cancer cells can be detected and T cells can be engineered to recognize and kill cells that express such cancer cells. However, simply engineering an immune cell to detect a cancer antigen (e.g., by engineering the immune cell to express a NeoTCR that is specific to the cancer antigen) to elicit a cascade of events leading to the killing of the cancer antigen-expressing cell may not be sufficient for the treatment of cancers. In certain circumstances, in addition to the expression of the NeoTCR, it is also advantageous to knock in one or more additional genes into the immune cell. Furthermore, expression of NeoTCRs results in personalized therapies for each patient in need thereof. Specifically, each patient will have a different cancer phenotype and thus the NeoTCRs need to be identified in each patient for a cell therapy that is designed specifically for such patient. In order to do this, viral gene-editing methods are not practical or feasible. Instead, non-viral gene-editing methods are needed to efficiently and cost-effectively engineer immune cells for personalized therapies. Accordingly, there is a need to develop methods to express at least one NeoTCR and at least a Payload using non-viral methods.
The present disclosure provides cells comprising an exogenous TCR and at least one Payload.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an exogenous enhancer, an insulator, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an exogenous enhancer, a pause element, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an insulator, a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an insulator, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR, a first sequence encoding a Payload, and a second sequence encoding a Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR and the first sequence encoding a Payload are under control of an endogenous promoter and the second sequence encoding a Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell and is under control of an endogenous promoter.
In certain embodiments, the insulator is an HS4 insulator or an IS2 insulator. In certain embodiments, the insulator comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19. In certain embodiments, the insulator comprises the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19.
In certain embodiments, the WPRE comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments, the WPRE comprises the nucleotide sequence set forth in SEQ ID NO: 20.
In certain embodiments, the exogenous enhancer is a CMV enhancer, a TCRα enhancer, or a TCRβ enhancer. In certain embodiments, the exogenous enhancer is a TCRα enhancer. In certain embodiments, the TCRα enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the TCRα enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the exogenous enhancer is a CMV enhancer. In certain embodiments, the CMV enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO. 33. In certain embodiments, the CMV enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 33.
In certain embodiments, the exogenous promoter is a constitutive promoter. In certain embodiments, the constitutive promoter is an MDN promoter, an EF1α promoter, an ACTB promoter, a PGK promoter, or a U6 promoter. In certain embodiments, the constitutive promoter is an MDN promoter. In certain embodiments, the constitutive promoter is an EF1α promoter. In certain embodiments, the exogenous promoter is an inducible promoter. In certain embodiments, the inducible promoter is an AP1 promoter, an NFAT promoter, an NF-κB promoter, or an NR4A-responsive promoter.
In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence or a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR further comprises a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof. In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence, a TCRβ gene sequence, a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof.
In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, and a TCRα gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRα gene sequence, and a poly-adenylation sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRα gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRβ gene sequence, and a poly-adenylation sequence.
In certain embodiments, the at least one Payload is selected from the group consisting of a cytokine receptors trap, a ligand trap, an angiogenesis factor, an apoptotic factor, an inhibitory protein, an extracellular matrix modulator, a soluble TCR, a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, a protein that binds to receptors and sterically hinders receptor function, and an inhibitory RNA molecule.
In certain embodiments, the 3′ of the at least one Payload comprises a STOP codon. In certain embodiments, the 3′ of the at least one Payload comprises a sequence encoding a 2A peptide and a sequence encoding a protease cleavage peptide. In certain embodiments, the 3′ of the at least one Payload comprises a poly-adenylation sequence.
In certain embodiments, the at least one Payload is an inhibitory RNA molecule. In certain embodiments, the inhibitory RNA molecule is a shRNA, a miRNA, or a miRNA cluster. In certain embodiments, the inhibitory RNA molecule is a miRNA. In certain embodiments, the miRNA comprises a first flanking sequence and a second flanking sequence. In certain embodiments, the first flanking sequence and the second flanking sequence are derived from miR-155, miR-30, miR-17/92, miR-122, or miR-21. In certain embodiments, the inhibitory RNA molecule is flanked by a splice donor site or a splice acceptor site. In certain embodiments, the inhibitory RNA molecule is flanked by a splice donor site and a splice acceptor site.
In certain embodiments, the sequences encoding a P2A peptide are codon diverged. In certain embodiments, the sequences encoding a protease cleavage peptide are codon diverged. In certain embodiments, the sequences encoding a signal sequence are codon diverged.
In certain embodiments, the exogenous TCR recognizes a cancer neoantigen. In certain embodiments, the neoantigen is a private neoantigen. In certain embodiments, the sequence encoding an exogenous TCR is obtained from a subject.
In certain embodiments, the cell is a primary cell. In certain embodiments, the cell is a patient-derived cell. In certain embodiments, the cell is a lymphocyte. In certain embodiments, the cell is a T cell. In certain embodiments, the cell is a young T cell. In certain embodiments, the cell is CD45RA+, CD62L+, CD28+, CD95−, CCR7+, and CD27+. In certain embodiments, the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+. In certain embodiments, the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
In certain embodiments, the endogenous locus within the genome of the cell is a TCR locus. In certain embodiments, the TCR locus is a TRAC locus or a TRBC locus. In certain embodiments, the TCR locus is a TRAC locus and a TRBC locus. In certain embodiments, the endogenous promoter is a TRAC promoter. In certain embodiments, the endogenous promoter is a TRBC promoter.
In certain embodiments, the cell, the sequence encoding an exogenous TCR, and the sequence of the neoantigen are obtained from the same subject.
In certain embodiments, the present disclosure provides a polynucleotide comprising an exogenous enhancer, an insulator, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an exogenous enhancer, a pause element, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an insulator, a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an insulator, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, a first sequence encoding a Payload, and a second sequence encoding a Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the second sequence encoding a Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a sequence encoding a first homology arm, a second homology arm, an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus.
In certain embodiments, the insulator is an HS4 insulator or an IS2 insulator. In certain embodiments, the insulator comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19. In certain embodiments, the insulator comprises the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 18. In certain embodiments, the WPRE comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments, the WPRE comprises the nucleotide sequence set forth in SEQ ID NO: 20.
In certain embodiments, the exogenous enhancer is a CMV enhancer, a TCRα enhancer, or a TCRβ enhancer. In certain embodiments, the exogenous enhancer is a TCRα enhancer. In certain embodiments, the TCRα enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the TCRα enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the exogenous enhancer is a CMV enhancer. In certain embodiments, the CMV enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 33. In certain embodiments, the CMV enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 33.
In certain embodiments, the exogenous promoter is a constitutive promoter. In certain embodiments, the constitutive promoter is an MDN promoter, an EF1α promoter, an ACTB promoter, a PGK promoter, or a U6 promoter. In certain embodiments, the constitutive promoter is an MDN promoter. In certain embodiments, the constitutive promoter is an EF1α promoter. In certain embodiments, the exogenous promoter is an inducible promoter. In certain embodiments, the inducible promoter is an AP1 promoter, an NFAT promoter, an NF-κB promoter, or an NR4A-responsive promoter.
In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence or a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR further comprises a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof. In certain embodiments, the sequence encoding an exogenous TCR comprises a TCRα gene sequence, a TCRβ gene sequence, a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof.
In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, and a TCRα gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRα gene sequence, and a poly-adenylation sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRα gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRβ gene sequence, and a poly-adenylation sequence. In certain embodiments, the at least one Payload is selected from the group consisting of a cytokine receptors trap, a ligand trap, an angiogenesis factor, an apoptotic factor, an inhibitory protein, an extracellular matrix modulator, a soluble TCR, a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, a protein that binds to receptors and sterically hinders receptor function, and an inhibitory RNA molecule.
In certain embodiments, the 3′ of the at least one Payload comprises a STOP codon. In certain embodiments, the 3′ of the at least one Payload comprises a sequence encoding a 2A peptide and a sequence encoding a protease cleavage peptide. In certain embodiments, the 3′ of the at least one Payload comprises a poly-adenylation sequence.
In certain embodiments, the at least one Payload is an inhibitory RNA molecule. In certain embodiments, the inhibitory RNA molecule is a shRNA, a miRNA, or a miRNA cluster. In certain embodiments, the inhibitory RNA molecule is a miRNA. In certain embodiments, the miRNA comprises a first flanking sequence and a second flanking sequence. In certain embodiments, the first flanking sequence and the second flanking sequence are derived from miR-155, miR-30, miR-17/92, miR-122, or miR-21. In certain embodiments, the inhibitory RNA molecule is flanked by a splice donor site or a splice acceptor site. In certain embodiments, the inhibitory RNA molecule is flanked by a splice donor site and a splice acceptor site.
In certain embodiments, the sequences encoding a P2A peptide are codon diverged. In certain embodiments, the sequences encoding a protease cleavage peptide are codon diverged. In certain embodiments, the sequences encoding a signal sequence are codon diverged. In certain embodiments, the exogenous TCR recognizes a cancer neoantigen. In certain embodiments, the neoantigen is a private neoantigen. In certain embodiments, the sequence encoding an exogenous TCR is obtained from a single subject.
In certain embodiments, the polynucleotide is a circular polynucleotide. In certain embodiments, the circular polynucleotide is a plasmid or a nanoplasmid. In certain embodiments, the polynucleotide is a linear polynucleotide.
In certain embodiments, the present disclosure further provides a vector comprising any one of the polynucleotide disclosed herein. In certain embodiments, the vector is a non-viral vector. In certain embodiments, the present disclosure provides a cell comprising any one of the polynucleotides or vectors disclosed herein.
In certain embodiments, the present disclosure provides a method of modifying a cell. In certain embodiments, the method comprises introducing into the cell any one of the polynucleotides or vectors disclosed herein. In certain embodiments, the method further comprises recombining the polynucleotide or vector into an endogenous locus of the cell.
In certain embodiments, the introducing occurs via electroporation. In certain embodiments, the recombining comprises cleavage of the endogenous locus by a nuclease. In certain embodiments, the recombining further comprises recombination of the polynucleotide into the endogenous locus by homology-directed repair.
In certain embodiments, the nuclease is a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) family nuclease, or a functional fragment thereof. In certain embodiments, the nuclease further comprises a gRNA.
In certain embodiments, the method further comprises culturing the cell in the presence of at least one cytokine. In certain embodiments, the at least one cytokine comprises IL2, IL7, IL15, or a combination thereof. In certain embodiments, the at least one cytokine comprises IL7 and IL15.
In certain embodiments, the cell is a primary cell. In certain embodiments, the cell is a patient-derived cell. In certain embodiments, the cell is a lymphocyte. In certain embodiments, the cell is a T cell. In certain embodiments, the cell is a young T cell. In certain embodiments, the cell is CD45RA+, CD62L+, CD28+, CD95−, CCR7+, and CD27+. In certain embodiments, the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+. In certain embodiments, the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
In certain embodiments, the present disclosure also provides a cell modified by any one of the methods disclosed herein.
In certain embodiments, the present disclosure provides a composition comprising an effective amount of the any one of the cells disclosed herein. In certain embodiments, the composition is a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient. In certain embodiments, the composition is administered to a patient in need thereof for the treatment of cancer.
In certain embodiments, the composition comprises a cryopreservation agent. In certain embodiments, the composition comprises serum albumin. In certain embodiments, the composition comprises Plasma-Lyte A, HSA, and CryoStor CS10.
In certain embodiments, the present disclosure provides methods of treating cancer in a subject in need thereof. In certain embodiments, the method comprises administering a therapeutically effective amount of any one of the cells disclosed herein. In certain embodiments, the method comprises administering a therapeutically effective amount of any one of the compositions disclosed herein. In certain embodiments, prior to administering, a non-myeloablative lymphodepletion regimen is administered to the subject.
In certain embodiments, the cancer is a solid tumor or a liquid tumor. In certain embodiments, the solid tumor is selected from the group consisting of melanoma, thoracic cancer, lung cancer, ovarian cancer, breast cancer, pancreatic cancer, head and neck cancer, prostate cancer, gynecological cancer, central nervous system cancer, cutaneous cancer, HPV+ cancer, esophageal cancer, thyroid cancer, gastric cancer, hepatocellular cancer, cholangiocarcinomas, renal cell cancers, testicular cancer, sarcomas, and colorectal cancer. In certain embodiments, the liquid tumor is selected from the group consisting of follicular lymphoma, leukemia, and multiple myeloma.
In certain embodiments, the present disclosure provides a kit comprising any one of the cells, the polynucleotides, the vectors, or the compositions disclosed herein. In certain embodiments, the kit further comprises written instructions for treating cancer.
The present disclosure provides adoptive cell therapies comprising a first and a second exogenous gene and having enhanced activity and efficacy against tumor cells. The present disclosure is based, in part, on the ability of the inventors to decouple the gene expression of the first and second exogenous genes resulting in elevated and maintained expression levels of a sequence encoding an exogenous TCR (e.g., a NeoTCR) and a Payload that potentiates and improves the activity of the cells (e.g., cytotoxicity, cell proliferation, and/or cell persistence). The present disclosure also provides methods for producing the cells, and compositions disclosed herein. Finally, the present disclosure provides methods of using such cells and composition for treating and/or preventing cancer.
Non-limiting embodiments of the present disclosure are described by the present description and examples. For purposes of clarity of disclosure and not by way of limitation, the detailed description is divided into the following subsections:
Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art. The following references provide one of skill with a general definition of many of the terms used in the presently disclosed subject matter: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.
It is understood that aspects and embodiments of the invention described herein include “comprising,” “consisting,” and “consisting essentially of” aspects and embodiments. The terms “comprises” and “comprising” are intended to have the broad meaning ascribed to them in U.S. Patent Law and can mean “includes”, “including” and the like.
As used herein, the term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 3 or more than 3 standard deviations, per the practice in the art. Alternatively, “about” can mean a range of up to 20%, e.g., up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, e.g., within 5-fold or within 2-fold, of a value.
The term “antibody” as used herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific and tri-specific antibodies), and antibody fragments (e.g., bis-Fabs) so long as they exhibit the desired antigen-binding activity. “Antibody Fragment” as used herein refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds. Examples of antibody fragments include but are not limited to bis-Fabs; Fv; Fab; Fab, Fab′-SH; F(ab′)2; diabodies; linear antibodies; single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments.
The terms “Cancer” and “Tumor” are used interchangeably herein. As used herein, the terms “Cancer” or “Tumor” refer to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms are further used to refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth/proliferation. Cancer can affect a variety of cell types, tissues, or organs, including but not limited to an organ selected from the group consisting of bladder, bone, brain, breast, cartilage, glia, esophagus, fallopian tube, gallbladder, heart, intestines, kidney, liver, lung, lymph node, nervous tissue, ovaries, pancreas, prostate, skeletal muscle, skin, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea, urogenital tract, ureter, urethra, uterus, and vagina, or a tissue or cell type thereof. Cancer includes cancers, such as sarcomas, carcinomas, or plasmacytomas (a malignant tumor of the plasma cells). Examples of cancer include, but are not limited to, those described herein. The terms “Cancer” or “Tumor” and “Proliferative Disorder” are not mutually exclusive as used herein.
As used herein, “sequence identity” or “identity” (in the context of two nucleic acid or polypeptide sequences) refers to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When the percentage of sequence identity is used about proteins it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity.” Means for making this adjustment are well known to those of skill in the art.
As used herein, “percentage of sequence identity” refers to the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window can comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for the optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity. Methods of alignment of sequences for comparison include, without any limitation, the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local homology algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-similarity-method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Computer implementations of these mathematical algorithms include, without any limitation, CLUSTAL, CLUSTALW, CLUSTALOMEGA, ALIGN, ALIGN PLUS, GAP, BESTFIT, BLAST, FASTA, TFASTA, BLASTN, BLASTX, BLASTP, TBLASTN, and TBLASTX.
A “conservative substitution” or a “conservative amino acid,” refers to the substitution of amino acid with a chemically or functionally similar amino acid. Conservative substitution tables providing similar amino acids are well known in the art. In certain embodiments, acidic amino acids D and E are conservative substitutions for one another; basic amino acids K, R, and H are conservative substitutions for one another; hydrophilic uncharged amino acids S, T, N. and Q are conservative substitutions for one another; aliphatic uncharged amino acids G, A, V, L, and I are conservative substitutions for one another; non-polar uncharged amino acids C, M, and P are conservative substitutions for one another; aromatic amino acids F, Y, and W are conservative substitutions for one another; A, S, and T are conservative substitutions for one another; D and E are conservative substitutions for one another; N and Q are conservative substitutions for one another; R and K are conservative substitutions for one another; I, L, and M are conservative substitutions for one another; F, Y, and W are conservative substitutions for one another; A and G are conservative substitutions for one another; D and E are conservative substitutions for one another; N and Q are conservative substitutions for one another; R, K and H are conservative substitutions for one another; I, L, M, and V are conservative substitutions for one another; F, Y and W are conservative substitutions for one another; S and T are conservative substitutions for one another; and C and M are conservative substitutions for one another. Additional conservative substitutions may be found, for example, in Creighton, Proteins: Structures and Molecular Properties 2nd ed. (1993) W. H. Freeman & Co., New York, NY.
“Treat,” “Treatment,” and “treating” are used interchangeably and as used herein mean obtaining beneficial or desired results including clinical results. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In certain embodiments, the NeoTCR Product of the invention is used to delay the development of a proliferative disorder (e.g., cancer) or to slow the progression of such disease.
“Dextramer” as used herein means a multimerized neoepitope-HLA complex that specifically binds to its cognate NeoTCR.
The term “tumor antigen” as used herein refers to an antigen (e.g., a polypeptide) that is uniquely or differentially expressed on a tumor cell compared to a normal or non-neoplastic cell. In certain embodiments, a tumor antigen includes any polypeptide expressed by a tumor that is capable of activating or inducing an immune response via an antigen-recognizing receptor or capable of suppressing an immune response via receptor-ligand binding.
As used herein, the terms “neoantigen”, “neoepitope” or “neoE” refer to a newly formed antigenic determinant that arises, e.g., from a somatic mutation(s) and is recognized as “non-self” A mutation giving rise to a “neoantigen”, “neoepitope” or “neoE” can include a frameshift or non-frameshift indel, missense or nonsense substitution, splice site alteration (e.g., alternatively spliced transcripts), genomic rearrangement or gene fusion, any genomic or expression alterations, or any post-translational modifications. In certain embodiments, the neoantigen can be a private neoantigen. As used herein, the term “private neoantigen” refers to neoantigens that are exclusively expressed and present in a subject having certain cancer. For clarity, a private neoantigen is a neoantigen that cannot be used for another patient. In certain embodiments, the neoantigen can be a “public neoantigen”. The term “public neoantigen,” as used herein, refers to neoantigens that are shared by more than one subject.
“NeoTCR” and “NeoE TCR,” as used herein, mean a neoepitope-specific T cell receptor that is introduced into a T cell, e.g., by gene-editing methods. As used herein, the term “exogenous TCR” may be used in place of “NeoTCR”.
“NeoTCR Cells” as used herein means one or more cells precision-engineered to express one or more NeoTCRs. In certain embodiments, the cells are T cells. In certain embodiments, the T cells are CD8+ and/or CD4+ T cells. In certain embodiments, the CD8+ and/or CD4+ T cells are autologous cells from the patient for whom a NeoTCR Product will be administered. The terms “NeoTCR Cells” and “NeoTCR-P1 T cells” and “NeoTCR-P1 cells” are used interchangeably herein.
“NeoTCR Product” as used herein means a pharmaceutical formulation comprising one or more NeoTCR Cells. NeoTCR Product consists of autologous precision genome-engineered CD8+ and CD4+ T cells. Using a targeted DNA-mediated non-viral precision genome engineering approach, expression of the endogenous TCR is eliminated and replaced by a patient-specific NeoTCR isolated from peripheral CD8+ T cells targeting the tumor-exclusive neoepitope. In certain embodiments, the resulting engineered CD8+ or CD4+ T cells express NeoTCRs on their surface of native sequence, native expression levels, and native TCR function. The sequences of the NeoTCR external binding domain and cytoplasmic signaling domains are unmodified from the TCR isolated from native CD8+ T cells. Regulation of the NeoTCR gene expression is driven by the native endogenous TCR promoter positioned upstream of where the NeoTCR gene cassette is integrated into the genome. Through this approach, native levels of NeoTCR expression are observed in unstimulated and antigen-activated T cell states. The NeoTCR Product manufactured for each patient represents a defined dose of autologous CD8+ and/or CD4+ T cells that are precision genome engineered to express a single neoE-specific TCR cloned from neoE-specific CD8+ T cells individually isolated from the peripheral blood of that same patient.
“NeoTCR Viral Product” as used herein has the same definition of NeoTCR Product except that the genome engineering is performed using viral-mediated methods.
“Secondary Promoter Construct” as used herein refers to a construct comprising elements to express a NeoTCR and elements to express a Payload. Formats 1-4, along with the variations thereof described herein, are representative examples of Secondary Promoter Constructs. Additional information can be found in Section 3 below.
“Secondary Promoter Cell” as used herein refers to a NeoTCR Cell that is engineered to express a Payload under the control of a different promoter than the promoter used to express the NeoTCR.
“Secondary Promoter Product” as used herein refers to a NeoTCR Product that is engineered to express a Payload under the control of a different promoter than the promoter used to express the NeoTCR.
“Payload” as used herein refers to a second or more gene, in addition to the NeoTCR, to be knocked into an immune cell using gene editing methods described herein. Examples of Payloads include but are not limited to the one disclosed in Section 3.1.1. below.
“Pharmaceutical Formulation” refers to a preparation that is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered. For clarity, DMSO at quantities used in a NeoTCR Product is not considered unacceptably toxic.
“Promoter region” or “promoter” as used herein means the region of the construct that encodes a promoter that controls the expression of the Payload in the Secondary Promoter Constructs.
As used herein, the term “enhancer” refers to a DNA control element that enhances the levels of expression of the gene when a specific transcription factor is bound. Unlike a promoter, an enhancer does not stimulate the expression of the gene on its own. Enhancers are frequently found in the upstream (5′) region of the gene.
A “subject,” “patient,” or an “individual” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. Preferably, the mammal is human.
“TCR” as used herein means T cell receptor.
“2A” and “2A peptide” are used interchangeably herein and mean a class of 18-22 amino acid long, viral, self-cleaving peptides that are able to mediate cleavage of peptides during translation in eukaryotic cells. Four well-known members of the 2A peptide class are T2A, P2A, E2A, and F2A.
The T2A peptide was first identified in the Thosea asigna virus 2A. The P2A peptide was first identified in the porcine teschovirus-1 2A. The E2A peptide was first identified in the equine rhinitis A virus. The F2A peptide was first identified in the foot-and-mouth disease virus. The self-cleaving mechanism of the 2A peptides is a result of ribosome skipping the formation of a glycyl-prolyl peptide bond at the C-terminus of the 2A. Specifically, the 2A peptides have a C-terminal conserved sequence that is necessary for the creation of steric hindrance and ribosome skipping. The ribosome skipping can result in one of three options: 1) successful skipping and recommencement of translation resulting in two cleaved proteins (the upstream of the 2A protein which is attached to the complete 2A peptide except for the C-terminal proline and the downstream of the 2A protein which is attached to one proline at the N-terminal; 2) successful skipping but ribosome fall-off that results in discontinued translation and only the protein upstream of the 2A; or 3) unsuccessful skipping and continued translation (i.e., a fusion protein).
The term “endogenous” as used herein refers to a nucleic acid molecule or polypeptide that is normally expressed in a cell or tissue.
The term “exogenous” as used herein refers to a nucleic acid molecule or polypeptide that is not endogenously present in a cell. The term “exogenous” would therefore encompass any recombinant nucleic acid molecule or polypeptide expressed in a cell, such as foreign, heterologous, and over-expressed nucleic acid molecules and polypeptides. By “exogenous” nucleic acid is meant a nucleic acid not present in a native wild-type cell; for example, an exogenous nucleic acid may vary from an endogenous counterpart by sequence, by position/location, or both. For clarity, an exogenous nucleic acid may have the same or different sequence relative to its native endogenous counterpart; it may be introduced by genetic engineering into the cell itself or a progenitor thereof, and may optionally be linked to alternative control sequences, such as a non-native promoter or secretory sequence.
“Young” or “Younger” or “Young T cell” as it relates to T cells means memory stem cells (TMSC) and central memory cells (TCM). These cells have T cell proliferation upon specific activation and are competent for multiple cell divisions. They also have the ability to engraft after re-infusion, to rapidly differentiate into effector T cells upon exposure to their cognate antigen and target and kill tumor cells, as well as to persist for ongoing cancer surveillance and control.
“WPRE,” as used herein, refers to a woodchuck hepatitis virus post-transcriptional regulatory element that increases transgene expression.
As used herein, a “STOP codon” or “termination codon” is a nucleotide triplet within a messenger RNA that signals the termination of the translation process of a protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which can ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.
“Kozak” or “Kozak sequence,” as used herein, refers to a nucleic acid motif that functions as the protein translation initiation site in certain eukaryotic mRNA transcripts.
“Insulator” or “transcriptional insulator,” as used herein, refer to a class of DNA sequence elements that possess a common ability to protect genes from inappropriate signals emanating from their surrounding environment. Insulators can be used to restrict the interaction of enhancers or silencers on promoters in a gene expression system. Insulators can set boundaries on the actions of enhancer and silencer elements and so partition the eukaryotic genome into regulatory domains. Physiologically, the transcriptional repressor CTCF (CCCTC-binding factor) binds through multiple zinc fingers (of which it has eleven) to a range of unrelated DNA sequences and functions as a transcriptional insulator, repressor, or activator, depending on the context of the binding site.
“Signal sequence” as used herein is a peptide that can be included at the N-terminus of a newly synthesized protein for the purpose of trafficking the newly synthesized protein to its intended and/or engineered location inside or outside of the cell.
In certain embodiments, using the gene-editing technology and NeoTCR isolation technology described in PCT/US2020/17887 and PCT/US2019/025415, which are incorporated herein in their entireties, NeoTCRs are cloned in autologous CD8+ and CD4+ T cells from the same patient with cancer by precision genome engineered (using a DNA-mediated (non-viral) method as described in
Ex vivo mechanism-of-action studies were also performed with NeoTCR Products manufactured with T cells from patients with cancer. Comparable gene editing efficiencies and functional activities, as measured by antigen-specificity of T cell killing activity, proliferation, and cytokine production, were observed demonstrating that the manufacturing process described herein is successful in generating products with T cells from patients with cancer as starting material.
In certain embodiments, the NeoTCR Product manufacturing process involves electroporation of dual ribonucleoprotein species of CRISPR-Cas9 nucleases bound to guide RNA sequences, with each species targeting the genomic TCRα and the genomic TCRβ loci. The specificity of targeting Cas9 nucleases to each genomic locus has been previously described in the literature as being highly specific. Comprehensive testing of the NeoTCR Product was performed in vitro and in silico analyses to survey possible off-target genomic cleavage sites, using COSMID and GUIDE-seq, respectively. Multiple NeoTCR Products or comparable cell products from healthy donors were assessed for cleavage of the candidate off-target sites by deep sequencing, supporting the published evidence that the selected nucleases are highly specific. Further aspects of the precision genome engineering process have been assessed for safety. No evidence of genomic instability following precision genome engineering was found in assessing multiple NeoTCR Products by targeted locus amplification (TLA) or standard FISH cytogenetics. No off-target integration anywhere into the genome of the NeoTCR sequence was detected. No evidence of residual Cas9 was found in the cell product.
The comprehensive assessment of the NeoTCR Product and precision genome engineering process indicates that the NeoTCR Product will be well tolerated following infusion back to the patient.
The genome engineering approach described herein enables the highly efficient generation of bespoke NeoTCR Cells (i.e., NeoTCR Products) for personalized adoptive cell therapy for patients with solid and liquid tumors. Furthermore, the engineering method is not restricted to the use in T cells and has also been applied successfully to other primary cell types, including natural killer and hematopoietic stem cells.
In certain embodiments, the present disclosure provides Secondary Promoter Products. In certain embodiments, the NeoTCR Cells described can express a Payload under the control of a different promoter than the promoter used to express the NeoTCR to produce a Secondary Promoter Cell. In certain embodiments, the NeoTCR Cells described herein are further engineered to express a Payload under the control of a different promoter than the promoter used to express the NeoTCR to produce a Secondary Promoter Cell. Such Secondary Promoter Cells can be formulated into Secondary Promoter Products for the treatment of an immune disease or disorder.
In certain embodiments, the immune disease or disorder is a primary immune disease or disorder (i.e., a disease or disorder that a subject is born with). In certain embodiments, the immune disease or disorder is a secondary disorder (i.e., acquired disease or disorder). In certain embodiments, the immune disease selected from the group comprising cancers, autoimmune diseases and disorders, viral infections, bacterial infections, retroviral infections, and neurological diseases and disorders. In certain embodiments, the immune disease is cancer. In certain embodiments, the immune disease is an autoimmune disease.
In certain embodiments, a single-step precision genome engineering method is performed in order for the NeoTCR insertion and the Payload insertion into a primary cell to occur in the same reaction. In certain embodiments, the NeoTCR and the Payload are encoded by the same polynucleotide. In certain embodiments, the primary cell is a T cell. In certain embodiments, the primary cell is an NK cell. In certain embodiments, this single-step process reduces potential T cell heterogeneity that would otherwise be present if multiple reactions and multiple polynucleotides (e.g., DNA templates) were used. In certain embodiments, this single-step process reduces potential NK cell heterogeneity that would otherwise be present if multiple reactions and multiple polynucleotides (e.g., DNA templates) were used.
In certain embodiments, the single-step precision genome engineering method described herein allows for one or more Payloads to be engineered in and/or one or more removal (i.e., silencing) of one or more genes endogenous to the primary cell.
In certain embodiments, the Secondary Promoter Cells of the Secondary Promoter Products are designed to target molecules on the tumor. Non-limiting examples of molecules expressed on tumors that the Secondary Promoter Cells and Secondary Promoter Products can target include but are not limited to antigens, neoantigens, private neoantigens, public neoantigens, receptors, cell surface molecules, cytokine receptors, and oncogenic pathway inhibitors or enhancers.
In certain embodiments, the Secondary Promoter Cells of the Secondary Promoter Products are designed to express a protein made by the Payload only upon activation of the Secondary Promoter Cells. In certain embodiments, the activated Secondary Promoter Cells are activated T cells.
In certain embodiments, the Secondary Promoter Cells of the Secondary Promoter Products are designed to secrete a protein made by the Payload only upon activation of the Secondary Promoter Cells. In certain embodiments, the activated Secondary Promoter Cells are activated T cells.
In certain embodiments, the Secondary Promoter Cells of the Secondary Promoter Products are designed to constitutively express a protein made by the Payload.
In certain embodiments, the Secondary Promoter Cells of the Secondary Promoter Products are designed to constitutively secrete a protein made by the Payload.
Secondary Promoter Constructs disclosed herein (including but not limited to Formats 1-4 described herein and diagramed in the figures) are designed to allow for the dual expression of an exogenous TCR (e.g., a NeoTCR) and a Payload when transfected or transduced into a cell. In certain embodiments, the method of gene insertion is non-viral transfection. In certain embodiments, the non-viral transfection methods used are those described herein. In certain embodiments, the cell is a primary human cell. In certain embodiments, the primary human cell is a T cell.
In certain embodiments, one or more of the following key elements are included in the Secondary Promoter Constructs: an element to promote translation of transcripts (e.g., enhancer), a poly-adenylation (poly-A) sequence, a promoter, a pause element, a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), a scaffold/matrix attachment region, and an insulator.
In certain embodiments, the Secondary Promoter Constructs are modular, as each element should be thought of as a broad and general category. For instance, any poly-A signal sequence known to one of skill in the art could be used in the modular construct. For instance, any element to promote translation of transcripts applicable to the intended cell and Payload known to one of skill in the art could be used in the modular construct. For instance, any applicable promoter for the intended cell and Payload known to one of skill in the art could be used in the modular construct. For instance, any applicable insulator for the intended cell and Payload known to one of skill in the art could be used in the modular construct.
In certain embodiments, the Secondary Promoter Construct designs comprise a Payload, a regulatory element to increase the translation of the Payload transcript, a transcription stop signal, a promoter, and optionally one or more insulators. In certain embodiments, the Secondary Promoter Construct design is described in
3.1.1. Payloads
In certain embodiments, the Secondary Promoter Constructs disclosed herein include a Payload. In certain embodiments, the Payload of the Secondary Promoter Constructs is selected from the group comprising a cytokine receptors trap or ligand trap, an angiogenesis factors, an apoptotic factor, an inhibitory protein for various cell processes (e.g., inhibition of macrophage activation), an extracellular matrix modulator, a soluble TCRs, a soluble chimeric antigen receptor (CAR), a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, and a protein that binds to receptors and sterically hinders receptor function.
In certain embodiments, the Payload is a cytokine receptor trap or a ligand trap. In certain embodiments, the cytokine receptor trap or ligand trap selected as a Payload acts as a cytokine sink. Cytokine receptor traps recognize certain inflammatory cytokines with high affinity and specificity but are structurally incapable of signaling or presenting the agonist to signaling receptor complexes. They act as a molecular trap for the agonist and signaling receptor components. Non-limiting examples of cytokine receptor trap include TNFR1, TNFR2, TGFBR1, TGFBR2, TGFBR3, IL4, CSF1R, CXCR1, CXCR2, CCR2, and CCR5. In certain embodiments, the cytokine receptor trap is a TGFBR2. In certain embodiments, the TGFBR2 comprises an amino acid sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the amino sequence set forth in SEQ ID NO: 1. In certain embodiments, the TGFBR2 comprises the amino sequence set forth in SEQ ID NO: 1. In certain embodiments, the TGFBR2 consists of the amino sequence set forth in SEQ ID NO: 1. SEQ ID NO: 1 is provided below.
In certain embodiments, the TGFBR2 is encoded by the nucleotide sequence set forth in SEQ ID NO: 2 provided below.
Additional information and examples of cytokine traps can be found in Economides et al., Nature medicine 9.1 (2003): 47-52.
In certain embodiments, the Payload is an angiogenesis factor. In certain embodiments, the angiogenesis factor selected as a Payload reshapes tumor vasculature. Non-limiting examples of angiogenesis factors include FGF1, FGF2, VEGF, PDGF, ANGPT1, ANGPT2, DLL4, MMP1, MMP2, MMP3, MMP47, MMP8, MMP9, MMP10, MMP11, MMP12, MMP13, MMP14, MMP15, MMP16, MMP17, MMP24, MMP25, MMP28, SEMA3A, SEMA3B, SEMA3C, SEMA3D, SEMA3E, SEMA3F, SEMA3G, urokinase, and tissue plasminogen activator.
In certain embodiments, the Payload is an apoptotic factor. In certain embodiments, the apoptotic factor selected as a Payload protects a Secondary Promoter Cell from apoptosis. In certain embodiments, the apoptotic factor selected as a Payload induces apoptosis in a target cell (e.g., a tumor cell). Non-limiting examples of apoptotic factors include FAS, FASL, TNFα, XIAP, cIAPI, c-IAP2, NAIP, API4, Bcl-2, cFLIP, BNIP3, FADD, AKT, and NK-κB.
In certain embodiments, the Payload is an inhibitory protein. In certain embodiments, the inhibitory protein selected as a Payload inhibits macrophage activity. Non-limiting examples of inhibitory proteins include anti-TIM3 antibodies, anti-PD1 antibodies, anti-CD32b antibodies, and anti-CD200R antibodies.
In certain embodiments, the Payload is an anti-PD1 antibody. In certain embodiment, the Payload is an anti-PD1 svFv. In certain embodiments, the anti-PD1 svFv comprises an amino acid sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the amino sequence set forth in SEQ ID NO: 3. In certain embodiments, the anti-PD1 svFv comprises the amino sequence set forth in SEQ ID NO: 3. In certain embodiments, the anti-PD1 svFv consists of the amino sequence set forth in SEQ ID NO: 3. SEQ ID NO: 3 is provided below.
In certain embodiments, the anti-PD1 svFv is encoded by the nucleotide sequence set forth in SEQ ID NO: 4 provided below.
In certain embodiments, the Payload is an extracellular matrix modulator. In certain embodiments, the extracellular matrix modulator selected as a Payload makes the tumor more physically accessible to immune cells. Non-limiting examples of extracellular matrix modulator include MATN1, MATN2, MATN3, MATN4, CTSB, CTSG, CEMIP, HPSE, HYAL1, HYAL2, HYAL3, HYAL4, HYAL5, PLOD1, PLOD2, PLOD3, ELANE, PLG, SULF1, SULF2, and TMPRSS6.
In certain embodiments, the Payload is a homing signal. This homing signal can guide the Secondary Construct Cell towards the tumor core through chemotaxis mechanisms. In certain embodiments, the homing signal is a cytokine or a chemokine. In certain embodiments, the homing signal is a cytokine receptor or a chemokine receptor. Non-limiting examples of homing signal include IFNGR2, IL6R+IL6ST, IL12RB1, IL12RB2, CXCR3, CXCR6, CCR2, CCR5, CCR7, CCR1, CCR3, CCR4, CCR6, CCR8, CX3CR1, CXCR1, CXCR2, CXCR4, CXCR6, XCR1, and CCR10.
In certain embodiments, the Payload is a modulator of reactive oxygen species (ROS). In certain embodiments, the modulators of reactive oxygen species are selected as a Payload because cancer cells typically have elevated ROS burden and neutrophils do create oxidative bursts as a way of destroying cancer cells. Non-limiting examples of modulators of ROS include nicotinamide adenine dinucleotide phosphate oxidase, nitric oxide synthase, and xanthine oxidase.
In certain embodiments, the competitive ligand inhibitor selected as a Payload binds to receptors on tumor cells and prevents activation.
In certain embodiments, the Payload of the Secondary Promoter Constructs is a transcription factor, florescent proteins, cytokine/chemokine and their receptor, cytokine fusion, cytokine receptor fusion, switch receptor (an extracellular domain which binds an inhibitory signal and an intracellular stimulatory domain), costimulatory receptor and their ligand, dominant-negative and null mutant immune checkpoint receptor, immune checkpoint antagonist, antigen-binding receptor or fragment and their coreceptor, coreceptor fusion, metabolic regulator, antibody, transpeptidase, protease, sheddase, growth factor and growth regulator, scaffold protein, adaptor protein, kinase, phosphatase, ITAM containing receptor, methyltransferase loss of function or null mutant, methylcytosine loss of function or null mutant, toll-like receptor, glycosylase, glycosidase, glycosyltransferase, DNA repair protein, inducible caspase, Truncated LNGFR or EGFR, cytosolic DNA sensor, GPCR and their ligand, leucine zipper fusion, Cas protein, guide RNA, short hairpin RNA, innate immune agonist, or drug resistance marker.
3.1.2. Inhibitory RNA Molecules
In certain embodiments, the Secondary Promoter Constructs disclosed herein include an inhibitory RNA molecule. In certain embodiments, the Payload is an inhibitory RNA molecule. As used here, the terms “inhibitory RNA” or “inhibitory RNA molecule” refer to an RNA molecule capable of interfering with, or suppressing, the expression of a gene (e.g., RNA interference or RNAi). In certain embodiments, the inhibitory RNA molecule is capable of interfering with, or suppressing, the expression of a single gene. In certain embodiments, the inhibitory RNA molecules are capable of interfering with, or suppressing, the expression of at least two or more, at least three or more, at least four or more, or at least five or more genes. In certain embodiments, the inhibitory RNA molecule comprises a small interference RNA (siRNA), a small hairpin RNA (shRNA), a microRNA (miRNA), or a combination thereof.
In certain embodiments, the inhibitory RNA molecules are positioned in the Secondary Promoter Construct in a series or multiplex arrangement such that multiple inhibitory RNA molecules are simultaneously expressed from a single polycistronic transcript. In certain embodiments, the inhibitory RNA molecules are positioned in the Payload in a series or multiplex arrangement such that multiple inhibitory RNA molecules are simultaneously expressed from a single polycistronic transcript. In certain embodiments, the inhibitory RNA molecules can be linked to each other by non-functional linker sequence(s).
In certain embodiments, the inhibitory RNA molecule comprises a small hairpin RNA (shRNA). In certain embodiments, the inhibitory RNA molecule comprises a microRNA (miRNA). A miRNA is an RNA molecule (artificial or naturally occurring) of about 22 nucleotides in length that can be used to silence target gene expression via RNA interference (RNAi).
In certain embodiments, the inhibitory RNA molecule is a naturally occurring miRNA. In certain embodiments, the inhibitory RNA molecule is an artificial miRNA. Artificial miRNAs can be produced by placing an RNA sequence directed against a target gene in a miRNA framework (e.g., microRNA sequences for processing and loop). In certain embodiments, the inhibitory RNA molecule comprises, from 5′ to 3′, a first miRNA flanking sequence, a first stem, a loop, a second stem that is partially or fully complementary to the first stem, and a second miRNA flanking sequence. In certain embodiments, the first and second miRNA flanking sequences are derived from a naturally occurring miRNA. For example, without any limitation, the first and second miRNA flanking sequences are derived from miR-155, miR-30, miR-17/92, miR-122, and miR-21. In certain embodiments, the first and second miRNA flanking sequences are derived from a miR-155. In certain embodiments, the first and second miRNA flanking sequences are derived from a miR-30. In certain embodiments, the first and second miRNA flanking sequences are derived from a miR-30a.
In certain embodiments, the inhibitory RNA molecule comprises a SIBR scaffold. In certain embodiments, the inhibitory RNA molecules comprise an eSIBR scaffold. Additional details on the eSIBR scaffold can be found in Fowler et al., Nucleic acids research 44.5 (2016): e48-e48, the content of which is incorporated by reference in its entirety.
In certain embodiments, the inhibitory RNA molecule comprises a miR-E scaffold. Additional details on the miR-E scaffold can be found in Fellmann et al., Cell reports 5.6 (2013): 1704-1713, the content of which is incorporated by reference in its entirety.
In certain embodiments, the inhibitory RNA molecules comprise a microRNA cluster. A miRNA cluster is a set of two or more miRNAs, which are transcribed from physically adjacent miRNA genes. miRNA genes can be found either in protein-coding or non-coding regions of transcription units (TUs). Typically, miRNAs in a cluster are transcribed in the same orientation and are not separated by a transcription unit or a miRNA in the opposite orientation. In certain embodiments, the miRNA cluster includes two miRNAs. In certain embodiments, the miRNA cluster includes three miRNAs. In certain embodiments, the miRNA cluster includes four miRNAs. In certain embodiments, the miRNA cluster includes five miRNAs. In certain embodiments, the miRNA cluster includes six miRNAs. In certain embodiments, the miRNA cluster derives from naturally occurring miRNA clusters. Non-limiting examples of naturally occurring miRNA clusters include miR-17/92, miR-23b/27b/24, and miR-106.
In certain embodiments, the inhibitory RNA molecules target a gene selected from the group consisting of A2AR, CBLB, TGFBR2, or a combination thereof.
In certain embodiments, the inhibitory RNA molecule targets a CBLB transcript. In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 5. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 5. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 5.
In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 6. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 6. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 6.
In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 7. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 7. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 7. SEQ ID NOs: 5-7 are provided below.
In certain embodiments, the inhibitory RNA molecule targets a CBLB transcript and an A2AR transcript. In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 8. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 8. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 8.
In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 9. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 9. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 9. SEQ ID NO: 8 and SEQ ID NO: 9 are provided below.
In certain embodiments, the inhibitory RNA molecule targets a CBLB transcript, an A2AR transcript, and a TGFBR2. In certain embodiments, the inhibitory RNA molecule comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 10. In certain embodiments, the inhibitory RNA molecule comprises the nucleotide sequence set forth in SEQ ID NO: 10. In certain embodiments, the inhibitory RNA molecule consists of the nucleotide sequence set forth in SEQ ID NO: 10. SEQ ID NO: 10 is provided below.
In certain embodiments, the inhibitory RNA molecule is flanked by a splice acceptor site. A “splice acceptor site” is a polynucleotide site at the 3′ of an intron and regulates the splicing of RNA. In certain embodiments, the inhibitory RNA molecule is flanked by a splice donor site. A “splice donor site” is a polynucleotide site at the 5′ of an intron and regulates the splicing of RNA. In certain embodiments, the inhibitory RNA molecule is flanked by a splice acceptor site and a splice donor site. In certain embodiments, the inhibitory RNA molecule is flanked at its 5′ by a splice acceptor site. In certain embodiments, the inhibitory RNA molecule is flanked at its 3′ by a splice acceptor site. In certain embodiments, the inhibitory RNA molecule is flanked at its 5′ by a splice donor site. In certain embodiments, the inhibitory RNA molecule is flanked at its 3′ by a splice donor site.
In certain embodiments, the splice acceptor site comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 11. In certain embodiments, the splice acceptor site comprises the nucleotide sequence set forth in SEQ ID NO. 11. In certain embodiments, the splice acceptor site consists of the nucleotide sequence set forth in SEQ ID NO: 11. SEQ ID NO: 11 is provided below.
In certain embodiments, the splice acceptor site comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 12. In certain embodiments, the splice acceptor site comprises the nucleotide sequence set forth in SEQ ID NO: 12. In certain embodiments, the splice acceptor site consists of the nucleotide sequence set forth in SEQ ID NO: 12. SEQ ID NO: 12 is provided below.
In certain embodiments, the splice donor site comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 13. In certain embodiments, the splice donor site comprises the nucleotide sequence set forth in SEQ ID NO: 13. In certain embodiments, the splice donor site consists of the nucleotide sequence set forth in SEQ ID NO: 13. SEQ ID NO: 13 is provided below.
3.1.3. Poly-Adenylation Sequence (Poly-A)
In certain embodiments, the Secondary Promoter Constructs disclosed herein include a poly-adenylation signal sequence (poly-A). The poly-A signal sequence is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule. Typically, a poly-A signal sequence is between about 100 and about 250 residues long. The poly-A signal sequence makes the RNA molecule more stable and prevents its degradation. Additionally, the poly-A signal sequence allows the mature messenger RNA molecule to be exported from the nucleus and translated into a protein by ribosomes in the cytoplasm.
In certain embodiments, the poly-adenylation signal sequence is a type of DNA sequence that mediates the addition of a poly-A signal sequence to the 3′ end of the mRNA transcript. In certain embodiments, the poly-A signal sequence acts as a transcription stop signal. In certain embodiments, the addition of a poly-A signal sequence is required for the production of mature mRNA. In certain embodiments, the poly-A signal sequence is important for nuclear export, translation, and mRNA stability.
In certain embodiments, a poly-A signal sequence is only included after the TCR gene to decouple transcription of the TCR genes from the transcription of a Payload. In essence, adding the poly-A signal sequence at this position leads to the production of two separate transcripts. Accordingly, when combined with a secondary promoter, the poly-A signal sequence allows the decoupling of the expression of the Payload from the expression of the TCR. In certain embodiments and as shown in Format 2, a second poly-A signal was added even though only the first poly-A signal sequence is required for the production of two distinct transcripts.
In certain embodiments, the Secondary Promoter Construct includes one poly-A signal sequence. In certain non-limiting embodiments, the poly-A signal sequence can be a simian virus 40 (SV40) poly-A signal sequence, an SV40 poly-A signal sequence, a human growth hormone (hGH) poly-A signal sequence, a bovine growth hormone (BGH) poly-A signal sequence, or a rabbit beta-globin (rbGlob) poly-A signal sequence. In certain embodiments, the Secondary Promoter Construct includes two poly-A signal sequences. In certain embodiments, the two poly-A signal sequences are the same. In certain embodiments, the two poly-A signal sequences are different.
In certain embodiments, the poly-A signal sequence used in the Secondary Promoter Constructs is the BGH poly-A signal sequence. In certain embodiments, the BGH poly-A signal sequence comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 14. In certain embodiments, the BGH poly-A signal sequence comprises the nucleotide sequence set forth in SEQ ID NO: 14. In certain embodiments, the BGH poly-A signal sequence consists of the nucleotide sequence set forth in SEQ ID NO: 14. SEQ ID NO: 14 is provided below.
In certain embodiments, the poly-A signal sequence used in the Secondary Promoter Constructs is the SV40 poly-A signal sequence. In certain embodiments, the SV40 poly-A signal sequence comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 15. In certain embodiments, the SV40 poly-A signal sequence comprises the nucleotide sequence set forth in SEQ ID NO: 15. In certain embodiments, the SV40 poly-A signal sequence consists of the nucleotide sequence set forth in SEQ ID NO: 15. SEQ ID NO: 15 is provided below.
In certain embodiments, the SV40 poly-A signal sequence further comprises an SV40 upstream element. In certain embodiments, the SV40 upstream element comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 3. In certain embodiments, the SV40 upstream element comprises the nucleotide sequence set forth in SEQ ID NO: 16. In certain embodiments, the SV40 upstream element consists of the nucleotide sequence set forth in SEQ ID NO: 16. SEQ ID NO: 16 is provided below.
In certain embodiments, the poly-A signal sequence used in the Secondary Promoter Constructs is a 6T sequence. In certain embodiments, the 6T sequence comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 17. In certain embodiments, the 6T poly-A signal sequence comprises the nucleotide sequence set forth in SEQ ID NO: 17. In certain embodiments, the 6T poly-A signal sequence consists of the nucleotide sequence set forth in SEQ ID NO: 17. SEQ ID NO: 17 is provided below.
In certain embodiments, the poly-A signal sequence used in the Secondary Promoter Constructs shown in
In certain embodiments, the first poly-A signal sequence used in the Secondary Promoter Constructs shown in
In certain embodiments, the first poly-A signal sequence used in the Secondary Promoter Constructs shown in
In certain embodiments, the poly-A signal sequence used in the Secondary Promoter Constructs shown in
3.1.4. Insulators
In certain embodiments, the Secondary Promoter Constructs disclosed herein include a transcriptional insulator or insulator. Insulators are a type of DNA sequence that helps divide the genome into distinct “genetic neighborhoods.” Insulators can help prevent regulatory elements designed to affect the expression of one gene from also affecting the expression of another nearby gene.
In certain embodiments, insulators can reduce promoter interference. Promoter interference is a molecular event characterized by the perturbation of one transcription unit by another. For example, without any limitation, promoter interference can occur between the transcription units of the genes of the Secondary Promoter Constructs (e.g., the sequence encoding an exogenous TCR and the Payload). Additional information on promoter interference can be found in Eszterhas et al., Molecular and Cellular Biology 22.2 (2002): 469-479.
In certain embodiments, promoter interference occurs when the expression of the Payload reduces the TCR expression. Accordingly, in certain embodiments, an insulator can be inserted into the Secondary Promoter Construct to prevent reduction in TCR expression.
In certain embodiments, insulators reduce promoter leakiness. Accordingly, in certain embodiments, insulators can be used to reduce transgene silencing.
In certain embodiments, an insulator is added to the construct between the TCR gene and the Payload. In certain embodiments, an insulator is added to the construct between the TCR genes and the promoter region.
In certain embodiments, the insulators used in the Secondary Promoter Constructs are HS4 or IS2. Additional examples of insulators encompassed by the present disclosure include, without any limitation, CTCF insulator, Cohesin insulator, TFIIIC insulator, Condensin insulator, p68 insulator, PARP1 insulator, Bptf insulator, TGF-β insulator, and Kaiso insulator. Further information and examples of insulators can be found in Liu et al., Nature biotechnology 33.2 (2015): 198-203.
In certain embodiments, the insulator is an HS4 insulator. In certain embodiments, the HS4 insulator comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 18. In certain embodiments, the HS4 insulator comprises the nucleotide sequence set forth in SEQ ID NO: 18. In certain embodiments, the HS4 insulator consists of the nucleotide sequence set forth in SEQ ID NO: 18. SEQ ID NO: 18 is provided below:
In certain embodiments, the insulator is an IS2 insulator. In certain embodiments, the IS2 insulator comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 19. In certain embodiments, the IS2 insulator comprises the nucleotide sequence set forth in SEQ ID NO: 19. In certain embodiments, the IS2 insulator consists of the nucleotide sequence set forth in SEQ ID NO: 19. SEQ ID NO: 19 is provided below:
In certain embodiments, the Secondary Promoter Construct includes one insulator. In certain embodiments, the Secondary Promoter Construct includes two insulators. In certain embodiments, the two insulators are the same. In certain embodiments, the two insulators are different.
In certain embodiments, the insulator used in Format 1 constructs is HS4 (
In certain embodiments, the insulator used in Format 2 constructs that only use 1 insulator is HS4 (
In certain embodiments, while not shown in the figures, insulators can be inserted in any construct disclosed herein, and where constructs contain an insulator a second insulator can be added.
3.1.5. Additional Elements to Increase Translation of Transcripts
In mammalian cells, mRNA lacking in intronic regions do not get properly processed. This results in the production of abysmally low levels of proteins. Introns are ubiquitous in most eukaryotes, yet intron-free genes are commonly used for gene delivery as a method of significantly decreasing the Payload size and nucleic acid toxicity.
In certain embodiments, sequence elements that promote translation of transcripts are introduced into the Secondary Promoter Constructs. In certain embodiments, sequence elements that promote normal processing of intron-free transcripts are introduced into the Secondary Promoter Constructs.
In certain embodiments, the Secondary Promoter Construct includes an element to increase the translation of transcripts. In certain embodiments, the element to increase translation of transcripts is a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). The WPRE can increase gene expression from a variety of vectors and is most effective when placed downstream of the gene, proximal to the polyadenylation signal.
In certain embodiments, the sequence element that promotes normal processing of intron-free transcripts and that is introduced into the Secondary Promoter Construct is a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). In certain embodiments, WPREs are often used to promote normal processing of intron-free transcripts, resulting in normal levels of protein expression.
In certain embodiments, the WPRE is a WPRE3 element. In certain embodiments, the WPRE3 element comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments, the WPRE3 element comprises the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments, the WPRE3 element consists of the nucleotide sequence set forth in SEQ ID NO: 20. SEQ ID NO: 20 is provided below:
In certain embodiments, the element to increase translation of transcripts is a transcriptional pause element. This “pause element” can regulate gene expression at the level of RNA synthesis in both prokaryotes and eukaryotes, serving to coordinate the appearance of RNA with its utilization in cellular functions, and to modulate the interaction of regulatory proteins with RNA polymerase (RNAP).
In certain embodiments, the pause element is a MAZ4 pause element. In certain embodiments, the MAZ4 pause element comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 21. In certain embodiments, the MAZ4 pause element comprises the nucleotide sequence set forth in SEQ ID NO: 21. In certain embodiments, the MAZ4 pause element consists of the nucleotide sequence set forth in SEQ ID NO: 21. SEQ ID NO: 21 is provided below:
In certain embodiments, the Secondary Promoter Constructs described herein are designed to integrate into the genome in a manner such that the transcripts of the TCR and the Payload include intronic regions (see, e.g., Format 1;
In certain embodiments, the WPRE element shown in
In certain embodiments, the WPRE element shown in
In certain embodiments, the WPRE element shown in
3.1.6. Secondary Promoters
In certain embodiments, the Secondary Promoter Construct includes a promoter. In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct can be a eukaryotic promoter, a mammalian promoter, a viral promoter, a synthetic promoter, a minimal promoter, a hybrid promoter, a tissue-specific promoter, an inducible promoter, or a constitutive promoter.
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct is a constitutive promoter (i.e., a promoter that displays stable gene expression patterns over time). In certain embodiments, a constitutive promoter is selected in cases where the Payload of interest has a low toxicity profile and in cases where there is no clear benefit in linking protein expression to a specific time or place. In certain non-limiting examples, the constitutive promoter is the EF-1α promoter, the hACTB promoter, the hPGK promoter, the MND promoter, or the U6 promoter.
In certain embodiments, the constitutive promoter is an EF-1α promoter. In certain embodiments, the EF-1α promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 22. In certain embodiments, the EF-1α promoter comprises the nucleotide sequence set forth in SEQ ID NO: 22. In certain embodiments, the EF-1α promoter consists of the nucleotide sequence set forth in SEQ ID NO: 22. SEQ ID NO: 22 is provided below:
In certain embodiments, the EF-1α promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 23. In certain embodiments, the EF-1α promoter comprises the nucleotide sequence set forth in SEQ ID NO: 23. In certain embodiments, the EF-1α promoter consists of the nucleotide sequence set forth in SEQ ID NO: 23. SEQ ID NO: 23 is provided below:
In certain embodiments, the constitutive promoter is a hACTB promoter. In certain embodiments, the hACTB promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 24. In certain embodiments, the hACTB promoter comprises the nucleotide sequence set forth in SEQ ID NO: 24. In certain embodiments, the hACTB promoter consists of the nucleotide sequence set forth in SEQ ID NO: 24. SEQ ID NO: 24 is provided below.
In certain embodiments, the constitutive promoter is an hPGK promoter. In certain embodiments, the hPGK promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 25. In certain embodiments, the hPGK promoter comprises the nucleotide sequence set forth in SEQ ID NO: 25. In certain embodiments, the hPGK promoter consists of the nucleotide sequence set forth in SEQ ID NO: 25. SEQ ID NO: 25 is provided below:
In certain embodiments, the constitutive promoter is an MND promoter. In certain embodiments, the MND promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 26. In certain embodiments, the MND promoter comprises the nucleotide sequence set forth in SEQ ID NO: 26. In certain embodiments, the MND promoter consists of the nucleotide sequence set forth in SEQ ID NO: 26. SEQ ID NO: 26 is provided below:
In certain embodiments, the constitutive promoter is a U6 promoter. In certain embodiment the U6 promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 27. In certain embodiments, the U6 promoter comprises the nucleotide sequence set forth in SEQ ID NO: 27. In certain embodiments, the U6 promoter consists of the nucleotide sequence set forth in SEQ ID NO: 27. SEQ ID NO: 27 is provided below:
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct is an inducible promoter (i.e., a type of conditional promoter where the promoter is in its “on” state only under certain conditions). In certain embodiments, the inducible promoter is generally in its “off” state, unless and until it receives a signal that induces switching into the “on” state. In certain embodiments, the inducible promoter allows for a basal level of gene expression even if in the “off” state (i.e., a phenomenon known as promoter leakiness).
In certain embodiments, the inducible promoter is a TCR activation triggered inducible promoter. In certain embodiments, the TCR activation triggered inducible promoter works as follows: upon TCR engagement a transcription factor is activated (i.e. AP-1, NFAT, NF-κB); these activated transcription factors will bind the inducible promoter and initiate a switch from the “off” state to the “on” state. In certain embodiments, the TCR activation triggered inducible promoter may contain either additional or a reduced number of response elements when compared to the wild-type promoter. In certain embodiments, the TCR activation triggered inducible promoter is used to localize a Payload of interest to the tumor site. In certain embodiments, the benefit of localizing a Payload of interest to the tumor site is to allow for high levels of the Payload to be predominantly expressed in response to TCR signaling at the tumor site. In certain embodiments, this is the site maximal TCR engagement. In certain embodiments, localizing a Payload of interest to the tumor site allows for the use of Payloads with high toxicity profiles because the use of an inducible promoter can limit the systemic availability of toxic Payloads. In certain embodiments, the TCR activation trigged inducible promoter comprises a sequence of at least one regulatory element of transcription factors induced by TCR activation. In certain embodiments, the TCR activation triggered inducible promoter is the AP-1 responsive, NFAT responsive, NF-κB responsive promoter, or an NR4A-responsive promoter.
In certain embodiments, the TCR activation triggered inducible promoter is a promoter that can be activated by pathways associated with the TCR activation or T cell pathways or by induction with an activation agent (for example but not limited to a small molecule or polypeptide).
In certain embodiments, the inducible promoter is an AP-1 promoter. In certain embodiments, the AP-1 promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 28. In certain embodiments, the AP-1 promoter comprises the nucleotide sequence set forth in SEQ ID NO: 28. In certain embodiments, the AP-1 promoter consists of the nucleotide sequence set forth in SEQ ID NO: 28. SEQ ID NO: 28 is provided below:
In certain embodiments, the inducible promoter is an NFAT promoter. In certain embodiments, the NFAT promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 29. In certain embodiments, the NFAT promoter comprises the nucleotide sequence set forth in SEQ ID NO: 29. In certain embodiments, the NFAT promoter consists of the nucleotide sequence set forth in SEQ ID NO: 29. SEQ ID NO: 29 is provided below:
In certain embodiments, the inducible promoter is an NF-κB promoter. In certain embodiments, the NF-κB promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 30. In certain embodiments, the NF-κB promoter comprises the nucleotide sequence set forth in SEQ ID NO: 30. In certain embodiments, the NF-κB promoter consists of the nucleotide sequence set forth in SEQ ID NO: 30. SEQ ID NO: 30 is provided below:
In certain embodiments, the inducible promoter is an NR4A-responsive promoter. In certain embodiments, the NR4A-responsive promoter comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 31. In certain embodiments, the NR4A-responsive promoter comprises the nucleotide sequence set forth in SEQ ID NO: 31. In certain embodiments, the NR4A-responsive promoter consists of the nucleotide sequence set forth in SEQ ID NO: 31. SEQ ID NO: 31 is provided below:
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct is an EF1a core (cEF1a) promoter, an hACTB promoter, an hPGK promoter, an MND promoter, an AP-1 responsive promoter, an NFAT responsive promoter, or an NF-κB responsive promoter.
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct is a TRAC promoter. In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct is a TCRβ promoter. In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct of Format 3 (
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct of Format 1 (
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct of Format 2 (
In certain embodiments, the promoter for the expression of the Payload of the Secondary Promoter Construct of Format 3 (
3.1.7. Enhancers
In certain embodiments, the Secondary Promoter Construct includes an enhancer. Enhancers are cis-acting elements of DNA, usually about 10 to about 300 bp in length, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes. For example, without any limitation, enhancer sequences are derived from the globin gene, the elastase gene, the albumin gene, the α-fetoprotein gene, and the insulin gene.
In certain embodiments, the enhancer is a T cell receptor (TCR) enhancer. In certain embodiments, the TCR enhancer can be a TCRα enhancer, a TCRβ enhancer, a TCRγ enhancer, or a TCRδ enhancer. In certain embodiments, the TCR enhancer comprises a TCRα enhancer. In certain embodiments, the TCRα enhancer comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the TCRα enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments, the TCRα enhancer consists of the nucleotide sequence set forth in SEQ ID NO: 32. SEQ ID NO: 32 is provided below:
In certain embodiments, the enhancer derives from a eukaryotic cell virus. Non-limiting examples of enhancers derived from eukaryotic cell virus include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
In certain embodiments, the enhancer is a cytomegalovirus (CMV) enhancer. In certain embodiments, the CMV comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 33. In certain embodiments, the CMV enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 33. In certain embodiments, the CMV enhancer consists of the nucleotide sequence set forth in SEQ ID NO: 33. SEQ ID NO: 33 is provided below:
In certain embodiments, the enhancer can be operably linked to a Kozak sequence. In certain embodiments, the Kozak sequence comprises the nucleotide sequence set forth in SEQ ID NO: 34. In certain embodiments, the Kozak sequence consists of the nucleotide sequence set forth in SEQ ID NO: 34. SEQ ID NO: 34 is provided below.
3.1.8. Homology Recombination Templates
In certain embodiments, the Secondary Promoter Construct is a homologous recombination (HR) template nucleic acid sequence for insertion into an endogenous locus of a cell.
In certain embodiments, the present disclosure provides genome editing of a cell by introducing and recombining a homologous recombination (HR) template nucleic acid sequence into an endogenous locus of a cell. In certain embodiments, the HR template nucleic acid sequence is linear. In certain embodiments, the HR template nucleic acid sequence is circular. In certain embodiments, the circular HR template can be a plasmid, minicircle, or nanoplasmid. In certain embodiments, the HR template nucleic acid sequence comprises a first homology arm and second homology arm. In certain embodiments, the homology arms can be of about 300 bases to about 2,000 bases. For example, each homology arm can be 1,000 bases. In certain embodiments, the homology arms can be homologous to first and second endogenous sequences of the cell. In certain embodiments, the endogenous locus is a TCR locus. For example, the first and second endogenous sequences are within a TCR alpha locus or a TCR beta locus.
In certain embodiments, the first homology arm comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 35. In certain embodiments, the first homology arm comprises the nucleotide sequence set forth in SEQ ID NO: 35. In certain embodiments, the first homology arm consists of the nucleotide sequence set forth in SEQ ID NO: 35. In certain embodiments, the first homology arm comprises about 300 consecutive bases, about 400 consecutive bases, about 500 consecutive bases, about 600 consecutive bases, about 700 consecutive bases, about 800 consecutive bases, or about 900 consecutive bases of SEQ ID NO: 35. In certain embodiments, the first homology arm comprises about 300 consecutive bases of SEQ ID NO: 35. In certain embodiments, the first homology arm comprises about 400 consecutive bases of SEQ ID NO: 35. In certain embodiments, the first homology arm comprises about 600 consecutive bases of SEQ ID NO: 35.
In certain embodiments, the second homology arm comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 36. In certain embodiments, the second homology arm comprises the nucleotide sequence set forth in SEQ ID NO: 36. In certain embodiments, the second homology arm consists of the nucleotide sequence set forth in SEQ ID NO: 36. In certain embodiments, the second homology arm comprises about 300 consecutive bases, about 400 consecutive bases, about 500 consecutive bases, about 600 consecutive bases, about 700 consecutive bases, about 800 consecutive bases, or about 900 consecutive bases of SEQ ID NO: 36. In certain embodiments, the second homology arm comprises about 300 consecutive bases of SEQ ID NO: 36. In certain embodiments, the second homology arm comprises about 400 consecutive bases of SEQ ID NO: 36. In certain embodiments, the second homology arm comprises about 600 consecutive bases of SEQ ID NO: 36.
SEQ ID NO: 35 and SEQ ID NO: 36 are provided below.
In certain embodiments, the HR template comprises a TCR gene sequence. In non-limiting embodiments, the TCR gene sequence is a patient-specific TCR gene sequence. In non-limiting embodiments, the TCR gene sequence is tumor-specific. In non-limiting embodiments, the TCR gene sequence encodes a TCR recognizing a neoantigen. In certain embodiments, the neoantigen is a private neoantigen. In non-limiting embodiments, the TCR gene sequence can be identified and obtained using the methods described in PCT/US2020/017887, the content of which is herein incorporated by reference. In certain embodiments, the HR template comprises a TCR alpha gene sequence and a TCR beta gene sequence.
In certain embodiments, the HR template is a polycistronic polynucleotide. In certain embodiments, the HR template comprises sequences encoding for flexible polypeptide sequences (e.g., Gly-Ser-Gly sequence). In certain embodiments, the HR template comprises sequences encoding an internal ribosome entry site (IRES). In certain embodiments, the HR template comprises a 2A peptide (e.g., P2A, T2A, E2A, and F2A). In certain embodiments, the HR template comprises a protease cleavage site. In certain embodiments, the HR template comprises a signal sequence.
In certain embodiments, the flexible polypeptide encodes a glycine-serine-glycine sequence. In certain embodiments, the flexible polypeptide is encoded by a nucleotide sequence comprising the nucleotide sequence set forth in SEQ ID NO: 37 or SEQ ID NO: 38. In certain embodiments, the flexible polypeptide is encoded by a nucleotide sequence consisting of the nucleotide sequence set forth in SEQ ID NO: 37 or SEQ ID NO: 38. SEQ ID NO: 37 and SEQ ID NO: 38 are provided below.
In certain embodiments, the 2A peptide is a P2A peptide. In certain embodiments, the P2A peptide comprises the amino acid sequence set forth in SEQ ID NO: 39. In certain embodiments, the P2A peptide consists of the amino acid sequence set forth in SEQ ID NO: 39. In certain embodiments, the P2A peptide is encoded by a nucleotide sequence comprising the nucleotide sequence set forth in SEQ ID NO: 40 or SEQ ID NO: 41. In certain embodiments, the P2A peptide is encoded by a nucleotide sequence consisting of the nucleotide sequence set forth in SEQ ID NO: 40 or SEQ ID NO: 41. SEQ ID NOs: 39-41 are provided below.
In certain embodiments, the P2A peptide comprises, at its N-end, a flexible polypeptide comprising a glycine-serine-glycine sequence. In certain embodiments, the P2A peptide comprises, at its N-end, a flexible polypeptide consisting of a glycine-serine-glycine sequence.
In certain embodiments, the protease cleavage site is a Furin cleavage site. In certain embodiments, the Furin cleavage site is encoded by a nucleotide sequence comprising the nucleotide sequence set forth in SEQ ID NO: 42. In certain embodiments, the Furin cleavage site is encoded by a nucleotide sequence consisting of the nucleotide sequence set forth in SEQ ID NO: 42. SEQ ID NO: 42 is provided below.
In certain embodiments, the signal sequence is a human growth hormone (HGH) signal sequence. In certain embodiments, the HGH signal sequence comprises the amino acid sequence set forth in SEQ ID NO: 43. In certain embodiments, the HGH signal sequence consists of the amino acid sequence set forth in SEQ ID NO: 43. In certain embodiments, the HGH signal sequence is encoded by a nucleotide sequence comprising the nucleotide sequence set forth in SEQ ID NO: 44 or SEQ ID NO: 45. In certain embodiments, the HGH signal sequence is encoded by a nucleotide sequence consisting of the nucleotide sequence set forth in SEQ ID NO: 44 or SEQ ID NO: 45. SEQ ID NOs: 43-45 are provided below.
In certain embodiments, the Secondary Promoter Constructs include multiple 2A peptides, flexible polypeptides, protease cleavage peptides, signal peptides, or combinations thereof. In certain embodiments, the multiple 2A peptides can have the same amino acid sequence. In certain embodiments, the multiple flexible polypeptides can have the same amino sequence. In certain embodiments, the multiple protease cleavage peptides can have the same amino acid sequence. In certain embodiments, the multiple signal peptides can have the same amino acid sequence. In certain embodiments, when the Secondary Promoter Constructs include multiple 2A peptides, flexible polypeptides, protease cleavage peptides, signal peptides, or combinations thereof, these amino acid sequences are encoded by codon diverged nucleotide sequences. Additional information on the HR template nucleic acids and methods of modifying a cell thereof can be found in International Patent Application no. PCT/US2018/058230, the content of which is herein incorporated by reference.
3.1.9. Exemplified Secondary Promoter Constructs
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the Secondary Promoter Construct further comprises a promoter and an insulator. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, an insulator, a promoter, a Payload, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a first poly-A signal sequence and a second poly-A signal sequence. In certain embodiments, the Secondary Promoter Construct further comprises a promoter, an insulator, and a WPRE element. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a first poly-A signal sequence, an insulator, a promoter, a Payload, a WPRE element, a second poly-A signal sequence, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a first poly-A signal sequence, a first insulator, a promoter, a Payload, a second poly-A signal sequence, a second insulator, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a first poly-A signal sequence, an insulator, a promoter, a Payload, a second poly-A signal sequence, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the Secondary Promoter Construct further comprises a promoter and a WPRE element. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a WPRE element, a Payload, a promoter, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a Payload, a protease cleavage site, a second 2A peptide, a second signal sequence, a TCRβ gene sequence, a second protease cleavage site, a third 2A peptide, a third signal sequence peptide, and a TRCα gene sequence.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence and an insulator. In certain embodiments, the 3′ of the at least one Payload comprises a STOP codon. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, an insulator, a promoter, a Payload having at its 3′ a termination codon, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the 3′ of the at least one Payload comprises a protease cleavage site and a 2A peptide. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a Payload, a second protease cleavage site, a third 2A peptide, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct comprises an enhancer. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence and a pause element. In certain embodiments, the 3′ of the at least one Payload comprises protease cleavage site and a 2A peptide. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, an enhancer, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a pause element, a promoter, a Payload, a second protease cleavage site, a third 2A peptide, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct comprises an enhancer. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence and an insulator. In certain embodiments, the 3′ of the at least one Payload comprises a protease cleavage site and a 2A peptide. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, an enhancer, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, an insulator, a promoter, a Payload, a second protease cleavage site, a third 2A peptide, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence, an enhancer, and an insulator. In certain embodiments, the 3′ of the at least Payload comprises a STOP codon. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, an enhancer, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, an insulator, a promoter, a Payload having at its 3′ a termination codon, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, an inhibitory RNA molecule, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence and a termination sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, an inhibitory RNA molecule, a termination sequence, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the 3′ of the at least one Payload comprises a protease cleavage site and a 2A peptide. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a first Payload, a second Payload, a second protease cleavage site, a third 2A peptide, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the at least one Payload comprises with a protease cleavage site and a 2A peptide. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a first Payload, a second protease cleavage site, a third 2A peptide, a second Payload, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the inhibitory RNA molecule is flanked by a splice acceptor site, a splice donor site, or a combination thereof. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a splice donor site, an inhibitory RNA molecule, a splice acceptor site, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the Secondary Promoter Construct further comprises a splice acceptor site. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, an inhibitory RNA molecule, a splice acceptor site, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, an inhibitory RNA molecule, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises an inhibitory RNA molecule. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a first Payload, a second Payload, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the at least one Payload comprises a first inhibitory RNA molecule. In certain embodiments, the at least one Payload comprises a second inhibitory RNA molecule. In certain embodiments, the first and second inhibitory RNA molecules knock down the gene expression of a same gene. In certain embodiments, the first and second inhibitory RNA molecules knock down the gene expression of different genes. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a first inhibitory RNA molecule, a second inhibitory RNA molecule, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least one Payload. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the Payload is a miRNA cluster. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a miRNA cluster, and a second homology arm.
In certain embodiments, the Secondary Promoter Construct comprises a sequence encoding an exogenous TCR and at least two Payloads. In certain embodiments, the sequence encoding an exogenous TCR encodes a TRCα gene sequence and a TCRβ gene sequence. In certain embodiments, the sequence encoding an exogenous TCR comprises a first 2A peptide and a second 2A peptide, a first signal peptide and a second signal peptide, and a protease cleavage site. In certain embodiments, the Secondary Promoter Construct further comprises a poly-A signal sequence. In certain embodiments, the first Payload is an inhibitory RNA molecule. In certain embodiments, the inhibitory RNA molecule is flanked by a splice acceptor site, a splice donor site, or a combination thereof. In certain embodiments, the Secondary Promoter Construct further comprises a promoter. In certain embodiments, the Secondary Promoter Construct further comprises a first homology arm and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a first Payload, a splice donor site, an inhibitory RNA molecule, a splice acceptor site, and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first Payload, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, a splice donor site, an inhibitory RNA molecule, a splice acceptor site, and a second homology arm. In certain embodiments, the Secondary Promoter Construct comprises, from 5′ to 3′, a first homology arm, a first 2A peptide, a first signal sequence peptide, a TCRβ gene sequence, a protease cleavage site, a second 2A peptide, a second signal sequence peptide, a TRCα gene sequence, a poly-A signal sequence, a promoter, an inhibitory RNA molecule, and a second homology arm.
In certain embodiments, when a Secondary Promoter Construct includes two or more sequences encoding a 2A peptide, the sequences encode for the same 2A peptide and can be codon diverged. For example, without any limitation, two sequences can encode for a P2A and be codon diverged. In certain embodiments, when a Secondary Promoter Construct includes a sequence encoding a 2A peptide, the Secondary Promoter Construct can include a sequence encoding for a GSG amino acid at the 5′ of the sequence encoding a 2A peptide. In certain embodiments, when a Secondary Promoter Construct includes two or more sequences encoding a signal peptide, the sequences encode for the same signal peptide and can be codon diverged. For example, without any limitation, two sequences can encode for a HGH signal peptide and be codon diverged.
In certain embodiments, the Secondary Promoter Construct comprises a TCRβ gene sequence comprising a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% identical to the nucleotide sequence set forth in SEQ ID NO: 46. In certain embodiments, the TCRβ gene sequence comprises the nucleotide sequence set forth in SEQ ID NO: 46. In certain embodiments, TCRβ gene sequence consists of the nucleotide sequence set forth in SEQ ID NO: 46.
In certain embodiments, the TCRβ gene sequence encodes an amino acid sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% identical to the amino acid sequence set forth in SEQ ID NO: 47. In certain embodiments, the TCRβ gene sequence encodes the amino acid sequence set forth in SEQ ID NO: 47. SEQ ID NOs: 46 and 47 are provided below.
In certain non-limiting embodiments, the Secondary Promoter Construct comprises a Payload encoding an mCherry protein. In certain embodiments, the Secondary Promoter Construct comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% identical to the nucleotide sequence set forth in SEQ ID NOs: 48-64. In certain embodiments, the Secondary Promoter Construct comprises the nucleotide sequence set forth in SEQ ID NOs: 48-64. In certain embodiments, the Secondary Promoter Construct consists of the nucleotide sequence set forth in SEQ ID NOs: 48-64.
In certain embodiments, the at least one Payload (e.g., mCherry protein) of any one of SEQ ID NOs: 48-64 can be replaced by any Payload disclosed herein. For example, but without any limitation, the at least one Payload can be replaced by a sequence encoding a cytokine receptors trap or ligand trap, an angiogenesis factors, an apoptotic factor, an inhibitory protein for various cell processes (e.g., inhibition of macrophage activation), an extracellular matrix modulator, a soluble TCRs, a soluble chimeric antigen receptor (CAR), a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, a protein that binds to receptors and sterically hinders receptor function, or an inhibitory RNA molecule.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3794 of SEQ ID NO: 48. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4503 to 7046 of SEQ ID NO: 48. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3821 and nucleotides 4503 to 7046 of SEQ ID NO: 48. SEQ ID NO: 48 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3837 of SEQ ID NO: 49. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4546 to 7520 of SEQ ID NO: 49. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3837 and nucleotides 4546 to 7520 of SEQ ID NO: 49. SEQ ID NO: 49 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3402 of SEQ ID NO: 50. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4111 to 7051 of SEQ ID NO: 50. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3402 and nucleotides 4111 to 7051 of SEQ ID NO: 50. SEQ ID NO: 50 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3931 of SEQ ID NO: 51. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4640 to 7258 of SEQ ID NO: 51. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4086 and nucleotides 4795 to 7413 of SEQ ID NO: 51. SEQ ID NO: 51 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4140 of SEQ ID NO: 52. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4849 to 7467 of SEQ ID NO: 52. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4140 and nucleotides 4849 to 7467 of SEQ ID NO: 52. SEQ ID NO: 52 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4004 of SEQ ID NO: 53. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4713 to 7331 of SEQ ID NO: 53. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4004 and nucleotides 4713 to 7331 of SEQ ID NO: 53 SEQ ID NO: 53 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4938 of SEQ ID NO: 54. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 5647 to 8265 of SEQ ID NO: 54. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4938 and nucleotides 5647 to 8265 of SEQ ID NO: 54 SEQ ID NO: 54 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4302 of SEQ ID NO: 55. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 5011 to 7629 of SEQ ID NO: 55. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4302 and nucleotides 5011 to 7629 of SEQ ID NO: 55 SEQ ID NO: 55 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4274 of SEQ ID NO: 56. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4983 to 7601 of SEQ ID NO: 56. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4274 and nucleotides 4983 to 7601 of SEQ ID NO: 56 SEQ ID NO: 56 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4105 of SEQ ID NO: 57. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4814 to 7432 of SEQ ID NO: 57. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4105 and nucleotides 4814 to 7432 of SEQ ID NO: 57 SEQ ID NO: 57 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4007 of SEQ ID NO: 58. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 4716 to 7334 of SEQ ID NO: 58. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 4007 and nucleotides 4716 to 7334 of SEQ ID NO: 58 SEQ ID NO: 58 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2881 of SEQ ID NO: 59. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 3759 to 5679 of SEQ ID NO: 59. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2881 and nucleotides 3759 to 5679 of SEQ ID NO: 59. SEQ ID NO: 59 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2887 of SEQ ID NO: 60. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 3837 to 5691 of SEQ ID NO: 60. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2887 and nucleotides 3837 to 5691 of SEQ ID NO: 60. SEQ ID NO: 60 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3007 of SEQ ID NO: 61. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 3165 to 5134 of SEQ ID NO: 61. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 3007 and nucleotides 3165 to 5134 of SEQ ID NO: 61. SEQ ID NO: 61 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 312 of SEQ TD NO: 62. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 470 to 4001 of SEQ TD NO: 62. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 312 and nucleotides 470 to 4001 of SEQ ID NO: 62. SEQ ID NO: 62 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2881 of SEQ ID NO: 63. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 3039 to 4893 of SEQ ID NO: 63. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2881 and nucleotides 3039 to 4893 of SEQ ID NO: 63. SEQ ID NO: 63 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2736 of SEQ ID NO: 64. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 2788 to 4648 of SEQ ID NO: 64. In certain embodiments, the Secondary Promoter Construct comprises nucleotides 1 to 2736 and nucleotides 2788 to 4648 of SEQ ID NO: 64. SEQ ID NO: 64 is provided below.
In certain embodiments, the Secondary Promoter Construct comprises a nucleotide sequence that is at least about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% identical to the nucleotide sequence set forth in SEQ ID NOs: 65-98. In certain embodiments, the Secondary Promoter Construct comprises the nucleotide sequence set forth in SEQ ID NOs: 65-98. In certain embodiments, the Secondary Promoter Construct comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, and 97. In certain embodiments, the Secondary Promoter Construct comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, and 98. In certain embodiments, the Secondary Promoter Construct comprises a first nucleotide sequence selected from the group consisting of SEQ ID NOs: 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, and 97, and a second nucleotide sequence selected from the group consisting of SEQ ID NOs: 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, and 98.
3.2. Methods of Producing Secondary Promoter Products with a Young Phenotype
In certain embodiments, the present disclosure relates, in part, to the production of engineered “young” T cells comprising the Secondary Promoter Constructs disclosed herein. In certain embodiments, the present disclosure comprises methods for producing antigen-specific cells, e.g., T cells, ex vivo, comprising activating, engineering, and expanding antigen-specific cells originally obtained from a subject or isolated from such sample.
In certain embodiments, the methods for activating cells comprise the steps of activating the TCR/CD3 complex. For example, without limitation, the T cells can be incubated and/or cultured with CD3 agonists, CD28 agonists, or a combination thereof.
In certain embodiments, engineered activated antigen-specific cells, e.g., engineered activated T cells, can be expanded by culturing the engineered activated antigen-specific cells, e.g., T cells, with cytokines, chemokine, soluble peptides, or combination thereof. In certain embodiments, the engineered activated antigen-specific cells, e.g., engineered activated T cells, can be cultured with one or more cytokines. In certain embodiments, the cytokines can be IL2, IL7, IL15, or combinations thereof. For example, engineered activated antigen-specific cells, e.g., engineered activated T cells, can be cultured with IL7 and IL15. In certain embodiments, the cytokine used in connection with the engineered activated antigen-specific cell, e.g., engineered activated T cell, culture can be present at a concentration from about 1 pg/ml to about 1 g/ml, from about 1 ng/ml to about 1 g/ml, from about 1 g/ml to about 1 g/ml, or from about 1 mg/ml to about 1 g/ml, and any values in between.
3.3. Gene-Editing Methods
In certain embodiments, the present disclosure involves, in part, methods of engineering human cells, e.g., engineered T cells or engineered human stem cells, comprising the Secondary Promoter Constructs disclosed herein. In certain embodiments, the present disclosure involves, in part, methods of engineering human cells, e.g., NK cells, NKT cells, macrophages, hematopoietic stem cells (HSCs), cells derived from HSCs, or dendritic/antigen-presenting cells. In certain embodiments, such engineering involves genome editing. For example, but not by way of limitation, such genome editing can be accomplished with nucleases targeting one or more endogenous loci, e.g., TCR alpha (TCRα) locus and TCR beta (TCRβ) locus. In certain embodiments, the nucleases can generate single-stranded DNA nicks or double-stranded DNA breaks in an endogenous target sequence. In certain embodiments, the nuclease can target coding or non-coding portions of the genome, e.g., exons, introns. In certain embodiments, the nucleases contemplated herein comprise homing endonuclease, meganuclease, megaTAL nuclease, transcription activator-like effector nuclease (TALEN), zinc-finger nuclease (ZFN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas nuclease. In certain embodiments, the nucleases can themselves be engineered, e.g., via the introduction of amino acid substitutions and/or deletions, to increase the efficiency of the cutting activity.
In certain embodiments, a CRISPR/Cas nuclease system is used to engineer human cells. In certain embodiments, the CRISPR/Cas nuclease system comprises a Cas nuclease and one or more RNAs that recruit the Cas nuclease to the endogenous target sequence, e.g., single guide RNA. In certain embodiments, the Cas nuclease and the RNA are introduced in the cell separately, e.g. using different vectors or compositions, or together, e.g., in a polycistronic construct or a single protein-RNA complex. In certain embodiments, the Cas nuclease is Cas9 or Cas12a. In certain embodiments, the Cas9 polypeptide is obtained from a bacterial species including, without limitation, Streptococcus pyogenes or Neisseria menengitidis. Additional examples of CRISPR/Cas systems are known in the art. See Adli, Mazhar. “The CRISPR tool kit for genome editing and beyond.” Nature communications vol. 9, 1 1911 (2018), herein incorporated by reference for all that it teaches.
In certain embodiments, genome editing occurs at one or more genome loci that regulate immunological responses. In certain embodiments, the loci include, without limitation, TCR alpha (TCRα) locus, TCR beta (TCRβ) locus, TCR gamma (TCRγ), and TCR delta (TCRδ). In certain embodiments, the locus for inserting a Secondary Promoter Construct is anywhere in the genome. In certain embodiments, the locus for inserting a Secondary Promoter Construct is the TRAC locus. In certain embodiments, the locus for inserting a Secondary Promoter Construct is one of the two TRBC loci. In certain embodiments, the locus for inserting a Secondary Promoter Construct is a locus other than the TRAC locus or TRAB loci. In certain embodiments, the Secondary Promoter Construct is inserted into a gene locus wherein such gene is knocked out.
In certain embodiments, genome editing is performed by using non-viral delivery systems. For example, a nucleic acid molecule can be introduced into a cell by administering the nucleic acid in the presence of lipofection (Feigner et al., Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger et al., Methods in Enzymology 101:512, 1983), asialoorosomucoid-polylysine conjugation (Wu et al., Journal of Biological Chemistry 263:14621, 1988; Wu et al., Journal of Biological Chemistry 264:16985, 1989), or by micro-injection under surgical conditions (Wolff et al., Science 247:1465, 1990). Other non-viral means for gene transfer include transfection in vitro using calcium phosphate, DEAE dextran, electroporation, and protoplast fusion. Liposomes can also be potentially beneficial for the delivery of DNA into a cell. Transplantation of normal genes into the affected tissues of a subject can also be accomplished by transferring a normal nucleic acid into a cultivatable cell type ex vivo (e.g., an autologous or heterologous primary cell or progeny thereof), after which the cell (or its descendants) are injected into a targeted tissue or are injected systemically.
In certain embodiments, genome editing is performed by using viral delivery systems. In certain embodiments, the viral methods include targeted integration (including but not limited to AAV) and random integration (including but not limited to lentiviral approaches). In certain embodiments, the viral delivery would be accomplished without integration of the nuclease. In such embodiments, the viral delivery system can be Lentiflash or another similar delivery system.
3.4. Compositions and Vectors
The presently disclosed subject matter provides compositions comprising cells (e.g., Secondary Promoter Cells) disclosed herein.
In certain embodiments, the presently disclosed subject matter provides nucleic acid compositions comprising a polynucleotide encoding the NeoTCR disclosed herein. In certain embodiments, the nucleic acid compositions disclosed herein comprise a polynucleotide encoding a Secondary Promoter Construct disclosed herein. Also provided are cells comprising such nucleic acid compositions.
In certain embodiments, the nucleic acid composition further comprises a promoter that is operably linked to the NeoTCR disclosed herein. In certain embodiments, the nucleic acid composition further comprises a promoter that is operably linked to the Secondary Promoter Construct disclosed herein.
In certain embodiments, the promoter is endogenous or exogenous. In certain embodiments, the exogenous promoter is selected from the group consisting of an elongation factor (EF)-1 promoter, a CMV promoter, an SV40 promoter, a PGK promoter, a long terminal repeat (LTR) promoter, and a metallothionein promoter. In certain embodiments, the promoter is an inducible promoter. In certain embodiments, the inducible promoter is selected from the group consisting of an NFAT transcriptional response element (TRE) promoter, a CD69 promoter, a CD25 promoter, an IL-2 promoter, an IL-12 promoter, a p40 promoter, and a Bcl-xL promoter.
The compositions and nucleic acid compositions can be administered to subjects or and/delivered into cells by art-known methods or as described herein. Genetic modification of a cell (e.g., a T cell) can be accomplished by transducing a substantially homogeneous cell composition with a recombinant DNA construct. In certain embodiments, a retroviral vector (either a gamma-retroviral vector or a lentiviral vector) is employed for the introduction of the DNA construct into the cell. Non-viral vectors may be used as well.
Possible methods of transduction also include direct co-culture of the cells with producer cells, e.g., by the method of Bregni, et al. (1992) Blood 80:1418-1422, or culturing with viral supernatant alone or concentrated vector stocks with or without appropriate growth factors and polycations, e.g., by the method of Xu, et al. (1994) Exp. Hemat. 22:223-230; and Hughes, et al. (1992) J. Clin. Invest. 89:1817.
Other transducing viral vectors can be used to modify a cell. In certain embodiments, the chosen vector exhibits high efficiency of infection and stable integration and expression (see, e.g., Cayouette et al., Human Gene Therapy 8:423-430, 1997; Kido et al., Current Eye Research 15:833-844, 1996; Bloomer et al., Journal of Virology 71:6641-6649, 1997; Naldini et al., Science 272:263-267, 1996; and Miyoshi et al., Proc. Natl. Acad. Sci. U.S.A. 94:10319, 1997). Other viral vectors that can be used include, for example, adenoviral, lentiviral, and adena-associated viral vectors, vaccinia virus, a bovine papilloma virus, or a herpes virus, such as Epstein-Barr Virus (also see, for example, the vectors of Miller, Human Gene Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis et al., BioTechniques 6:608-614, 1988; Tolstoshev et al., Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337:1277-1278, 1991; Cornetta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416, 1991; Miller et al., Biotechnology 7:980-990, 1989; LeGal La Salle et al., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995). Retroviral vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346).
Non-viral approaches can also be employed for genetic modification of a cell. For example, a nucleic acid molecule can be introduced into a cell by administering the nucleic acid in the presence of lipofection (Feigner et al., Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger et al., Methods in Enzymology 101:512, 1983), asialoorosomucoid-polylysine conjugation (Wu et al., Journal of Biological Chemistry 263:14621, 1988; Wu et al., Journal of Biological Chemistry 264:16985, 1989), or by micro-injection under surgical conditions (Wolff et al., Science 247:1465, 1990). Other non-viral means for gene transfer include transfection in vitro using calcium phosphate, DEAE dextran, electroporation, and protoplast fusion. Liposomes can also be potentially beneficial for the delivery of DNA into a cell. Transplantation of normal genes into the affected tissues of a subject can also be accomplished by transferring a normal nucleic acid into a cultivatable cell type ex vivo (e.g., an autologous or heterologous primary cell or progeny thereof), after which the cell (or its descendants) are injected into a targeted tissue or are injected systemically.
Polynucleotide therapy methods can be directed from any suitable promoter (e.g., the human cytomegalovirus (CMV), simian virus 40 (SV40), or metallothionein promoters), and regulated by any appropriate mammalian regulatory element or intron (e.g. the elongation factor 1a enhancer/promoter/intron structure). For example, if desired, enhancers known to preferentially direct gene expression in specific cell types can be used to direct the expression of a nucleic acid. The enhancers used can include, without limitation, those that are characterized as tissue- or cell-specific enhancers. Alternatively, if a genomic clone is used as a therapeutic construct, regulation can be mediated by the cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, including any of the promoters or regulatory elements described above.
The resulting cells can be grown under conditions similar to those for unmodified cells, whereby the modified cells can be expanded and used for a variety of purposes.
3.5. Cells
The presently disclosed subject matter provides cells comprising a presently disclosed Secondary Promoter Constructs. In certain embodiments, the cell is an immune cell (e.g., a lymphocyte). For example, but without any limitation, the cells can be T cells, Natural Killer (NK) cells, B cells, dendritic cells, hematopoietic stem cells, or pluripotent stem cells.
In certain embodiments, the cell is a T cell. Non-limiting examples of T cells encompassed by the present disclosure include helper T cells, cytotoxic T cells, memory T cells (including central memory T cells, stem-cell-like memory T cells (or stem-like memory T cells), and two types of effector memory T cells: e.g., TEM cells and TEMRA cells, Regulatory T cells (also known as suppressor T cells), tumor-infiltrating lymphocyte (TIL), Natural killer T cells, Mucosal associated invariant T cells, and γδ T cells. Cytotoxic T cells (CTL or killer T cells) are a subset of T lymphocytes capable of inducing the death of infected somatic or tumor cells. In certain embodiments, the T cell is a CD4+ T cell. In certain embodiments, the T cell is a CD8+ T cell.
In certain embodiments, the T cell is a peripheral T cell. Peripheral T cells are differentiated T cells that have undergone the maturation process. Peripheral T cells can be found in peripheral blood. In certain embodiments, the T cell is not a naïve T cell. Naïve T cells are precursors for effector and memory T cell subsets. Phenotypically, naïve T cells are small cells with little cytoplasm; they express surface markers, such as CD45RA, CCR7, CD62L, CD127, and CD132. Naïve T cells lack expression of markers of previous activation, such as CD25, CD44, CD69, CD45RO, or HLA-DR.
In certain embodiments, the cell is a NK cell. Natural killer (NK) cells can be lymphocytes that are part of cell-mediated immunity and act during the innate immune response. NK cells do not require prior activation to perform their cytotoxic effect on target cells.
In certain embodiments, the cells are autologous. In certain embodiments, the cells can be transduced with the presently disclosed Secondary Promoter Constructs to express an exogenous TCR (e.g., NeoTCR) and a Payload.
3.6. Pharmaceutical Formulations.
In certain embodiments, the present disclosure provides a pharmaceutical formulation comprising the Secondary Promoter Cells disclosed herein. In certain embodiments, pharmaceutical formulations of the Secondary Promoter Products are prepared by combining the Secondary Promoter Cells in a solution that can preserve the ‘young’ phenotype of the cells in a cryopreserved state.
In certain embodiments, pharmaceutically acceptable carriers, buffers, stabilizers, and/or preservatives can be added to the cryopreservation solution. Any cryopreservation agent and/or media can be used to cryopreserve the Secondary Promoter Product, including but not limited to CryoStor, CryoStor CS5, CELLBANKER, and custom cryopreservation media that optionally include DMSO.
The presently disclosed subject matter provides methods for inducing and/or increasing an immune response in a subject in need thereof. The Secondary Promoter Products can be used for treating and/or preventing a cancer in a subject. The Secondary Promoter Products can be used for prolonging the survival of a subject suffering from a cancer. The Secondary Promoter Products can also be used for treating and/or preventing a cancer in a subject. The Secondary Promoter Products can also be used for reducing tumor burden in a subject. Such methods comprise administering the Secondary Promoter Products in an amount effective or a composition (e.g., a pharmaceutical composition or formulation disclosed herein) comprising thereof to achieve the desired effect, be it palliation of an existing condition or prevention of recurrence. For treatment, the amount administered is an amount effective in producing the desired effect. An effective amount can be provided in one or a series of administrations. An effective amount can be provided in a bolus or by continuous perfusion.
In certain embodiments, the Secondary Promoter Products can be used for treating viral or bacterial diseases. In certain embodiments, the Secondary Promoter Products can be used for treating autoimmune diseases.
In certain embodiments, an effective amount of the Secondary Promoter Products are delivered through intravenous (IV) administration. In certain embodiments, the Secondary Promoter Products are delivered through intravenous administration in a single administration. In certain embodiments, the Secondary Promoter Products are delivered through intravenous administration in multiple administrations. In certain embodiments, the Secondary Promoter Products are delivered through intravenous administration in two or more administrations. In certain embodiments, the Secondary Promoter Products are delivered through intravenous administration in two administrations. In certain embodiments, the Secondary Promoter Products are delivered through intravenous administration in three administrations.
The presently disclosed subject matter provides methods for treating and/or preventing cancer in a subject. In certain embodiments, the method comprises administering an effective amount of the Secondary Promoter Products to a subject having cancer.
Non-limiting examples of cancer include blood cancers (e.g. leukemias, lymphomas, and myelomas), ovarian cancer, breast cancer, bladder cancer, brain cancer, colon cancer, intestinal cancer, liver cancer, lung cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, glioblastoma, throat cancer, melanoma, neuroblastoma, adenocarcinoma, glioma, soft tissue sarcoma, and various carcinomas (including prostate and small cell lung cancer). Suitable carcinomas further include any known in the field of oncology, including, but not limited to, astrocytoma, fibrosarcoma, myxosarcoma, liposarcoma, oligodendroglioma, ependymoma, medulloblastoma, primitive neural ectodermal tumor (PNET), chondrosarcoma, osteogenic sarcoma, pancreatic ductal adenocarcinoma, small and large cell lung adenocarcinomas, chordoma, angiosarcoma, endotheliosarcoma, squamous cell carcinoma, bronchoalveolarcarcinoma, epithelial adenocarcinoma, and liver metastases thereof, lymphangiosarcoma, lymphangioendotheliosarcoma, hepatoma, cholangiocarcinoma, synovioma, mesothelioma, Ewing's tumor, rhabdomyosarcoma, colon carcinoma, basal cell carcinoma, sweat gland carcinoma, papillary carcinoma, sebaceous gland carcinoma, papillary adenocarcinoma, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, testicular tumor, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, neuroblastoma, retinoblastoma, leukemia, multiple myeloma, Waldenstrom's macroglobulinemia, and heavy chain disease, breast tumors such as ductal and lobular adenocarcinoma, squamous and adenocarcinomas of the uterine cervix, uterine and ovarian epithelial carcinomas, prostatic adenocarcinomas, transitional squamous cell carcinoma of the bladder, B and T cell lymphomas (nodular and diffuse) plasmacytoma, acute and chronic leukemias, malignant melanoma, soft tissue sarcomas and leiomyosarcomas. In certain embodiments, the neoplasia is selected from the group consisting of blood cancers (e.g. leukemias, lymphomas, and myelomas), ovarian cancer, prostate cancer, breast cancer, bladder cancer, brain cancer, colon cancer, intestinal cancer, liver cancer, lung cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, glioblastoma, and throat cancer. In certain embodiments, the presently disclosed Secondary Promoter Products comprising young T cells can be used for treating and/or preventing blood cancers (e.g., leukemias, lymphomas, and myelomas) or ovarian cancer, which are not amenable to conventional therapeutic interventions.
In certain embodiments, the neoplasia is a solid cancer or a solid tumor. In certain embodiments, the solid tumor or solid cancer is selected from the group consisting of glioblastoma, prostate adenocarcinoma, kidney papillary cell carcinoma, sarcoma, ovarian cancer, pancreatic adenocarcinoma, rectum adenocarcinoma, colon adenocarcinoma, esophageal carcinoma, uterine corpus endometrioid carcinoma, breast cancer, skin cutaneous melanoma, lung adenocarcinoma, stomach adenocarcinoma, cervical and endocervical cancer, kidney clear cell carcinoma, testicular germ cell tumors, and aggressive B-cell lymphomas.
The subjects can have an advanced form of disease, in which case the treatment objective can include mitigation or reversal of disease progression, and/or amelioration of side effects. The subjects can have a history of the condition, for which they have already been treated, in which case the therapeutic objective will typically include a decrease or delay in the risk of recurrence.
Suitable human subjects for therapy typically comprise two treatment groups that can be distinguished by clinical criteria. Subjects with “advanced disease” or “high tumor burden” are those who bear a clinically measurable tumor. A clinically measurable tumor can be detected based on tumor mass (e.g., by palpation, CAT scan, sonogram, mammogram or X-ray; positive biochemical or histopathologic markers on their own are insufficient to identify this population). A pharmaceutical composition is administered to these subjects to elicit an anti-tumor response, to palliate their condition. Ideally, reduction in tumor mass occurs as a result, but any clinical improvement constitutes a benefit. Clinical improvement includes decreased risk or rate of progression or reduction in pathological consequences of the tumor.
The Secondary Promoter Products can be used in combination with articles of manufacture. Such articles of manufacture can be useful for the prevention or treatment of proliferative disorders (e.g., cancer). Examples of articles of manufacture include but are not limited to containers (e.g., infusion bags, bottles, storage containers, flasks, vials, syringes, tubes, and IV solution bags) and a label or package insert on or associated with the container. The containers may be made of any material that is acceptable for the storage and preservation of the Secondary Promoter Cells within the Secondary Promoter Products. In certain embodiments, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle. For example, the container may be a CryoMACS freezing bag. The label or package insert indicates that the Secondary Promoter Products are used for treating the condition of choice and the patient of origin. The patient is identified on the container of the Secondary Promoter Product because the Secondary Promoter Products is made from autologous cells and engineered as a patient-specific and individualized treatment.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; and 2) a second container with the same Secondary Promoter Product as the first container contained therein. Optionally, additional containers with the same Secondary Promoter Product as the first and second containers can be prepared and made. Optionally, additional containers containing a composition comprising a different cytotoxic or otherwise therapeutic agent may also be combined with the containers described above.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; and 2) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In certain embodiments, the article of manufacture can comprise: 1) a first container with two Secondary Promoter Products contained therein; and 2) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; and 3) optionally a third container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. In certain embodiments, the first and second Secondary Promoter Products are different Secondary Promoter Products. In certain embodiments, the first and second Secondary Promoter Products are the same Secondary Promoter Products.
In certain embodiments, the article of manufacture can comprise: 1) a first container with three Secondary Promoter Products contained therein; and 2) optionally a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein; and 4) optionally a fourth container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. In certain embodiments, the first, second, and third Secondary Promoter Products are different Secondary Promoter Products. In certain embodiments, the first, second, and third Secondary Promoter Products are the same Secondary Promoter Products. In certain embodiments, two of the first, second, and third Secondary Promoter Products are the same Secondary Promoter Products.
In certain embodiments, the article of manufacture can comprise: 1) a first container with four Secondary Promoter Products contained therein; and 2) optionally a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein; 4) a fourth container with a fourth Secondary Promoter Product contained therein; and 5) optionally a fifth container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. In certain embodiments, the first, second, third, and fourth Secondary Promoter Products are different Secondary Promoter Products. In certain embodiments, the first, second, third, and fourth Secondary Promoter Products are the same NeoTCR Products. In certain embodiments, two of the first, second, third, and fourth Secondary Promoter Products are the same NeoTCR Products. In certain embodiments, three of the first, second, third, and fourth Secondary Promoter Products are the same Secondary Promoter Products.
In certain embodiments, the article of manufacture can comprise: 1) a first container with five or more Secondary Promoter Products contained therein; and 2) optionally a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein; 4) a fourth container with a fourth Secondary Promoter Product contained therein; 5) a fifth container with a fifth Secondary Promoter Product contained therein; 6) optionally a sixth or more additional container with a sixth or more Secondary Promoter Product contained therein; and 7) optionally an additional container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. In certain embodiments, all of the containers of Secondary Promoter Products are different Secondary Promoter Products. In certain embodiments, all of the containers of Secondary Promoter Products are the same Secondary Promoter Products. In certain embodiments, there can be any combination of same or different Secondary Promoter Products in the five or more containers based on the availability of detectable Secondary Promoters in a patient's tumor sample(s), the need and/or desire to have multiple Secondary Promoter Products for the patient, and the availability of any Secondary Promoter Product that may require or benefit from one or more container.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein; 4) optionally a fourth container with a fourth Secondary Promoter Product contained therein.
In certain embodiments, the article of manufacture can comprise: 1) a first container with a Secondary Promoter Product contained therein; 2) a second container with a second Secondary Promoter Product contained therein; 3) a third container with a third Secondary Promoter Product contained therein; 4) a fourth container with a fourth Secondary Promoter Product contained therein; 5) optionally a fifth container with a fourth Secondary Promoter Product contained therein.
In certain embodiments, the article of manufacture can comprise a container with one Secondary Promoter Product contained therein. The article of manufacture may comprise a container with two Secondary Promoter Products contained therein. The article of manufacture can comprise a container with three Secondary Promoter Products contained therein. The article of manufacture can comprise a container with four Secondary Promoter Products contained therein. The article of manufacture can comprise a container with five Secondary Promoter Products contained therein.
In certain embodiments, the article of manufacture can comprise 1) a first container with one Secondary Promoter Product contained therein, and 2) a second container with two Secondary Promoter Products contained therein. In certain embodiments, the article of manufacture can comprise 1) a first container with two Secondary Promoter Products contained therein, and 2) a second container with one Secondary Promoter Product contained therein. In the examples above, a third and/or fourth container comprising one or more additional Secondary Promoter Products may be included in the article of manufacture. Additionally, a fifth container comprising one or more additional Secondary Promoter Products may be included in the article of manufacture.
Furthermore, any container of Secondary Promoter Product described herein can be split into two, three, or four separate containers for multiple time points of administration and/or based on the appropriate dose for the patient.
In certain embodiments, the Secondary Promoter Products are provided in a kit. The kit can, by means of non-limiting examples, contain package insert(s), labels, instructions for using the Secondary Promoter Product(s), syringes, disposal instructions, administration instructions, tubing, needles, and anything else a clinician would need in order to properly administer the Secondary Promoter Product(s).
As described herein, plasmid DNA-mediated precision genome engineering process for Good Manufacturing Practice (GMP) manufacturing of Secondary Promoter Products was developed. Targeted integration of the patient-specific NeoTCR was accomplished by electroporating CRISPR endonuclease ribonucleoproteins (RNPs) together with the personalized NeoTCR gene cassette, encoded by the plasmid DNA. In addition to the NeoTCR, the Secondary Promoter Constructs were inserted by incorporating them into the NeoTCR vector and then electroporating with CRISPR endonuclease ribonucleoproteins (RNPs) as described above.
In certain embodiments, the Secondary Promoter Products can be formulated into a drug product using the clinical manufacturing process. Under this process, the Secondary Promoter Products are cryopreserved in CryoMACS Freezing Bags. One or more bags may be shipped to the site for each patient depending on patient needs. In certain embodiments, the product is composed of apheresis-derived, patient-autologous, and CD4/CD8 T cells that have been precision genome engineered to express one or more autologous NeoTCRs targeting a neoepitope (e.g., against a private neoantigen) complexed to one of the endogenous HLA receptors presented exclusively on the surface of that patient's tumor cells and a Payload. In certain embodiments, the cell includes a Secondary Promoter Construct disclosed herein.
In certain embodiments, the final product contains about 5% dimethyl sulfoxide (DMSO), human serum albumin, and Plasma-Lyte. In certain embodiments, the final cell product contains the list of components provided in Table 1.
The presently disclosed subject matter provides kits for inducing and/or enhancing immune response and/or treating and/or preventing cancer or a pathogen infection in a subject. In certain embodiments, the kit comprises an effective amount of presently disclosed cells (e.g. Secondary Promoter Cells) or a pharmaceutical composition comprising thereof (e.g., Secondary Promoter Products). In certain embodiments, the kit comprises a sterile container; such containers can be boxes, ampules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments. In certain non-limiting embodiments, the kit includes an isolated nucleic acid molecule encoding a presently disclosed HR template.
If desired, the cells and/or nucleic acid molecules are provided together with instructions for administering the cells or nucleic acid molecules to a subject having or at risk of developing cancer or pathogen, or immune disorder. The instructions generally include information about the use of the composition for the treatment and/or prevention of cancer or a pathogen infection. In certain embodiments, the instructions include at least one of the following: description of the therapeutic agent; dosage schedule and administration for treatment or prevention of a neoplasia, pathogen infection, or immune disorder or symptoms thereof, precautions; warnings; indications; counter-indications; over-dosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container. The resulting cells can be grown under conditions similar to those for unmodified cells, whereby the modified cells can be expanded and used for a variety of purposes.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an exogenous enhancer, an insulator, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an exogenous enhancer, a pause element, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an insulator, a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising an insulator, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR is under control of an endogenous promoter and the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR, a first sequence encoding a Payload, and a second sequence encoding a Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell, wherein the sequence encoding an exogenous TCR and the first sequence encoding a Payload are under control of an endogenous promoter and the second sequence encoding a Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a cell comprising an exogenous polynucleotide comprising a sequence encoding an exogenous TCR and a sequence encoding at least one Payload, wherein the exogenous polynucleotide is integrated at an endogenous locus within the genome of the cell and is under control of an endogenous promoter.
In certain embodiments of the cells disclosed herein, the insulator is an HS4 insulator or an IS2 insulator. In certain embodiments of the cells disclosed herein, the insulator comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19. In certain embodiments of the cells disclosed herein, the insulator comprises the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19.
In certain embodiments of the cells disclosed herein, the WPRE comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments of the cells disclosed herein, the WPRE comprises the nucleotide sequence set forth in SEQ ID NO: 20.
In certain embodiments of the cells disclosed herein, the exogenous enhancer is a CMV enhancer, a TCRα enhancer, or a TCRβ enhancer. In certain embodiments of the cells disclosed herein, the exogenous enhancer is a TCRα enhancer. In certain embodiments of the cells disclosed herein, the TCRα enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments of the cells disclosed herein, the TCRα enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments of the cells disclosed herein, the exogenous enhancer is a CMV enhancer. In certain embodiments of the cells disclosed herein, the CMV enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 33. In certain embodiments of the cells disclosed herein, the CMV enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 33.
In certain embodiments of the cells disclosed herein, the exogenous promoter is a constitutive promoter. In certain embodiments of the cells disclosed herein, the constitutive promoter is an MDN promoter, an EF1α promoter, an ACTB promoter, a PGK promoter, or a U6 promoter. In certain embodiments of the cells disclosed herein, the constitutive promoter is an MDN promoter. In certain embodiments of the cells disclosed herein, the constitutive promoter is an EF1α promoter. In certain embodiments of the cells disclosed herein, the exogenous promoter is an inducible promoter. In certain embodiments of the cells disclosed herein, the inducible promoter is an AP1 promoter, an NFAT promoter, an NF-κB promoter, or an NR4A-responsive promoter.
In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence or a TCRβ gene sequence. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence and a TCRβ gene sequence. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR further comprises a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence, a TCRβ gene sequence, a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof.
In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, and a TCRα gene sequence. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRα gene sequence, and a poly-adenylation sequence. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRα gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRβ gene sequence, and a poly-adenylation sequence.
In certain embodiments of the cells disclosed herein, the at least one Payload is selected from the group consisting of a cytokine receptors trap, a ligand trap, an angiogenesis factor, an apoptotic factor, an inhibitory protein, an extracellular matrix modulator, a soluble TCR, a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, a protein that binds to receptors and sterically hinders receptor function, and an inhibitory RNA molecule.
In certain embodiments of the cells disclosed herein, the 3′ of the at least one Payload comprises a STOP codon. In certain embodiments of the cells disclosed herein, the 3′ of the at least one Payload comprises a sequence encoding a 2A peptide and a sequence encoding a protease cleavage peptide. In certain embodiments of the cells disclosed herein, the 3′ of the at least one Payload comprises a poly-adenylation sequence.
In certain embodiments of the cells disclosed herein, the at least one Payload is an inhibitory RNA molecule. In certain embodiments of the cells disclosed herein, the inhibitory RNA molecule is a shRNA, a miRNA, or a miRNA cluster. In certain embodiments of the cells disclosed herein, the inhibitory RNA molecule is a miRNA. In certain embodiments of the cells disclosed herein, the miRNA comprises a first flanking sequence and a second flanking sequence. In certain embodiments of the cells disclosed herein, the first flanking sequence and the second flanking sequence are derived from miR-155, miR-30, miR-17/92, miR-122, or miR-21. In certain embodiments of the cells disclosed herein, the inhibitory RNA molecule is flanked by a splice donor site or a splice acceptor site. In certain embodiments of the cells disclosed herein, the inhibitory RNA molecule is flanked by a splice donor site and a splice acceptor site.
In certain embodiments of the cells disclosed herein, the sequences encoding a P2A peptide are codon diverged. In certain embodiments of the cells disclosed herein, the sequences encoding a protease cleavage peptide are codon diverged. In certain embodiments of the cells disclosed herein, the sequences encoding a signal sequence are codon diverged.
In certain embodiments of the cells disclosed herein, the exogenous TCR recognizes a cancer neoantigen. In certain embodiments of the cells disclosed herein, the neoantigen is a private neoantigen. In certain embodiments of the cells disclosed herein, the sequence encoding an exogenous TCR is obtained from a subject.
In certain embodiments of the cells disclosed herein, the cell is a primary cell. In certain embodiments of the cells disclosed herein, the cell is a patient-derived cell. In certain embodiments of the cells disclosed herein, the cell is a lymphocyte. In certain embodiments of the cells disclosed herein, the cell is a T cell. In certain embodiments of the cells disclosed herein, the cell is a young T cell. In certain embodiments of the cells disclosed herein, the cell is CD45RA+, CD62L+, CD28+, CD95−, CCR7+, and CD27+. In certain embodiments of the cells disclosed herein, the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+. In certain embodiments of the cells disclosed herein, the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
In certain embodiments of the cells disclosed herein, the endogenous locus within the genome of the cell is a TCR locus. In certain embodiments of the cells disclosed herein, the TCR locus is a TRAC locus or a TRBC locus. In certain embodiments of the cells disclosed herein, the TCR locus is a TRAC locus and a TRBC locus. In certain embodiments of the cells disclosed herein, the endogenous promoter is a TRAC promoter. In certain embodiments of the cells disclosed herein, the endogenous promoter is a TRBC promoter.
In certain embodiments of the cells disclosed herein, the cell, the sequence encoding an exogenous TCR, and the sequence of the neoantigen are obtained from the same subject.
In certain embodiments of the polynucleotides disclosed herein, the present disclosure provides a polynucleotide comprising an exogenous enhancer, an insulator, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an exogenous enhancer, a pause element, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an insulator, a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising an insulator, a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the sequence encoding at least one Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a first homology arm, a second homology arm, a sequence encoding an exogenous TCR, a first sequence encoding a Payload, and a second sequence encoding a Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus and wherein the second sequence encoding a Payload is under control of an exogenous promoter.
In certain embodiments, the present disclosure provides a polynucleotide comprising a sequence encoding a first homology arm, a second homology arm, an exogenous TCR, and a sequence encoding at least one Payload, wherein the first and second homology arms are homologous to a TRAC or TRBC locus.
In certain embodiments of the polynucleotides disclosed herein, the insulator is an HS4 insulator or an IS2 insulator. In certain embodiments of the polynucleotides disclosed herein, the insulator comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 19. In certain embodiments of the polynucleotides disclosed herein, the insulator comprises the nucleotide sequence set forth in SEQ ID NO: 18 or SEQ ID NO: 18. In certain embodiments of the polynucleotides disclosed herein, the WPRE comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 20. In certain embodiments of the polynucleotides disclosed herein, the WPRE comprises the nucleotide sequence set forth in SEQ ID NO: 20.
In certain embodiments of the polynucleotides disclosed herein, the exogenous enhancer is a CMV enhancer, a TCRα enhancer, or a TCRβ enhancer. In certain embodiments of the polynucleotides disclosed herein, the exogenous enhancer is a TCRα enhancer. In certain embodiments of the polynucleotides disclosed herein, the TCRα enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments of the polynucleotides disclosed herein, the TCRα enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 32. In certain embodiments of the polynucleotides disclosed herein, the exogenous enhancer is a CMV enhancer. In certain embodiments of the polynucleotides disclosed herein, the CMV enhancer comprises a nucleotide sequence that is at least about 80% identical to the nucleotide sequence set forth in SEQ ID NO: 33. In certain embodiments of the polynucleotides disclosed herein, the CMV enhancer comprises the nucleotide sequence set forth in SEQ ID NO: 33.
In certain embodiments of the polynucleotides disclosed herein, the exogenous promoter is a constitutive promoter. In certain embodiments of the polynucleotides disclosed herein, the constitutive promoter is an MDN promoter, an EF1α promoter, an ACTB promoter, a PGK promoter, or a U6 promoter. In certain embodiments of the polynucleotides disclosed herein, the constitutive promoter is an MDN promoter. In certain embodiments of the polynucleotides disclosed herein, the constitutive promoter is an EF1α promoter. In certain embodiments of the polynucleotides disclosed herein, the exogenous promoter is an inducible promoter. In certain embodiments of the polynucleotides disclosed herein, the inducible promoter is an AP1 promoter, an NFAT promoter, an NF-κB promoter, or an NR4A-responsive promoter.
In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence or a TCRβ gene sequence. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence and a TCRβ gene sequence. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR further comprises a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises a TCRα gene sequence, a TCRβ gene sequence, a sequence encoding a P2A peptide, a sequence encoding a signal sequence, a sequence encoding a protease cleavage peptide, or a combination thereof.
In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, and a TCRα gene sequence. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRβ gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRα gene sequence, and a poly-adenylation sequence. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR comprises, from 5′ end to 3′ end, a first sequence encoding a P2A peptide, a first sequence encoding a signal sequence, a TCRα gene sequence, a sequence encoding a protease cleavage peptide, a second sequence encoding a P2A peptide, a second sequence encoding a signal sequence, a TCRβ gene sequence, and a poly-adenylation sequence. In certain embodiments of the polynucleotides disclosed herein, the at least one Payload is selected from the group consisting of a cytokine receptors trap, a ligand trap, an angiogenesis factor, an apoptotic factor, an inhibitory protein, an extracellular matrix modulator, a soluble TCR, a homing signal, an enzyme, a modulator of reactive oxygen species, a competitive ligand inhibitor, a protein that binds to receptors and sterically hinders receptor function, and an inhibitory RNA molecule.
In certain embodiments of the polynucleotides disclosed herein, the 3′ of the at least one Payload comprises a STOP codon. In certain embodiments of the polynucleotides disclosed herein, the 3′ of the at least one Payload comprises a sequence encoding a 2A peptide and a sequence encoding a protease cleavage peptide. In certain embodiments of the polynucleotides disclosed herein, the 3′ of the at least one Payload comprises a poly-adenylation sequence.
In certain embodiments of the polynucleotides disclosed herein, the at least one Payload is an inhibitory RNA molecule. In certain embodiments of the polynucleotides disclosed herein, the inhibitory RNA molecule is a shRNA, a miRNA, or a miRNA cluster. In certain embodiments of the polynucleotides disclosed herein, the inhibitory RNA molecule is a miRNA. In certain embodiments of the polynucleotides disclosed herein, the miRNA comprises a first flanking sequence and a second flanking sequence. In certain embodiments of the polynucleotides disclosed herein, the first flanking sequence and the second flanking sequence are derived from miR-155, miR-30, miR-17/92, miR-122, or miR-21. In certain embodiments of the polynucleotides disclosed herein, the inhibitory RNA molecule is flanked by a splice donor site or a splice acceptor site. In certain embodiments of the polynucleotides disclosed herein, the inhibitory RNA molecule is flanked by a splice donor site and a splice acceptor site.
In certain embodiments of the polynucleotides disclosed herein, the sequences encoding a P2A peptide are codon diverged. In certain embodiments of the polynucleotides disclosed herein, the sequences encoding a protease cleavage peptide are codon diverged. In certain embodiments of the polynucleotides disclosed herein, the sequences encoding a signal sequence are codon diverged. In certain embodiments of the polynucleotides disclosed herein, the exogenous TCR recognizes a cancer neoantigen. In certain embodiments of the polynucleotides disclosed herein, the neoantigen is a private neoantigen. In certain embodiments of the polynucleotides disclosed herein, the sequence encoding an exogenous TCR is obtained from a single subject.
In certain embodiments of the polynucleotides disclosed herein, the polynucleotide is a circular polynucleotide. In certain embodiments of the polynucleotides disclosed herein, the circular polynucleotide is a plasmid or a nanoplasmid. In certain embodiments of the polynucleotides disclosed herein, the polynucleotide is a linear polynucleotide.
In certain embodiments, the present disclosure further provides a vector comprising any one of the polynucleotide disclosed herein. In certain embodiments of the vectors disclosed herein, the vector is a non-viral vector. In certain embodiments, the present disclosure provides a cell comprising any one of the polynucleotides or vectors disclosed herein.
In certain embodiments, the present disclosure provides a method of modifying a cell. In certain embodiments of the methods disclosed herein, the method comprises introducing into the cell any one of the polynucleotides or vectors disclosed herein. In certain embodiments of the methods disclosed herein, the method further comprises recombining the polynucleotide or vector into an endogenous locus of the cell.
In certain embodiments of the methods disclosed herein, the introducing occurs via electroporation. In certain embodiments of the methods disclosed herein, the recombining comprises cleavage of the endogenous locus by a nuclease. In certain embodiments of the methods disclosed herein, the recombining further comprises recombination of the polynucleotide into the endogenous locus by homology-directed repair.
In certain embodiments of the methods disclosed herein, the nuclease is a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) family nuclease, or a functional fragment thereof. In certain embodiments of the methods disclosed herein, the nuclease further comprises a gRNA.
In certain embodiments of the methods disclosed herein, the method further comprises culturing the cell in the presence of at least one cytokine. In certain embodiments of the methods disclosed herein, the at least one cytokine comprises IL2, IL7, IL15, or a combination thereof. In certain embodiments of the methods disclosed herein, the at least one cytokine comprises IL7 and IL15.
In certain embodiments of the methods disclosed herein, the cell is a primary cell. In certain embodiments of the methods disclosed herein, the cell is a patient-derived cell. In certain embodiments of the methods disclosed herein, the cell is a lymphocyte. In certain embodiments of the methods disclosed herein, the cell is a T cell. In certain embodiments of the methods disclosed herein, the cell is a young T cell. In certain embodiments of the methods disclosed herein, the cell is CD45RA+, CD62L+, CD28+, CD95−, CCR7+, and CD27+. In certain embodiments of the methods disclosed herein, the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+. In certain embodiments of the methods disclosed herein, the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
In certain embodiments, the present disclosure also provides a cell modified by any one of the methods disclosed herein.
In certain embodiments, the present disclosure provides a composition comprising an effective amount of the any one of the cells disclosed herein. In certain embodiments of the compositions disclosed herein, the composition is a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient. In certain embodiments of the compositions disclosed herein, the composition is administered to a patient in need thereof for the treatment of cancer. In certain embodiments of the compositions disclosed herein, the composition comprises a cryopreservation agent. In certain embodiments of the compositions disclosed herein, the composition comprises serum albumin. In certain embodiments of the compositions disclosed herein, the composition comprises Plasma-Lyte A, HSA, and CryoStor CS10.
In certain embodiments, the present disclosure provides methods of treating cancer in a subject in need thereof. In certain embodiments of the methods disclosed herein, the method comprises administering a therapeutically effective amount of any one of the cells disclosed herein. In certain embodiments of the methods disclosed herein, the method comprises administering a therapeutically effective amount of any one of the compositions disclosed herein. In certain embodiments of the methods disclosed herein, prior to administering, a non-myeloablative lymphodepletion regimen is administered to the subject.
In certain embodiments of the methods disclosed herein, the cancer is a solid tumor or a liquid tumor. In certain embodiments of the methods disclosed herein, the solid tumor is selected from the group consisting of melanoma, thoracic cancer, lung cancer, ovarian cancer, breast cancer, pancreatic cancer, head and neck cancer, prostate cancer, gynecological cancer, central nervous system cancer, cutaneous cancer, HPV+ cancer, esophageal cancer, thyroid cancer, gastric cancer, hepatocellular cancer, cholangiocarcinomas, renal cell cancers, testicular cancer, sarcomas, and colorectal cancer. In certain embodiments of the methods disclosed herein, the liquid tumor is selected from the group consisting of follicular lymphoma, leukemia, and multiple myeloma.
In certain embodiments, the present disclosure provides a kit comprising any one of the cells, the polynucleotides, the vectors, or the compositions disclosed herein. In certain embodiments of the kits disclosed herein, the kit further comprises written instructions for treating cancer.
In certain embodiments, the present disclosure provides a method of modifying a cell. In certain embodiments of the methods disclosed herein, the method comprises introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises a Secondary Promoter Construct, and recombining the HR template nucleic acid into an endogenous locus of the cell. In certain embodiments of the methods disclosed herein, the Secondary Promoter Construct comprises Format 1, 2, or 3. In certain embodiments of the methods disclosed herein, the Secondary Promoter Construct comprises Format 4.
In certain embodiments, the present disclosure provides a cell modified by any of the methods disclosed herein. In certain embodiments, the present disclosure provides a composition comprising a Secondary Cell Product made according to any of the methods disclosed herein. In certain embodiments of the compositions disclosed herein, the composition is a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient. In certain embodiments of the compositions disclosed herein, the composition is administered to a patient in need thereof for the treatment of cancer.
In certain embodiments, the present disclosure provides a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of any one of the cells or compositions disclosed herein. In certain embodiments of the methods disclosed herein, prior to administering, a non-myeloablative lymphodepletion regimen is administered to the subject. In certain embodiments of the methods disclosed herein, the cancer is a solid tumor. In certain embodiments of the methods disclosed herein, the cancer is liquid tumor. In certain embodiments of the methods disclosed herein, the solid tumor is selected from the group consisting of melanoma, thoracic cancer, lung cancer, ovarian cancer, breast cancer, pancreatic cancer, head and neck cancer, prostate cancer, gynecological cancer, central nervous system cancer, cutaneous cancer, HPV+ cancer, esophageal cancer, thyroid cancer, gastric cancer, hepatocellular cancer, cholangiocarcinomas, renal cell cancers, testicular cancer, sarcomas, and colorectal cancer. In certain embodiments of the methods disclosed herein, the liquid tumor is selected from the group consisting of follicular lymphoma, leukemia, and multiple myeloma.
In certain embodiments, the present disclosure provides a composition or a method of any of the embodiments described herein.
The following are examples of methods and compositions of the invention. It is understood that various other embodiments may be practiced, given the general description provided above.
Neoepitope-specific TCRs identified by the imPACT Isolation Technology described in PCT/US2020/17887 (which is herein incorporated by reference in its entirety) were used to generate homologous recombination (HR) DNA templates. These HR templates were transfected into primary human T cells in tandem with site-specific nucleases (see
The precision of NeoTCR-T cell genome engineering was evaluated by Targeted Locus Amplification (TLA) for off-target integration hot spots or translocations, and by next-generation sequencing based off-target cleavage assays and found to lack evidence of unintended outcomes.
As shown in
It was determined that P2A peptides were superior to other 2A peptides for Cell Products because of their efficient cleavage. Accordingly, two (2) P2A peptides and codon divergence were used to express the gene of interest without introducing any exogenous epitopes from the remaining amino acids on either end of the gene of interest from the P2A peptide. The benefit of the gene-edited cell having no exogenous epitopes (i.e., no flanking P2A peptide amino acids on either side of the gene of interest) is that immunogenicity is drastically decreased and there is less likelihood of a patient infused with a Cell Product containing the gene-edited cell to have an immune reaction against the gene-edited cell.
As described in PCT/US/2018/058230, NeoTCRs were integrated into the TCRα locus of T cells. Specifically, a homologous repair template containing a NeoTCR coding sequence flanked by left and right HR Arms was used. In addition, the endogenous TCRβ locus was disrupted leading to the expression of only TCR sequences encoded by the NeoTCR construct. The general strategy was applied using circular HR templates as well as linear templates.
The target TCRα locus (Ca) is shown along with the plasmid HR template, and the resulting edited sequence and downstream mRNA/protein products in
Once integrated into the genome (
Additionally, three repeated protein sequences are codon diverged within the HR template to promote genomic stability. The two P2A are codon diverged relative to each other, as well as the two HGH signal sequences relative to each other, within the TCR gene cassette to promote stability of the introduced NeoTCR cassette sequences within the genome of the ex vivo engineered T cells. Similarly, the re-introduced 5′ end of TRAC exon 1 (vertical stripe) reduces the likelihood of the entire cassette being lost over time through the removal of an intervening sequence of two direct repeats.
In addition to NeoTCR Products, this method can be used for any Secondary Promoter Product.
In-Out PCR was used to confirm the precise target integration of the NeoE TCR cassette. Agarose gels show the results of a PCR using primers specific to the integration cassette and site generate products of the expected size only for cells treated with both nuclease and DNA template (KOKI and KOKIKO), demonstrating site-specific and precise integration.
Furthermore, Targeted Locus Amplification (TLA) was used to confirm the specificity of targeted integration. Crosslinking, ligation, and use of primers specific to the NeoTCR insert were used to obtain sequences around the site(s) of integration. The reads mapped to the genome are binned in 10 kb intervals. Significant read depths were obtained only around the intended site the integration site on chromosome 14, showing no evidence of common off-target insertion sites.
Antibody staining for endogenous TCR and peptide-HLA staining for NeoTCR revealed that the engineering results in high frequency knock-in of the NeoTCR, with some TCR-cells and few WT T cells remaining. Knock-in is evidenced by NeoTCR expression in the absence of an exogenous promoter. Engineering was carried out multiple times using the same NeoTCR with similar results. Therefore, efficient and consistent expression of the NeoTCR and knockout of the endogenous TCR in engineered T cells was achieved.
Format 1. Format 1 of the modular Secondary Promoter Constructs is exemplified in
The 2A sequences of Format 1 can be two P2As, one P2A, and one T2A, or two T2As. However, the preferred format used to design the construct and make mCherry Payload Secondary Promoters and resulting Secondary Promoter Cells and Products used two P2As.
In Format 1, each of the 2A sequences is preceded by a GSG linker or functionally equivalent linker and the Secondary Promoter region may be followed by a Kozak sequence.
As shown in
As shown in
Furthermore,
Format 2. Format 2 of the modular Secondary Promoter Constructs is exemplified in
The 2A sequences of Format 2 can be two P2As, one P2A, and one T2A, or two T2As. However, the preferred format used to design the construct and make mCherry Payload Secondary Promoters and resulting Secondary Promoter Cells and Products used two P2As.
In Format 2, each of the 2A sequences is preceded by a GSG linker or functionally equivalent linker and the Secondary Promoter region may be followed by a Kozak sequence.
As shown in
As shown in
Furthermore,
Format 3. Format 3 of the modular Secondary Promoter Constructs is exemplified in
The 2A sequences of Format 3 can be two P2As, one P2A, and one T2A, or two T2As. However, the preferred format used to design the construct and make mCherry Payload Secondary Promoters and resulting Secondary Promoter Cells and Products used two P2As.
In Format 3, each of the 2A sequences is preceded by a GSG linker or functionally equivalent linker and the Secondary Promoter region may be followed by a Kozak sequence.
As shown in
As shown in
T cell Isolation and Editing. CD4 and CD8 T cells were isolated from healthy donor PBMCs using the Miltenyi Prodigy or Miltenyi MACS separation columns according to the manufacturers' instructions. Positively-selected CD4 and CD8 T cells were used fresh or cryopreserved in 1% human serum albumin (Gemini), 49% Plasmalyte (Baxter), and 50% CS10 (Sigma). Cryopreserved cells were thawed, washed in media, and seeded at a density of 2×106 cells per mL culture medium. One day after thaw, or immediately if used fresh, the cells were washed and re-seeded at a density of 1.46×106 cells per mL in culture medium+12.5 ng/mL IL7+12.5 ng/mL IL15+a T cell activation reagent by volume. Two days after activation, T cells were electroporated with a plasmid (containing a Secondary Promoter Construct) for the production of Secondary Promoter Cells and a Secondary Promoter Product. T cells were electroporated expanded in culture medium supplemented with 12.5 ng/mL IL7+12.5 ng/mL IL15. Supplemented medium was exchanged every 2-3 days or as needed until the end of the study, 13 days after activation.
comPACT and comPACT-Dextramer preparation. Neoantigen-specific peptide-HLA complex polypeptides (each a “comPACT”) were prepared according to the method as described in PCT/US2019/025415, hereby incorporated by reference in its entirety. A comPACT-dextramer complex was made for the labeling of NeoTCR expressing T cells. Biotinylated comPACT protein was incubated with a streptavidin-conjugated fluorophore for 10 min at room temperature (RT). Biotin-40-dextran (NANOCS) was added to the mixture and incubated at RT for an additional 10 minutes. The comPACT-Dextramer was stored at 4° C.
Confirmation of comPACT binding to NeoTCR edited T cells. T cells were stained for flow cytometry. Cells were first stained with viability dye for 20 minutes at 4° C., then washed and stained with the comPACT-dextramer for 10 minutes at 4° C. Surface antibodies (anti-CD8a, anti-CD80, anti-CD4) were added to the suspension of cells and comPACT-dextramer, and the cells are incubated for an additional 20 minutes at 4° C. Cells were then washed and fixed in intracellular fixation buffer (BD Biosciences). All cells were acquired on an Attune NxT Flow Cytometer (ThermoFisher Scientific) and data were analyzed with either FCS Express or FlowJo.
Cytometric Bead Array (CBA). Streptavidin-coated plates (Eagle Biosciences) were washed 3 times with wash buffer (PBS supplemented with 1% BSA and 0.05% tween20) and then coated with comPACTs at different concentrations ranging from 100-0.01 ng/well. Wells with no comPACT and wells coated with mismatched comPACT were used as controls. The plates were incubated for 2 hr at room temperature, washed three times with wash buffer, and then washed three times with TexMACS supplemented with 3% human AB serum to remove the tween20. T cells were given two washes with TexMACS supplemented with 3% human AB serum and resuspended at 1 million cells/mL in TexMACS supplemented with 3% human AB serum and 1×penicillin-streptomycin solution. T cells were plated onto the comPACT coated plate at 100 μL/well and incubated at 37° C., 5% CO2. After 24 h the supernatant was collected, and the cytokine concentrations were analyzed using the BD Cytometric Bead Array (CBA) Human Th1/Th2 Cytokine Kit II (Catalog No. 551809) following the manufacturer's protocol. Capture beads were mixed with culture supernatant, incubated with the detection reagent for 3 hr at RT protected from light, washed, and resuspended in wash buffer. Samples were assayed on an Attune NxT Flow Cytometer and data analyzed with FlowJo. The EC50 represents the concentration of cognate comPACT that elicits 50% of the maximum response and is calculated utilizing a least-squares fit of IFNγ secretion over a range of comPACT concentrations.
Intracellular Staining. T cells were stained for flow cytometry on the indicated days. T cells are first stained with viability dye for 20 minutes at 4° C., then washed and incubated with surface antibodies (anti-CD8α, anti-CD8β, anti-CD4) for an additional 20 minutes at 4° C. T cells are then washed and permeabilized for intracellular staining. T cells are stained with anti-2A peptide or with anti-IFNγ, anti-TNF, or anti-IL2 in permeabilization buffer for 20 minutes at 4° C. T cells are fixed in intracellular fixation buffer (BD Biosciences). Samples are assayed on an Attune NxT Flow Cytometer (ThermoFisher Scientific) and data analyzed with either FCS Express or FlowJo.
T cell Proliferation Assay. Edited CD4 and CD8 T cells are labeled with the e450 proliferation dye (eBioscience) according to the manufacturer's instructions. Labeled cells were stimulated on comPACT coated plates with a range of concentrations as described above. T cells were harvested over 48-96 hours and analyzed for proliferation as measured by dilution of the e450 dye.
T cell Killing Assay. HLA-matched cell lines were pulsed with the cognate neoantigen peptide or mismatched peptide for 1 h at 37° C., 5% C02. The cells were washed 3 times with media to remove any unbound peptide and then co-cultured with edited CD4 and CD8 T cells that are labeled with the e450 proliferation dye described above. Co-cultures were incubated for 48 h at 37° C. with 5% C02 before harvest. Cells were washed and stained with a fixable viability dye to determine killing efficiency. The e450 proliferation dye was used to distinguish edited T cells from target cells.
The present example provides several Secondary Promoter Constructs in order to decouple the expression of exogenous TCRs (e.g., NeoTCR) from the expression of a secondary Payload. It was observed that the introduction of a second promoter to express a Payload (i.e., a Secondary Promoter Construct) had a negative impact on the expression of the exogenous TCR (see
Based on the observations from Example 4, several Secondary Promoter Constructs were designed in order to decouple the expression of the NeoTCR from the Payload. The used constructs are depicted in
The “base construct” encodes for a T cell receptor and includes a left homology arm, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, and a right homology arm.
The “original MND” Secondary Promoter Construct encodes for a T cell receptor and a Payload and includes a left homology arm, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, an insulator, an MND promoter, a Payload, a STOP codon, and a right homology arm. The original MND Secondary Promoter Construct encoding mCherry as Payload is also identified as “TCR-HS4-MND>mCherry-STOP.”
The “second generation MND” Secondary Promoter Construct encodes for a T cell receptor and a Payload and includes a left homology arm, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, an MND promoter, a Payload, a sequence encoding a second Furin cleavage sequence, a sequence encoding a third GSG linker, a sequence encoding a third P2A sequence, and a right homology arm. The second-generation MND Secondary Promoter Construct encoding mCherry as Payload is also identified as “TCR-MND>mCherry-2A.”
The “alternative MND” Secondary Promoter Construct encodes for a T cell receptor and a Payload and includes a left homology arm, a TCR gene enhancer, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a poly-adenylation sequence, a pause element, an MND promoter, a Payload, a sequence encoding a second Furin cleavage sequence, a sequence encoding a third GSG linker, a sequence encoding a third P2A sequence, and a right homology arm. The alternative MND Secondary Promoter Construct encoding mCherry as Payload is also identified as “3E-TCR-HS4-MND>mCherry-2A.”
The “original EF-1α” Secondary Promoter Construct encodes for a T cell receptor and a Payload and includes a left homology arm, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, an insulator, an EF-1α promoter, a Payload, a STOP codon, and a right homology arm. The original EF-1α Secondary Promoter Construct encoding mCherry as Payload is also identified as “TCR-HS4-cEF1α>mCherry-STOP.”
The “second generation EF-1α” Secondary Promoter Construct encodes for a T cell receptor and a Payload and includes a left homology arm, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, an EF-1α promoter, a Payload, a sequence encoding a second Furin cleavage sequence, a sequence encoding a third GSG linker, a sequence encoding a third P2A sequence, and a right homology arm. The second generation EF-1α Secondary Promoter Construct encoding mCherry as Payload is also identified as “TCR-cEF1α>mCherry-2A.”
Alternatively, the second generation EF-1α Secondary Promoter Construct includes a left homology arm, a TCRα gene enhancer, a sequence encoding a GSG linker, a sequence encoding a P2A sequence, a sequence encoding an HGH signal sequence, a full length TCRβ gene sequence, a sequence encoding a Furin cleavage sequence, a sequence encoding a second GSG linker, a sequence encoding a second P2A sequence, a full length TCRα gene sequence, a polyadenylation sequence, an insulator, an EF-1α promoter, a Payload, a STOP codon, and a right homology arm. The second generation EF-1α Secondary Promoter Construct encoding mCherry as Payload and including enhancer and insulator is also identified as “3E-TCR-HS4-cEF1α>mCherry-STOP.”
The Secondary Promoter Constructs described in Example 5 were used to determine the decoupling of gene expression of NeoTCR and Payload. As seen in
Next, experiments were conducted to confirm whether the TCRα enhancer (e.g., the 3′ portion of the protein coding sequence) could increase the expression of NeoTCR when using an EF-1α promoter. As shown in
These results show that removal of STOP codon improves the expression of TCR genes (e.g., NeoTCR) and Payload in all tested constructs. Further, the addition of enhancers did not improve the NeoTCR expression in presence of an MND promoter.
Since Secondary Promoter Constructs including an enhancer had improved NeoTCR expression, new constructs were designed to determine the relationship between enhancers and promoters. As seen in
These data show that Secondary Promoter Constructs including an MND promoter perform best when in presence of a CMV enhancer, an HS4 insulator, and P2A peptides.
The present example discloses additional Secondary Promoter Constructs including an inhibitory RNA molecule disclosed herein.
The present example describes several approaches to include an inhibitory RNA in a Secondary Promoter Construct. CBLB was used as target gene for knockdown analysis.
Initially, it was determined whether NeoTCR expression could be improved in Secondary Promoter Constructs including an inhibitory RNA molecule as a Payload.
Next, it was verified whether addition of a second Payload could be achieved.
Next, it was tested whether addition of certain secondary promoters upstream of an inhibitory RNA molecules would increase the knockdown of the CBLB target gene. Analysis of gene expression levels confirmed that U6 promoters significantly reduced the expression of the CBLB target gene without negatively impacting the expression of the NeoTCRs (
Further, Secondary Promoter Constructs including multiple inhibitory RNA molecules were designed and tested to evaluate the knockdown of the multiple target genes such as CBLB and A2AR (
Finally, it was determined whether miRNA clusters could target multiple genes. Cells were transfected with the constructs depicted in
Collectively, these data demonstrated that the inclusion of promoters upstream of Payloads improved the knockdown of target genes induced by inhibitory RNA molecules without altering the expression of NeoTCRs.
Next, it was hypothesized that flanking inhibitory RNA molecules by splice acceptor sites (SA) and/or splice donor sites (SD) could improve the knockdown of target genes.
While the present invention has been described at some length and with some particularity with respect to the several described embodiments, it is not intended that it should be limited to any such particulars or embodiments or any particular embodiment, but it is to be construed with references to the appended claims so as to provide the broadest possible interpretation of such claims in view of the prior art and, therefore, to effectively encompass the intended scope of the invention.
All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, section headings, the materials, methods, and examples are illustrative only and not intended to be limiting.
This application is a continuation application of International Patent Application No. PCT/US21/56737, filed on Oct. 27, 2021, which claims priority to U.S. Provisional Application No. 63/106,122, filed on Oct. 27, 2020, the contents of each of which are incorporated in their entirety, and to each of which priority is claimed.
| Number | Date | Country | |
|---|---|---|---|
| 63106122 | Oct 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US2021/056737 | Oct 2021 | US |
| Child | 18306927 | US |
