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  • C12N15/90—Stable introduction of foreign DNA into chromosome
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  • C12N2310/00—Structure or type of the nucleic acid
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  • C12N2510/00—Genetically modified cells

Definitions

• TCR T cell receptor
• CD4 and CD8 are membrane proteins that are expressed on T helper cells and cytotoxic T lymphocytes that serve as coreceptors that augment TCR signaling by stabilizing the interactions between the peptide-major histocompatibility (pMHC) ligands and the TCR (Li QJ, et al. (2004) CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nat Immunol 5:791-799; Holler PD, Kranz DM (2003) Quantitative analysis of the contribution of TCR/pepMHC affinity and CD8 to T cell activation. Immunity 18:255-264).
• pMHC peptide-major histocompatibility
• the CD4 and CD8 coreceptors are essential for the initiation of signaling because they facilitate the recruitment of a kinase to the TCR-pMHC complex. Furthermore, research has shown that while the CD4 and CD8 coreceptors both augment T cell sensitivity to its ligands, only CD8 plays a role in the stabilization of TCR-pMHC interactions.
• CD4 T cells when engineered with high affinity NeoTCRs, are thus able to recognize peptide-MHC-I targets and trigger effector T cell functions.
• lower affinity TCRs are dependent on CD8 co receptors to trigger T cell activation.
• NeoTCR cell therapy that is engineered to have CD8 co-receptor expression could stabilize the TCR-pMHC interactions and increase the efficacy of NeoTCR cell therapies that comprise low affinity TCRs that are dependent on such CD8 co-receptors.
• the presently disclosed subject matter provides a cell, comprising an exogenous T cell receptor (TCR), and an exogenous CD8.
• the exogenous CD8 comprises at least one monomer.
• the at least one monomer of the exogenous CD8 comprises an extracellular domain, a transmembrane domain, an intracellular domain, fragments thereof, or combinations thereof.
• the extracellular domain comprises a CD8a extracellular domain or a CD8P extracellular domain.
• the transmembrane a CD8a transmembrane domain or a CD8P transmembrane domain.
• the intracellular domain comprises a CD8a intracellular domain or a CD8P intracellular domain.
• the intracellular domain comprises a CD4 intracellular domain.
• the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain. In certain embodiments, the at least one monomer comprises a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain. In certain embodiments, the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain. In certain embodiments, the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain. In certain embodiments, the at least one monomer comprises a signal peptide. In certain embodiments, the signal peptide is a CD8 signal peptide.
• the extracellular domain comprises the amino acid sequence set forth in SEQ ID NO: 140, or SEQ ID NO: 145.
• the transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 141, or SEQ ID NO: 146.
• the intracellular domain comprises the amino acid sequence set forth in SEQ ID NO: 142, SEQ ID NO: 147, or SEQ ID NO: 148.
• the signal peptide comprises the amino acid sequence set forth in SEQ ID NO: 139, or SEQ ID NO: 144.
• the exogenous CD8 comprises a 2A sequence. In certain embodiments, the exogenous CD8 comprises a linker. In certain embodiments, the linker comprises the amino acid sequence set forth in SEQ ID NO: 137. In certain embodiments, the exogenous CD8 comprises a protease cleavage site. In certain embodiments, the protease cleavage site is a Furin cleavage site.
• the exogenous TCR is a patient derived TCR.
• the exogenous TCR comprises a signal sequence, a first and second 2A sequence, and a TCR polypeptide sequence.
• the exogenous TCR recognizes a cancer antigen.
• the cancer antigen is a neoantigen.
• the cancer antigen is a patient specific antigen.
• 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 if 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+.
• the cell further comprises a gene modification to enhance cell persistence and/or enhances memory cell differentiation.
• killing activity of the cell is increased between about 10% to about 500% as compared to killing activity of a cell that does not have the exogenous CD8.
• proliferation of the cell upon binding of the TCR to the antigen is increased between about 10% to about 500% as compared to proliferation of a cell that does not have the exogenous CD8.
• secretion of pro-inflammatory cytokine upon binding of the TCR to the antigen by the cell is increased between about 10% to about 500% as compared to secretion by a cell that does not have the exogenous CD8.
• LCK affinity of the cell is increased between about 10% to about 500% as compared to LCK affinity of a cell that does not have the exogenous CD8.
• persistence of the cell is increased between about 10% to about 500% as compared to persistence of a cell that does not have the exogenous CD8.
• tumor infiltration ability of the cell is increased between about 10% to about 500% as compared to tumor infiltration ability of a cell that does not have the exogenous CD8.
• the exogenous TCR is a CD8-dependent TCR.
• the exogenous TCR is a CD8-independent TCR.
• the exogenous CD8 is encoded by a CD8 Construct 1, a CD8 Construct 2, a CD8 Construct 3, or a CD8 Construct 4.
• the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and aCD8p intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8P signal peptide (SEQ ID NO: 144), a CD8P extracellular domain (SEQ ID NO: 145), a CD8P transmembrane domain (SEQ ID NO: 146), and a CD8P intracellular domain (SEQ ID NO: 147); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID
• the presently disclosed subject matter provides a method of modifying a cell, the method comprising introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises first and second homology arms homologous to first and second target nucleic acid sequences, a TCR gene sequence positioned between the first and second homology arms, a CD8 gene sequence positioned between the first and the second homology arms, and recombining the HR template nucleic acid into an endogenous locus of the cell.
• HR homologous recombination
• the HR template comprises a first 2A-coding sequence positioned upstream of the CD8 gene sequence, a second 2A-coding sequence positioned downstream of the CD8 gene sequence and upstream of the TCR gene sequence, and a third 2A-coding sequence positioned downstream of the TCR gene sequence; wherein the first, second, and third 2A-coding sequences code for the same amino acid sequence and are codon-diverged relative to each other.
• the HR template comprises a sequence coding for the amino acid sequence Gly Ser Gly positioned immediately upstream of the first, second, and/or third 2A-coding sequences.
• the HR template further comprises a sequence coding for a Furin cleavage site positioned upstream of the first, second, and/or third 2A-coding sequences. In certain embodiments, the HR template further comprises a sequence encoding a signal sequence positioned immediately upstream of the TCR gene sequence and/or the CD8 gene sequence.
• the HR template comprises a second TCR sequence positioned between the third 2A-coding sequence and the second homology arm.
• the HR template comprises a sequence encoding a first signal sequence positioned immediately upstream the first TCR gene sequence, and a sequence encoding a second signal sequence positioned immediately upstream of the second TCR gene sequence.
• the HR template comprises a second CD8 gene sequence positioned between the first CD8 gene sequence and the second 2A-coding sequence.
• a 2A coding sequence is positioned between the first and second CD8 gene sequence.
• a sequence coding for the amino acid sequence Gly Ser Gly is positioned between the first and second CD8 gene sequences.
• a sequence coding for a Furin cleavage site is positioned between the first and second CD8 gene sequences.
• the CD8 gene sequence comprises a sequence encoding an extracellular domain, a sequence encoding an intracellular domain, a sequence encoding an intracellular domain, fragments thereof, or combinations thereof.
• the sequence encoding an extracellular domain comprises a sequence encoding a CD8a extracellular domain or a CD8P extracellular domain.
• the sequence encoding a transmembrane domain comprises a sequence encoding a CD8a transmembrane domain or a CD8P transmembrane domain.
• the sequence encoding an intracellular domain comprises a sequence encoding a CD8a intracellular domain or a CD8P intracellular domain.
• the sequence encoding an intracellular domain comprises a sequence encoding a CD4 intracellular domain.
• the CD8 gene sequence comprises a sequence encoding a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain.
• the CD8 gene sequence comprises a sequence encoding a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain.
• the CD8 gene sequence comprises a sequence encoding a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain.
• the CD8 gene sequence comprises a sequence encoding a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• the HR template comprises a sequence encoding a first signal sequence positioned immediately upstream the first CD8 gene sequence, and a sequence encoding a second signal sequence positioned immediately upstream of the second CD8 gene sequence.
• the signal sequence is a CD8 signal sequence, a human growth hormone signal sequence, fragments thereof, or combinations thereof.
• the first and second homology arms of the HR template are each from about 300 bases to about 2,000 bases in length. In certain embodiments, the first and second homology arms of the HR template are each from about 600 bases to about 2,000 bases in length.
• the exogenous TCR is a patient derived TCR.
• the exogenous TCR comprises a signal sequence, a first and second 2A sequence, and a TCR polypeptide sequence.
• the exogenous TCR recognizes a cancer antigen.
• the cancer antigen is a neoantigen.
• the cancer antigen is a patient specific antigen.
• the HR template is non-viral.
• the HR template is a circular DNA.
• the HR template is a linear DNA.
• the introducing occurs via electroporation.
• the recombining comprises cleavage of the endogenous locus by a nuclease, and recombination of the HR template nucleic acid sequence into the endogenous locus by homology directed repair.
• the nuclease is a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) family nuclease, or derivative thereof.
• the nuclease further comprises a gRNA.
• the method further comprises culturing the cell.
• the culturing is conducted in the presence of at least one cytokine.
• the culturing is conducted in the presence of IL2, IL7, IL15, or any combination thereof.
• the culturing is conducted in the presence of IL7 and IL15.
• the method comprises a gene modification to enhance cell persistence and/or enhances memory cell differentiation.
• 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+.
• killing activity of the cell is increased between about 10% to about 500% as compared to killing activity of a cell that does not have the CD8 gene sequence.
• proliferation of the cell upon binding of the TCR to the antigen is increased between about 10% to about 500% as compared to proliferation of a cell that does not have the CD8 gene sequence.
• secretion of pro-inflammatory cytokine upon binding of the TCR to the antigen by the cell is increased between about 10% to about 500% as compared to secretion by a cell that does not have the CD8 gene sequence.
• LCK affinity of the cell is increased between about 10% to about 500% as compared to LCK affinity of a cell that does not have the CD8 gene sequence.
• persistence of the cell is increased between about 10% to about 500% as compared to persistence of a cell that does not have the CD8 gene sequence.
• tumor infiltration ability of the cell is increased between about 10% to about 500% as compared to tumor infiltration ability of a cell that does not have the CD8 gene sequence.
• the TCR gene encodes a CD8-dependent TCR. In certain embodiments, the TCR gene encodes a CD8-independent TCR. In certain embodiments, the CD8 gene sequence is encoded by a CD8 Construct 1, a CD8 Construct 2, a CD8 Construct 3, or a CD8 Construct 4.
• the CD8 gene sequence comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain; or a CD8a extracellular domain, CD8a transmembrane domain, CD4 intracellular domain.
• the CD8 gene sequence comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8p signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembrane domain (SEQ ID NO: 146), and a O ⁇ 8b intracellular domain (SEQ ID NO: 147); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (S
• the presently disclosed subject matter provides a cell modified by any of the methods disclosed herein.
• the presently disclosed subject matter provides a composition comprising an effective amount of a cell disclosed herein.
• the composition is a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient.
• the composition is administered to a patient in need thereof for the treatment of cancer.
• the composition comprises a cryopreservation agent.
• the composition comprises serum albumin.
• the composition comprises Plasma-Lyte A, HSA, and CryoStor CS10.
• the presently disclosed subject matter provides a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of a cell or a composition disclosed herein.
• a non-myeloablative lymphodepletion regimen is administered to the subject.
• the cancer is a solid tumor. In certain embodiments, the cancer is a liquid tumor.
• 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.
• the liquid tumor is selected from the group consisting of follicular lymphoma, leukemia, and multiple myeloma.
• the presently disclosed subject matter provides a kit comprising a cell disclosed herein, reagents for performing a method disclosed herein, or a composition disclosed herein.
• the kit further comprises written instructions for treating a cancer.
• the presently disclosed subject matter provides a cell, comprising: an exogenous T cell receptor (TCR); and an exogenous CD8, comprising: a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR T cell receptor
• the presently disclosed subject matter provides a cell, comprising: an exogenous T cell receptor (TCR); and an exogenous CD8, comprising: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8P signal peptide (SEQ ID NO: 144), a CD8P extracellular domain (SEQ ID NO: 145), a CD8P transmembrane domain (SEQ ID NO: 146), and a CD8P intracellular domain (SEQ ID NO: 147
• the presently disclosed subject matter provides a method of modifying a cell, the method comprising: introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises: first and second homology arms homologous to first and second target nucleic acid sequences; a TCR gene sequence positioned between the first and second homology arms; a CD8 gene sequence positioned between the first and the second homology arms; and recombining the HR template nucleic acid into an endogenous locus of the cell, wherein the CD8 gene sequence comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8p extracellular domain, a CD8P transmembrane domain, and a CD8p intracellular domain; a CD8a extracellular domain, a CD8a transmembrination (HR
• the presently disclosed subject matter provides a method of modifying a cell, the method comprising: introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises: first and second homology arms homologous to first and second target nucleic acid sequences; a TCR gene sequence positioned between the first and second homology arms; a CD8 gene sequence positioned between the first and the second homology arms; and recombining the HR template nucleic acid into an endogenous locus of the cell, wherein the CD8 gene sequence comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a CD8
• the presently disclosed subject matter provides a composition comprising a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a O ⁇ 8b extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR T cell receptor
• the presently disclosed subject matter provides a composition comprising a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a O ⁇ 8b signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembrane domain (SEQ ID NO: 146),
• the presently disclosed subject matter provides a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a O ⁇ 8b extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a O ⁇ 8b intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR exogenous T cell receptor
• CD8a extracellular domain a CD8a transme
• the presently disclosed subject matter provides a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8P signal peptide (SEQ ID NO: 144), a CD8P extracellular domain (SEQ ID NO: 145),
• TCR ex
• Figures 1A-1C show an example of a NeoE TCR cassette and gene editing methods that can be used to make NeoTCR Products.
• Figure 1A shows a schematic representing the general targeting strategy used for integrating neoantigen- specific TCR constructs (neoTCRs) into the TCRa locus.
• Figures IB and 1C show a neoantigen-specific TCR construct design used for integrating a NeoTCR into the TCRa locus wherein the cassette is shown with signal sequences (“SS”), protease cleavage sites (“P”), and 2A peptides (“2A”).
• SS signal sequences
• P protease cleavage sites
• 2A 2A peptides
• Figure IB shows a target TCRa locus (endogenous TRAC, top panel) and its CRISPR Cas9 target site (horizontal stripes, cleavage site designated by the arrow), and the circular plasmid HR template (bottom panel) with the polynucleotide encoding the neoTCR, which is located between left and right homology arms (“LHA” and“RHA” respectively) prior to integration.
• Figure 1C shows the integrated neoTCR in the TCRa locus (top panel), the transcribed and spliced neoTCR mRNA (middle panel), and translation and processing of the expressed neoTCR (bottom panel).
• Figures 2A-2D show the circular plasmids used to encode CD8 constructs 1, 2, 3, and 4.
• Figure 2A shows CD8 Construct 1 used to produce the CD8 Product 1.
• Figure 2B shows CD8 Construct 2 used to produce the CD8 Product 2.
• Figure 2C shows CD8 Construct 3 used to produce the CD8 Product 3.
• Figure 2D shows CD8 Construct 4 used to produce the CD8 Product 4.
• SS stands for a signal sequence. As described in Figures 6, 7, 8, and 9, the SS may be HGH; however other signal sequences may be used as needed for appropriate trafficking.
• P stands for a protease cleavage site.
• the P may be Furin; however other protease cleavage sites may be used as appropriate to provide the cleavage action described herein.
• 2A-2D 2A stands for the 2A peptide.
• the 2A may be the P2A peptide; however, other 2A peptides may be used.
• Figures 3A-3D show the transcription/splicing and translation processing of each of CD8 Constructs 1, 2, 3, and 4 to yield CD8 Products 1, 2, 3, and 4.
• SS stands for a signal sequence.
• the SS may be HGH; however other signal sequences may be used as needed for appropriate trafficking.
• P stands for a protease cleavage site.
• the P may be Furin; however other protease cleavage sites may be used as appropriate to provide the cleavage action described herein.
• 2A stands for the 2A peptide.
• the 2A may be the P2A peptide; however, other 2A peptides may be used.
• Figures 4A and 4B Figure 4A shows translated products of CD8 Product 1 and CD8 Product 2.
• Figure 4B shows the translated products of CD8 Product 3 and CD8 Product 4.
• Figure 5 provides an exemplary DNA sequence of the NeoTCR construct described in Figures 1A-1C. Conservative substitutions of nucleic acids can be used throughout to result in the same translated product. Furthermore, where amino acids can be substituted without a change in function, substitutions of the nucleic acids provided in Figure 5 can also be used to achieve the substituted amino acids conferring a substantially similar or identical function of the translated proteins.
• Figure 6 provides an exemplary DNA sequence of the CD8 Construct
• Figure 7 provides an exemplary DNA sequence of the CD8 Construct
• Figure 8 provides an exemplary DNA sequence of the CD8 Construct 3 (and translated CD8 Product 3) described in Figures 2C, 3C, and 4B. Conservative substitutions of nucleic acids can be used throughout to result in the same translated product. Furthermore, where amino acids can be substituted without a change in function, substitutions of the nucleic acids provided in Figure 8 can also be used to achieve the substituted amino acids conferring a substantially similar or identical function of the translated proteins.
• Figure 9 provides an exemplary DNA sequence of the CD8 Construct 4 (and translated CD8 Product 4) described in Figures 2D, 3D, and 4B. Conservative substitutions of nucleic acids can be used throughout to result in the same translated product. Furthermore, where amino acids can be substituted without a change in function, substitutions of the nucleic acids provided in Figure 9 can also be used to achieve the substituted amino acids conferring a substantially similar or identical function of the translated proteins.
• Figure 10 presents a visual depiction of CD8 Products 1, 2, 3, and 4 along with the predicted LCK activity of each of CD8 Products 1, 2, 3, and 4.
• Figure 11A provides an exemplary expression construct of
• FIG. 11B provides an exemplary expression construct of CD8 Product 2.
• Figure 11C provides an exemplary expression construct of CD8 Product 3.
• Figure 11D provides an exemplary expression construct of CD8 Product 4.
• Figure 12 diagrams the design of an Incucyte experiment to show the killing ability of the CD8 Products.
• Figures 13A and 13B show the increased tumor killing ability of CD8 Product 4 compared to a NeoTCR Product with the same NeoTCR as the CD8 Product 4 in a population of CD4 T cells. Specifically, both the CD8 Product 4 and the NeoTCR Product express TCR097. However, the CD8 Product 4 also expresses CD8 Construct 4 which comprises the extracellular domain of CD8a and the intracellular domain of CD4.
• the effectontarget cell ratio (E:T Ration) was 1 : 1 ( Figure 13A) or 2: 1 ( Figure 13B) and each were normalized for gene editing per cell line.
• the SW620 COX6C R20Q heterozygous tumor cells used in this experiment was a cell line that expresses the cognate antigen for TCR097 (a CD8 dependent TCR). This shows that the low affinity binding of TCR097 can be saved by co-expressing the extracellular domain of CD8a and the intracellular domain of CD4.
• Figure 14 shows the increased tumor killing ability of CD8 Product 4 compared to a NeoTCR Product with the same NeoTCR as the CD8 Product 4 in a population of CD4 T cells.
• both the CD8 Product 4 and the NeoTCR Product express TCR097.
• the CD8 Product 4 also expresses CD8 Construct 4 which comprises the extracellular domain of CD8a and the intracellular domain of CD4.
• the effectontarget cell ratio (E:T Ration) was 1 : 1, 1 :2, or 1 :4 and each were normalized for gene editing per cell line.
• the SW620 COX6C R20Q homozygous tumor cells used in this experiment was a cell line that expresses the cognate antigen for TCR097.
• Figures 15A and 15B provide exemplary control experiments showing that there is an increased tumor killing ability of CD8 Product 4 compared to a NeoTCR Product with the same NeoTCR as the CD8 Product 4 in a population of CD4 T cells (top graphs in Figures 15A and 15B) or CD8 T cells (bottom graphs in Figures 15A and 15B) and that CD8 Product 4 is more effective at tumor killing than simply expressing the NeoTCR construct and CD8 Product 4 in CD8 T cells.
• Figure 15A shows an E:T ration of 2: 1
• Figure 15B shows an E:T ratio of 1 : 1.
• Figure 16 shows the surface expression of CD8 Construct 4.
• Peak #1 is a NeoTCR Product in CD4+/CD8- T cells (expressing TCR089).
• Peak #2 is a CD8 Product 4 in CD8+/CD4+ T cells.
• Peak #3 is a NeoTCR Product in CD8+/CD4- T cells.
• CD8 Construct 4 exhibited proper and comparable surface expression as the NeoTCR Products. Similar results were achieved with the other CD8 Constructs (data not shown).
• Figures 17A and 17B show that CD8a expression boosts CD4 T cell sensitivity while maintaining specificity.
• Figure 17A shows that the expression of CD8 Constructs 1-4 increases the sensitivity of the T cells and does not change the specificity of the CD8 Product to the NeoTCR. As shown, co-expression of the CD8 Constructs decreases the EC50 which shows the increased sensitivity to the NeoTCR.
• Figure 17B shows that the CD8 Products 1-4 are specific for the cognate antigen to NeoTCR 097 because there is only INFy production by the CD8 Cells of the CD8 Products 1-4 in the presence of cognate antigen (i.e., no INFy production by the CD8 Cells of the CD8 Products 1-4 in the presence of mismatched antigen).
• the same experiment as shown in Figures 17A and 17B were performed with CD 107a instead of INFy and the same increased sensitivity with maintained specificity to the NeoTCR was shown (data not shown) to confirm the results with INFy.
• Figure 18 shows that CD8a expression boosts CD4 T cell sensitivity among CD8-independent NeoTCRs.
• the figure shows data from the CD8-independent NeoTCR089. This shows that even when a NeoTCR is CD8-independent, there is an increase in sensitivity of CD8 Product 4. This was a surprising result to find that sensitivity can be increased even for CD8-independent TCRs. Similar results were achieved with CD8 Products 1-3 (data not shown).
• CD8-dependent (e.g., NeoTCR097) and CD8- independent (e.g., NeoTCR089) exhibit increased sensitivity compared to NeoTCR Products expressing the same NeoTCRs.
• 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.
• “about” can mean within 3 or more than 3 standard deviations, per the practice in the art.
• “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.
• the term can mean within an order of magnitude, e.g., within 5-fold or within 2-fold, of a value.
• 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 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.
• 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.
• 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 plasmacyto as (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.
• CD8 is a cell surface glycoprotein found on most cytotoxic T lymphocytes that mediates efficient cell-cell interactions within the immune system.
• the CD8 antigen acts as a coreceptor with the T-cell receptor on the T lymphocyte to recognize antigens displayed by an antigen presenting cell in the context of class I MHC molecules.
• CD8 Cells as used herein means one or more cells precision engineered to express one or more NeoTCRs and a CD8 Construct.
• CD8 Construct as used herein means any one of a CD8 Construct 1, a CD8 Construct 2, a CD8 Construct 3, or a CD8 Construct 4.
• CD8 Product as used herein means a product comprising CD8 Cells.
• CD8 Construct 1 and“CD8 Product 1” refer to a construct that comprises a NeoTCR and CD8a (CD8a extracellular domain, CD8a transmembrane domain, and CD8a intracellular domain) and the resulting product that comprises an expressed NeoTCR and CD8a.
• Non-limiting examples of a CD8 Product 1 is provided in Figures 2A, 3A, and 6.
• a non-limiting example of a CD8 Product 1 is provided in Figure 4A.
• CD8 Construct 2 and“CD8 Product 2” refer to a construct that comprises a NeoTCR, CD8a (CD8a extracellular domain, CD8a transmembrane domain, and CD8a intracellular domain), and CD8P (CD8P extracellular domain, CD8P transmembrane domain, and CD8P intracellular domain) and the resulting product that comprises an expressed NeoTCR, CD8a, and CD8p.
• a CD8 Product 2 is provided in Figures 2B, 3B, and 7.
• a non-limiting example of a CD8 Product 1 is provided in Figure 4A.
• CD8 Construct 3 and“CD8 Product 3” refer to a construct that comprises a NeoTCR, CD8a extracellular domain, CD8a transmembrane domain, and CD8P intracellular domain and the resulting product that comprises an expressed NeoTCR, CD8a extracellular domain, CD8a transmembrane domain, and CD8P intracellular domain.
• Non-limiting examples of a CD8 Product 3 is provided in Figures 2C, 3C, and 8.
• a non-limiting example of a CD8 Product 1 is provided in Figure 4B.
• CD8 Construct 4 and“CD8 Product 4” refer to a construct that comprises a NeoTCR, CD8a extracellular domain, CD8a transmembrane domain, and CD4 intracellular domain) and the resulting product that comprises an expressed NeoTCR, CD8a extracellular domain, CD8a transmembrane domain, and CD4 intracellular domain.
• Non-limiting examples of a CD8 Product 4 is provided in Figures 2D, 3D, and 9.
• a non limiting example of a CD8 Product 1 is provided in Figure 4B.
• A“conservative substitution” or a“conservative amino acid,” refers to the substitution of an amino acid with a chemically or functionally similar amino acid. Conservative substitution tables providing similar amino acids are well known in the art.
• 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,
• “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.
• the NeoTCR Product of the invention is used to delay 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.
• neoantigen 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.”
• NeoTCR NeoE TCR
• exogenous TCR mean a neoepitope-specific T cell receptor that is introduced into a T cell, e.g., by gene editing methods.
• TCR gene sequence refers to a NeoTCR gene sequence.
• NeoTCR cells as used herein means one or more cells precision engineered to express one or more NeoTCRs.
• the cells are T cells.
• the T cells are CD8+ and/or CD4+ T cells.
• 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-Pl T cells” and “NeoTCR-Pl 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.
• 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.
• 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.
• 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.
• “Pharmaceutical Formulation” refers to a preparation which 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.
• 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.
• the mammal is human.
• TCR as used herein means T cell receptor.
• tumor antigen 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.
• 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.
• 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.
• T2A The T2A peptide was first identified in the Thosea asigna virus 2A.
• the P2A peptide was first identified in the porcine teschovirus-1 2 A.
• 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.
• 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).
• endogenous refers to a nucleic acid molecule or polypeptide that is normally expressed in a cell or tissue.
• exogenous refers to a nucleic acid molecule or polypeptide that is not endogenously present in a cell.
• 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.
• 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.
• 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.
• T cells 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.
• TMSC memory stem cells
• TCM central memory cells
• 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 Figures 1A-1C) to express the neoTCR.
• the NeoTCRs that are tumor specific are identified in cancer patients, such NeoTCRs are then cloned, and then the cloned NeoTCRs are inserted into the cancer patient’s T cells.
• NeoTCR expressing T cells are then expanded in a manner that preserves a“young” T cell phenotypes, resulting in a NeoTCR-Pl product (i.e., a NeoTCR Product) in which the majority of the T cells exhibit T memory stem cell and T central memory phenotypes.
• a NeoTCR-Pl product i.e., a NeoTCR Product
• NeoTCR Product consisting significantly of ‘young’ T cell phenotypes, has the potential to benefit patients with cancer, through improved engraftment potential, prolonged persistence post-infusion, and rapid differentiation into effector T cells to eradicate tumor cells throughout the body.
• NeoTCR Product 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.
• 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 TCRa and the genomic TCRP 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 GUTDE-seq, respectively. Multiple NeoTCR Product 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.
• NeoTCR 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.
• NeoTCR T cells i.e., NeoTCR Products
• 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.
• MHC-I neoTCRs neoepitope-specific MHC class I-restricted TCRs
• DNA-mediated (non-viral) gene editing as described in Example 1 fresh CD8 and CD4 T cells from the same patient with cancer were engineered to express the MHC-I neoTCR (concomitant with elimination of the endogenous TCR).
• MHC-I TCRs While naturally occurring MHC-I TCRs were presumed to require concurrent CD8 co-receptor help to stabilize peptide-MHC binding, higher affinity TCRs were able to drive CD8-independent target binding and T cell activation.
• CD4 T cells when engineered with high affinity neoTCRs, were thus able to recognize peptide-MHC-I targets and trigger effector T cell functions.
• lower affinity TCRs were dependent on CD8 co receptors to trigger T cell activation.
• CD8 co-receptor genes together with the neoTCR into CD4 T cells, MHC-I neoTCRs were made competent to trigger antigen-specific effector T cell function.
• CD8 stabilizes TCR-pMHC interactions and synergizes with TCRs for avidity.
• CD8 also serves to enhance avidity from low affinity TCRs, while the intracellular domain of CD8a is critical for enhanced T cell activation.
• Expression of CD8 may enhance CD4 T cell responses, which may not respond to physiological concentrations of pMHC. Disruption of CD8 binding to MHC can convert catch-bond TCR-pMHC into slip-bonds, highlighting the importance of CD8-MHC interactions even for TCRs that bind pMHC independent of CD8.
• CD8a has a lower affinity to LCK than CD8P, suggesting that either co-expression of both CD8a and CD8P or generation of a chimeric CD8a-CD8p molecule which contains the extracellular CD8a and intracellular domain of CD8P can improve effectiveness.
• the CD8 Constructs described herein are:
• CD8a homodimer (CD8 Construct 1)
• CD8a-P2A-CD8p (CD 8 Construct 2)
• CD8a with CD8P intracellular domain (CD8 Construct 3)
• NeoTCR 4 CD8a homodimer with CD4 intracellular domain
• the NeoTCR Products described above include an additional modification to include the expression of CD8 Construct 1, CD8 Construct 2, CD8 Construct 3, or CD8 Construct 4 (each a CD8 Product).
• 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 Figures 1A-1C) to express the neoTCR.
• CD8 Constructs when expressed, result in CD8 Products.
• Table 1 provides a description of each construct and product.
• the CD8 Product 1 comprises a NeoTCR and a CD8 homodimer. In certain embodiments, the CD8 Product 1 comprises the expression of a NeoTCR, a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain. In certain embodiments, the CD8 Product 1 further includes the expression of a CD8a signal peptide. In certain embodiments, the CD8 Product 1 comprises the translated elements presented in Figure 3A.
• the CD8 Product 1 comprises a NeoTCR, a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142).
• sequence modifications of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, and CD8a intracellular domain can be made that conserve or substantially conserve function of each element. In certain embodiments, such sequence modifications are conservative substitutions of amino acids.
• the CD8 Product 1 is manufactured from a CD8 Construct 1 provided in Figure 6.
• the sequence of CD8 Construct 1 provided in Figure 6 can be modified in any number of ways so long as the translation of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, and CD8a intracellular domain leave each element with conserved function.
• the order of each element of the CD8 Construct 1 in Figure 6 remains the same but the sequences of each individual element can be changed so long as the amino acids that the nucleic acid encodes remain the same or only comprise conservative substitutions.
• the order of each element of the CD8 Construct 1 in Figure 6 remains the same but the sequences of each individual element can be changed so long as the function of the encoded proteins remains substantially unchanged.
• the CD8 Product 2 comprises a NeoTCR, a CD8a, and aCD8p.
• the CD8a and CD8P are separated by a protease cleavage site and a 2A peptide in the CD8 Product 2 construct for expression.
• the CD8 Product 2 comprises the expression of a NeoTCR, a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain.
• the CD8 Product 2 further comprises the expression of a CD8a signal peptide.
• the CD8 Product further comprises the expression of a CD8P signal peptide. In certain embodiments, the CD8 Product further comprises the expression of a CD8a signal peptide and a CD8P signal peptide. In certain embodiments, the CD8 Product 2 comprises the translated elements presented in Figure 3B.
• the CD8 Product 2 comprises a NeoTCR, a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8P signal peptide (SEQ ID NO: 144), a CD8P extracellular domain (SEQ ID NO: 145), a CD8P transmembrane domain (SEQ ID NO: 146), and a CD8P intracellular domain (SEQ ID NO: 147).
• sequence modifications of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, CD8a intracellular domain, O ⁇ 8b extracellular domain, O ⁇ 8b transmembrane domain, and O ⁇ 8b intracellular domain can be made that conserve or substantially conserve function of each element. In certain embodiments, such sequence modifications are conservative substitutions of amino acids.
• the CD8 Product 2 is manufactured from a CD8 Construct 2 provided in Figure 7.
• CD8a signal peptide CD8a extracellular domain, CD8a transmembrane domain, CD8a intracellular domain, CD8b extracellular domain, CD8b transmembrane domain, and CD8b intracellular domain leave each element with conserved function.
• the order of each element of the CD8 Construct 2 in Figure 7 remains the same but the sequences of each individual element can be changed so long as the amino acids that the nucleic acid encodes remain the same or only comprise conservative substitutions.
• the order of each element of the CD8 Construct 2 in Figure 7 remains the same but the sequences of each individual element can be changed so long as the function of the encoded proteins remains substantially unchanged.
• the CD8 Product 3 comprises aNeoTCR and a CD8a with CD8b intracellular domain. In certain embodiments, the CD8 Product 3 comprises the expression of a NeoTCR, a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8b intracellular domain. In certain embodiments, the CD8 Product 3 further includes the expression of a CD8a signal peptide. In certain embodiments, the CD8 Product 3 comprises the translated elements presented in Figure 3C.
• the CD8 Product 3 comprises a NeoTCR, a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a O ⁇ 8b intracellular domain (SEQ ID NO: 147).
• sequence modifications of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, and O ⁇ 8b intracellular domain can be made that conserve or substantially conserve function of each element. In certain embodiments, such sequence modifications are conservative substitutions of amino acids.
• the CD8 Product 3 is manufactured from a CD8 Construct 3 provided in Figure 8.
• CD8a signal peptide CD8a extracellular domain, CD8a transmembrane domain, and CD8P intracellular domain leave each element with conserved function.
• the order of each element of the CD8 Construct 3 in Figure 8 remains the same but the sequences of each individual element can be changed so long as the amino acids that the nucleic acid encodes remain the same or only comprise conservative substitutions.
• the order of each element of the CD8 Construct 3 in Figure 8 remains the same but the sequences of each individual element can be changed so long as the function of the encoded proteins remains substantially unchanged.
• the CD8 Product 4 comprises a NeoTCR and a CD8a homodimer with a CD4 intracellular domain. In certain embodiments, the CD8 Product 4 comprises the expression of a NeoTCR, a CD8a extracellular domain, aCD8a transmembrane domain, and a CD4 intracellular domain. In certain embodiments, the CD8 Product 4 further includes the expression of a CD8a signal peptide. In certain embodiments, the CD8 Product 4 comprises the translated elements presented in Figure 3D.
• the CD8 Product 4 comprises a NeoTCR, a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD4 intracellular domain (SEQ ID NO: 148).
• sequence modifications of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, and CD4 intracellular domain can be made that conserve or substantially conserve function of each element. In certain embodiments, such sequence modifications are conservative substitutions of amino acids.
• the CD8 Product 4 is manufactured from a CD8 Construct 4 provided in Figure 9.
• the sequence of CD8 Construct 4 provided in Figure 9 can be modified in any number of ways so long as the translation of the CD8a signal peptide, CD8a extracellular domain, CD8a transmembrane domain, and CD4 intracellular domain leave each element with conserved function.
• the order of each element of the CD8 Construct 4 in Figure 9 remains the same but the sequences of each individual element can be changed so long as the amino acids that the nucleic acid encodes remain the same or only comprise conservative substitutions.
• the order of each element of the CD8 Construct 4 in Figure 9 remains the same but the sequences of each individual element can be changed so long as the function of the encoded proteins remains substantially unchanged.
• the CD8 Products comprise a TET2 knockout or TET2 knockdown.
• the cells of the CD8 Product are further engineered to knockout the TET2 gene using non-viral methods.
• the cells of the CD8 Product are further engineered to knockout the TET2 gene using viral methods.
• the cells of the CD8 Product are further engineered to increase T cell persistence by knocking out, knocked down, or modifying the function of a gene associated with T cell persistence using non-viral methods.
• the cells of the CD8 Product are further engineered to increase T cell persistence by knocking out, knocking down, or modifying the function of a gene associated with T cell persistence using viral methods.
• the CD8 Products comprise cells that were engineered to express a NeoTCR and a CD8 Construct using viral methods (i.e., CD8 Viral Product).
• the cells of the CD8 Viral Product are further engineered to knockout the TET2 gene using non-viral methods.
• the cells of the CD8 Viral Product are further engineered to knockout the TET2 gene using viral methods.
• the cells of the CD8 Viral Product are further engineered to increase T cell persistence by knocking out, knocking down, or modifying the function of a gene associated with T cell persistence using non-viral methods.
• the cells of the CD8 Viral Product are further engineered to increase T cell persistence by knocking out, knocking down, or modifying the function of a gene associated with T cell persistence using viral methods.
• the T cell persistence gene that is knocked out, knocked down, or with a modified function is a gene that confers downregulation of T cell activity. In certain embodiments, the gene that is knocked out, knocked down, or modified is a gene that downregulates T cell memory function. In certain embodiments, the gene that is knocked out, knocked down, or modified is a gene that decreases T-cell function, proliferation, and/or survival.
• additional modifications to the CD8 Products and CD8 Cells thereof include modifications to increase tumor microenvironment resilience, increase T cell activity, increase tumor microenvironment homing/retention, increase T cell persistence, and increase ectopic effector functions of T cells.
• the tumor microenvironment resilience includes but is not limited to converting/counteracting negative environmental signals.
• TCR- mediated signal enhancements include but are not limited to increasing T cell activity.
• the tumor microenvironment homing/retention includes but is not limited to enhancing tumor infiltration.
• the functional T cell persistence includes but is not limited to metabolic and transcriptional regulation.
• the ectopic effector functions include but is not limited to TCR- induced antibody, cytokine, or peptide secretion.
• functional T cell persistence can be accomplished by genetic engineering as described herein, by co-administration of a pharmaceutical agent that improves the functional T cell persistence of a modified T cells (modified to incorporate at least a neoTCR as described herein), and by manufacturing and culture conditions of the modified T cells (modified to incorporate at least a neoTCR as described herein).
• the TCR-induced antibodies used to improve ectopic effector functions are any one of the antibodies or functional fragments thereof described herein.
• the TCR-induced cytokines used to improve ectopic effector functions are naturally occurring cytokines, modified cytokines, fusion proteins of the cytokines, or any combination thereof.
• the TCR-induced cytokines are not cytokines but rather other co-factors or expression elements that induce endogenous cytokine production.
• additional modifications to the CD8 Products and CD8 Cells thereof include modifications to knock in one or more additional genes and/or functional proteins.
• the genes and/or functional proteins knocked in include but are not limited c-Myb, dominant negative FAS, FAS truncations, FBXW7, CTP1A, OPA1, GLUT1, CA-STAT5A, dominant negative TGFpR, DNMT3a, dominant negative PD-1R, dominant negative PD-1 or PD-L1, or PD-L2, dominant negative SHIP- 1 protein, integrins, chemokine receptors, cytokines, and interleukins.
• the dominant negative form of a gene is an antibody or functional fragment thereof that is an antagonist of the gene.
• a dominant negative PD-1 can be an anti -PD-1 antibody or functional fragment thereof.
• any of the knock in genes and/or functional proteins is a functional fragment (including but not limited to truncations) of the gene and/or protein.
• additional modifications to the CD8 Products and CD8 Cells thereof include modifications to knock out or knock down of one or more additional genes and/or functional proteins.
• the genes and/or functional proteins knocked out or knocked down include but are not limited to TET2, IFNGRl, RICTOR, NR4A1, DNMT3A, SUV39H1, PPP2RD, adenosine 2A receptor, PP2A3, and PP2A4.
• a different gene can be modulated through genetic engineering described herein that upregulates the expression of the gene that would otherwise be knocked in.
• a different gene can be modulated through genetic engineering described herein that downregulates the expression of the gene that would otherwise be knocked out.
• the CD8 Product manufacturing process involves electroporation of dual ribonucleoprotein species of CRISPR-Cas9 nucleases bound to guide RNA sequences, with each species targeting the genomic TCRa and the genomic TCRP 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 CD8 Product was performed in vitro and in silico analyses to survey possible off-target genomic cleavage sites, using COSMID and GUTDE-seq, respectively.
• Multiple CD8 Product 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.
• the CD8 Products described herein can be T cells, NK cells, NKT cells, macrophages, hematopoietic stem cells (HSCs), cells derived from HSCs, or dendritic/antigen-presenting cells.
• T cells NK cells
• NKT cells NK cells
• macrophages hematopoietic stem cells (HSCs)
• HSCs hematopoietic stem cells
• dendritic/antigen-presenting cells dendritic/antigen-presenting cells.
• CD8 Cells are expanded in a manner that preserves a “young” T cell phenotypes, resulting in a CD8 Product in which the majority of the T cells exhibit T memory stem cell and T central memory phenotypes
• CD8 Product consisting significantly of‘young’ T cell phenotypes, has the potential to benefit patients with cancer, through improved engraftment potential, prolonged persistence post-infusion, and rapid differentiation into effector T cells to eradicate tumor cells throughout the body.
• the CD8 Cells of the CD8 Products predominantly comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 25% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 30% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 35% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm).
• At least 40% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 45% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 50% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 55% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm).
• At least 60% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 65% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 70% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm). In certain embodiments, at least 75% of the CD8 Cells of the CD8 Products comprise memory stem cells (Tmsc) and/or central memory cells (Tcm).
• Tmsc memory stem cells
• Tcm central memory cells
• Tmsc are characterized as cells that are CD45RA+CD62L+, CD28+CD95+, and CCR7+CD27+.
• Tcm are characterized as cells that are CD45RO+CD62L+, CD28+CD95+, and CCR7+CD27+CD127+. Both Tmsc and Tcm are characterized as having weak effector T cell function, robust proliferation, robust engraftment, and long telomeres.
• the CD8 cells disclosed herein show improved properties (e.g ., killing activity, cell proliferation, secretion of cytokines, LCK affinity, persistence, tumor infiltration ability) about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 100%, about 150%, about 200%, about 250%, about 300%, about 350%, about 400%, about 450%, or about 500% as compared to the cells that do not have a CD8 construct.
• improved properties e.g ., killing activity, cell proliferation, secretion of cytokines, LCK affinity, persistence, tumor infiltration ability
• the present disclosure relates, in part, on the production of engineered“young” T cells.
• 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.
• the methods for activating cells comprise the steps of activating the TCR/CD3 complex.
• the T cells can be incubated and/or cultured with CD3 agonists, CD28 agonists, or a combination thereof.
• engineered activated antigen-specific cells can be expanded by culturing the engineered activated antigen-specific cells, e.g., T cells, with cytokines, chemokine, soluble peptides, or combination thereof.
• the engineered activated antigen-specific cells e.g., engineered activated T cells
• the cytokines can be IL2, IL7, IL15, or combinations thereof.
• engineered activated antigen-specific cells e.g., engineered activated T cells, can be cultured with IL7 and IL15.
• 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 pg/ml to about 1 g/ml, or from about 1 mg/ml to about lg/ml, and any values in between.
• compositions of the CD8 Product are prepared by combining the CD8 Cells in a solution that can preserve the ‘young’ phenotype of the cells in a cryopreserved state.
• Table 1 provides an example of one such pharmaceutical formulation.
• pharmaceutical formulations of the CD8 Product can be prepared by combining the CD8 Cells in a solution that can preserve the‘young’ phenotype of the cells without the need to freeze or cryopreserve the product (i.e., the CD8 Product is maintained in an aqueous solution or as a non-frozen/cryopreserved cell pellet).
• cryopreservation solution or the aqueous storage solution (if the CD8 Product is not cryopreserved).
• Any cryopreservation agent and/or media can be used to cryopreserve the CD8 Product, including but not limited to CryoStor, CryoStor CS5, CELLBANKER, and custom cryopreservation media that optionally include DMSO. GENE-EDITING METHODS
• the present disclosure involves, in part, methods of engineering human cells, e.g., engineered T cells or engineered human stem cells.
• 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.
• such engineering involves genome editing.
• such genome editing can be accomplished with nucleases targeting one or more endogenous loci, e.g., TCR alpha (TCRa) locus and TCR beta (TCRP) locus.
• the nucleases can generate single-stranded DNA nicks or double-stranded DNA breaks in an endogenous target sequence.
• the nuclease can target coding or non-coding portions of the genome, e.g., exons, introns.
• 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.
• 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.
• a CRISPR/Cas nuclease system is used to engineer human cells.
• 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.
• 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.
• the Cas nuclease is Cas9 or Casl2a.
• 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 (2016), herein incorporated by reference for all that it teaches.
• genome editing occurs at one or more genome loci that regulate immunological responses.
• the loci include, without limitation, TCR alpha (TCRa) locus, TCR beta (TCRP) locus, TCR gamma (TCRy), and TCR delta (TCR5).
• the loci for inserting a CD8 Construct is anywhere in the genome.
• the loci for inserting a CD8 Construct is the TRAC locus.
• the loci for inserting a CD8 Construct is one of the two TRBC loci.
• the locus for inserting a CD8 Construct is a locus other than the TRAC locus or TRAB loci.
• the loci for inserting a CD8 Construct is inserted into a gene locus wherein such gene is knocked out.
• the desired phenotype of a CD8 Product is the expression of a NeoTCR
• the CD8 Construct can be inserted at the TET2 locus or AAVS1 locus.
• the insertion of the CD8 Construct is in tandem with the NeoTCR insertion.
• the insertion of the CD8 Construct is a separate locus than the NeoTCR insertion.
• genome editing is performed by using non-viral delivery systems.
• a nucleic acid molecule can be introduced into a cell by administering the nucleic acid in the presence of lipofection (Feigner et ak, Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et ak, Neuroscience Letters 17:259, 1990; Brigham et ak, Am. J. Med. Sci.
• 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.
• a cultivatable cell type ex vivo e.g., an autologous or heterologous primary cell or progeny thereof
• genome editing is performed by using viral delivery systems.
• the viral methods include targeted integration (including but not limited to AAV) and random integration (including but not limited to lentiviral approaches).
• the viral delivery would be accomplished without integration of the nuclease.
• the viral delivery system can be Lentiflash or another similar delivery system.
• 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.
• HR homologous recombination
• the HR template nucleic acid sequence is linear.
• the HR template nucleic acid sequence is circular.
• the circular HR template can be a plasmid, minicircle, or nanoplasmid.
• the HR template nucleic acid sequence comprises a first and a second homology arms.
• the homology arms can be of about 300 bases to about 2,000 bases. For example, each homology arm can be 1,000 bases.
• the homology arms can be homologous to a first and second endogenous sequences of the cell.
• the endogenous locus is a TCR locus.
• the first and second endogenous sequences are within a TCR alpha locus or a TCR beta locus.
• the HR template comprises a TCR gene sequences.
• the TCR gene sequence is a patient specific TCR gene sequence.
• the TCR gene sequence is tumor-specific.
• 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.
• the HR template comprises a TCR alpha gene sequence and a TCR beta gene sequence.
• the HR template is a polycistronic polynucleotide.
• the HR template comprises sequences encoding for flexible polypeptide sequences (e.g., Gly-Ser-Gly sequence).
• the HR template comprises sequences encoding an internal ribosome entry site (IRES).
• the HR template comprises a 2A peptide (e.g., P2A, T2A, E2A, and F2A). 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.
• the presently disclosed subject matter provides methods for inducing and/or increasing an immune response in a subject in need thereof.
• the CD8 Products can be used for treating and/or preventing a cancer in a subject.
• the CD8 Products can be used for prolonging the survival of a subject suffering from a cancer.
• the CD8 Products can also be used for treating and/or preventing a cancer in a subject.
• the CD8 Products can also be used for reducing tumor burden in a subject.
• Such methods comprise administering the CD8 Products in an amount effective or a composition (e.g ., a pharmaceutical composition) comprising thereof to achieve the desired effect, be it palliation of an existing condition or prevention of recurrence.
• 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.
• the CD8 Products can be used for treating viral or bacterial diseases. In certain embodiments, the CD8 Products can be used for treating autoimmune diseases.
• an effective amount of the CD8 Products are delivered through IV administration.
• the CD8 Products are delivered through IV administration in a single administration.
• the CD8 Products are delivered through IV administration in multiple administrations.
• the CD8 Products are delivered through IV administration in two or more administrations.
• the CD8 Products are delivered through IV administration in two administrations.
• the CD8 Products are delivered through IV administration in three administrations.
• the presently disclosed subject matter provides methods for treating and/or preventing cancer in a subject.
• the method comprises administering an effective amount of CD8 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).
• 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
• 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.
• blood cancers e.g. leukemias, lymphomas, and myelomas
• ovarian cancer e.g. leukemias, lymphomas, and myelomas
• the presently disclosed young T cells and compositions comprising thereof 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.
• the neoplasia is a solid cancer or a solid tumor.
• 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 is one that can be detected on the basis of 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, with the objective of palliating their condition.
• 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 CD8 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).
• 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 CD8 Cells within the CD8 Products.
• the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle.
• the container may be a CryoMACS freezing bag.
• the label or package insert indicates that the CD8 Products are used for treating the condition of choice and the patient of origin. The patient is identified on the container of the CD8 Product because the CD8 Products is made from autologous cells and engineered as a patient-specific and individualized treatment.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; and 2) a second container with the same CD8 Product as the first container contained therein.
• additional containers with the same CD8 Product as the first and second containers may be prepared and made.
• additional containers containing a composition comprising a different cytotoxic or otherwise therapeutic agent may also be combined with the containers described above.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; and 2) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
• the article of manufacture may comprise: 1) a first container with two CD8 Products contained therein; and 2) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD 8 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.
• the first and second CD8 Products are different CD8 Products.
• the first and second CD8 Products are the same CD8 Products.
• the article of manufacture may comprise: 1) a first container with three CD8 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.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD8 Product contained therein; 3) a third container with a third CD8 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.
• the first, second, and third CD8 Products are different CD8 Products.
• the first, second, and third CD8 Products are the same CD8 Products.
• two of the first, second, and third CD8 Products are the same CD8 Products.
• the article of manufacture may comprise: 1) a first container with four CD8 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.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD8 Product contained therein; 3) a third container with a third CD8 Product contained therein; 4) a fourth container with a fourth CD8 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.
• the first, second, third, and fourth CD8 Products are different CD8 Products.
• the first, second, third, and fourth CD8 Products are the same NeoTCR Products.
• two of the first, second, third, and fourth CD8 Products are the same NeoTCR Products.
• three of the first, second, third, and fourth CD8 Products are the same CD8 Products.
• the article of manufacture may comprise: 1) a first container with five or more CD8 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.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD8 Product contained therein; 3) a third container with a third CD8 Product contained therein; 4) a fourth container with a fourth CD8 Product contained therein; 5) a fifth container with a fifth CD8 Product contained therein; 6) optionally a sixth or more additional containers with a sixth or more CD8 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.
• all of the containers of CD8 Products are different CD8 Products.
• all of the containers of CD8 Products are the same CD8 Products.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD 8 Product contained therein; and 3) a third container with a third CD8 Product contained therein.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD8 Product contained therein; 3) a third container with a third CD8 Product contained therein; and 4) optionally a fourth container with a fourth CD8 Product contained therein.
• the article of manufacture may comprise: 1) a first container with a CD8 Product contained therein; 2) a second container with a second CD8 Product contained therein; 3) a third container with a third CD8 Product contained therein; 4) a fourth container with a fourth CD8 Product contained therein; and 5) optionally a fifth container with a fourth CD8 Product contained therein.
• the article of manufacture may comprise a container with one CD8 Product contained therein.
• the article of manufacture may comprise a container with two CD8 Products contained therein.
• the article of manufacture may comprise a container with three CD8 Products contained therein.
• the article of manufacture may comprise a container with four CD8 Products contained therein.
• the article of manufacture may comprise a container with five CD8 Products contained therein.
• the article of manufacture may comprise 1) a first container with one CD8 Product contained therein, and 2) a second container with two CD8 Products contained therein.
• the article of manufacture may comprise 1) a first container with two CD8 Products contained therein, and 2) a second container with one CD8 Product contained therein.
• a third and/or fourth container comprising one or more additional CD8 Products may be included in the article of manufacture.
• a fifth container comprising one or more additional CD8 Products may be included in the article of manufacture.
• any container of CD8 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.
• the CD8 Products are provided in a kit.
• the kit can, by means of non-limiting examples, contain package insert(s), labels, instructions for using the CD8 Product(s), syringes, disposal instructions, administration instructions, tubing, needles, and anything else a clinician would need in order to properly administer the CD8 Product(s).
• plasmid DNA-mediated precision genome engineering process for Good Manufacturing Practice (GMP) manufacturing of CD8 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.
• RNPs CRISPR endonuclease ribonucleoproteins
• CD8 Constructs were inserted by incorporating them into the neoTCR vector and then electroporating with CRISPR endonuclease ribonucleoproteins (RNPs) as described above.
• the CD8 Products can be formulated into a drug product using the clinical manufacturing process. Under this process, the CD8 Products are cryopreserved in CryoMACS Freezing Bags. One or more bags may be shipped to the site for each patient depending on patient needs.
• the product is composed of apheresis-derived, patient- autologous, CD8 and CD4 T cells that have been precision genome engineered to express one or more autologous neoTCRs targeting a neoepitope complexed to one of the endogenous HLA receptors presented exclusively on the surface of that patient’s tumor cells.
• the final product will contain 5% dimethyl sulfoxide (DMSO), human serum albumin, and Plasma-Lyte.
• DMSO dimethyl sulfoxide
• human serum albumin human serum albumin
• Plasma-Lyte Plasma-Lyte
• compositions comprising cells (e.g., immunoresponsive cells) disclosed herein.
• the presently disclosed subject matter provides nucleic acid compositions comprising a polynucleotide encoding the NeoTCR disclosed herein.
• the nucleic acid compositions disclosed herein comprise a polynucleotide encoding a CD8 Construct disclosed herein. Also provided are cells comprising such nucleic acid compositions.
• 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 CD8 Construct disclosed herein.
• the promoter is endogenous or exogenous.
• the exogenous promoter is selected from the group consisting of an elongation factor (EF)-l promoter, a CMV promoter, a SV40 promoter, a PGK promoter, a long terminal repeat (LTR) promoter and a metallothionein promoter.
• the promoter is an inducible promoter.
• the inducible promoter is selected from the group consisting of a 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.
• TRE NFAT transcriptional response element
• 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
• 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.
• transducing viral vectors can be used to modify a cell.
• 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).
• 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; Cometta 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 259:98
• 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.
• 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.
• 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.
• a cultivatable cell type ex vivo e.g., an autologous or heterologous primary cell or progeny thereof
• 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 la enhancer/promoter/intron structure).
• CMV human cytomegalovirus
• SV40 simian virus 40
• metallothionein promoters regulated by any appropriate mammalian regulatory element or intron (e.g. the elongation factor la enhancer/promoter/intron structure).
• 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.
• 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.
• kits for inducing and/or enhancing an immune response and/or treating and/or preventing a cancer or a pathogen infection in a subject comprises an effective amount of presently disclosed cells or a pharmaceutical composition comprising thereof.
• 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.
• the kit includes an isolated nucleic acid molecule encoding a presently disclosed HR template.
• 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 a cancer or pathogen or immune disorder.
• the instructions generally include information about the use of the composition for the treatment and/or prevention of a cancer or a pathogen infection.
• 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.
• the presently disclosed subject matter provides for a cell, comprising an exogenous T cell receptor (TCR), and an exogenous CD8.
• TCR T cell receptor
• CD8 comprises at least one monomer.
• A4 The foregoing cell of A2 or A3, wherein the transmembrane a CD8a transmembrane domain or a O ⁇ 8b transmembrane domain.
• A5 The foregoing cell of A2-A4, wherein the intracellular domain comprises a CD8a intracellular domain or a O ⁇ 8b intracellular domain.
• A6 The foregoing cell of A2-A4, wherein the intracellular domain comprises a CD4 intracellular domain.
• A7 The foregoing cell of A1-A5, wherein the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain.
• A8 The foregoing cell of A1-A5, wherein the at least one monomer comprises a CD8P extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain.
• A9 The foregoing cell of A1-A5, wherein the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a O ⁇ 8b intracellular domain.
• A10 The foregoing cell of A1-A6, wherein the at least one monomer comprises a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• A13 The foregoing cell of A2-A12, wherein the extracellular domain comprises the amino acid sequence set forth in SEQ ID NO: 140, or SEQ ID NO: 145.
• A14 The foregoing cell of A2-A13, wherein the transmembrane domain comprises the amino acid sequence set forth in SEQ ID NO: 141, or SEQ ID NO: 146.
• A15 The foregoing cell of A2-A14, wherein the intracellular domain comprises the amino acid sequence set forth in SEQ ID NO: 142, SEQ ID NO: 147, or SEQ ID NO: 148.
• A16 The foregoing cell of A11-A15, wherein the signal peptide comprises the amino acid sequence set forth in SEQ ID NO: 139, or SEQ ID NO: 144.
• A17 The foregoing cell of A-A16, wherein the exogenous CD8 comprises a 2A sequence.
• A20 The foregoing cell of A-A19, wherein the exogenous CD8 comprises a protease cleavage site.
• A21 The foregoing cell of A-A20, wherein the protease cleavage site is a Furin cleavage site.
• A22 The foregoing cell of A-A21, wherein the exogenous TCR is a patient derived TCR.
• A23 The foregoing cell of A-A22, wherein the exogenous TCR comprises a signal sequence, a first and second 2A sequence, and a TCR polypeptide sequence.
• A24 The foregoing cell of A-A23, wherein the exogenous TCR recognizes a cancer antigen.
• A25 The foregoing cell of A24, wherein the cancer antigen is a neoantigen.
• A26 The foregoing cell of A24, wherein the cancer antigen is a patient specific antigen.
• A27 The foregoing cell of A-A26, wherein the cell is a primary cell.
• A28 The foregoing cell of A-A26, wherein the cell is a patient-derived cell.
• A29 The foregoing cell of A-A26, wherein the cell is a lymphocyte.
• A30 The foregoing cell of A-A26, wherein the cell is a T cell.
• A31 The foregoing cell of A-A26, wherein the cell if a young T cell.
• A32 The foregoing cell of A31, wherein the cell is CD45RA+, CD62L+, CD28+, CD95-, CCR7+, and CD27+.
• A33 The foregoing cell of A31, wherein the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+.
• A34 The foregoing cell of A31, wherein the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
• A35 The foregoing cell of A-A34, further comprising a gene modification to enhance cell persistence and/or enhances memory cell differentiation
• A36 The foregoing cell of A- A35, wherein killing activity of the cell is increased between about 10% to about 500% as compared to killing activity of a cell that does not have the exogenous CD8.
• A37 The foregoing cell of A-A36, wherein proliferation of the cell upon binding of the TCR to the antigen is increased between about 10% to about 500% as compared to proliferation of a cell that does not have the exogenous CD8.
• A38 The foregoing cell of A-A37, wherein secretion of pro-inflammatory cytokine upon binding of the TCR to the antigen by the cell is increased between about 10% to about 500% as compared to secretion by a cell that does not have the exogenous CD8.
• A39 The foregoing cell of A-A38, wherein LCK affinity of the cell is increased between about 10% to about 500% as compared to LCK affinity of a cell that does not have the exogenous CD8.
• A40 The foregoing cell of A-A39, wherein persistence of the cell is increased between about 10% to about 500% as compared to persistence of a cell that does not have the exogenous CD8.
• A41 The foregoing cell of A-A40, wherein tumor infiltration ability of the cell is increased between about 10% to about 500% as compared to tumor infiltration ability of a cell that does not have the exogenous CD8.
• A42 The foregoing cell of A-A41, wherein the exogenous TCR is a CD8-dependent TCR.
• A43 The foregoing cell of A-A41, wherein the exogenous TCR is a CD8- independent TCR.
• A44 The foregoing cell of A-A43, wherein the exogenous CD8 is encoded by a CD8 Construct 1, a CD8 Construct 2, a CD8 Construct 3, or a CD8 Construct 4.
• the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and aCD8p intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a O ⁇ 8b signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembrane domain (SEQ ID NO: 146), and a O ⁇ 8b intracellular domain (SEQ ID NO: 147); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain
• the presently disclosed subject matter provides for a method of modifying a cell, the method comprising introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises first and second homology arms homologous to first and second target nucleic acid sequences, a TCR gene sequence positioned between the first and second homology arms, and a CD8 gene sequence positioned between the first and the second homology arms, and recombining the HR template nucleic acid into an endogenous locus of the cell.
• HR homologous recombination
• the HR template comprises a first 2A- coding sequence positioned upstream of the CD8 gene sequence, a second 2A-coding sequence positioned downstream of the CD8 gene sequence and upstream of the TCR gene sequence, and a third 2A-coding sequence positioned downstream of the TCR gene sequence; wherein the first, second, and third 2A-coding sequences code for the same amino acid sequence and are codon-diverged relative to each other.
• B13 The foregoing method of Bl l or B12, wherein the sequence encoding a transmembrane domain comprises a sequence encoding a CD8a transmembrane domain or a CD8P transmembrane domain.
• B14 The foregoing method of B11-B13, wherein the sequence encoding an intracellular domain comprises a sequence encoding a CD8a intracellular domain or a CD8P intracellular domain.
• B16 The foregoing method of B11-B15, wherein the CD8 gene sequence comprises a sequence encoding a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain.
• B17 The foregoing method of B11-B15, wherein the CD8 gene sequence comprises a sequence encoding a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain.
• B21 The foregoing method of B4-B20, wherein the signal sequence is a CD8 signal sequence, a human growth hormone signal sequence, fragments thereof, or combinations thereof.
• B25 The foregoing method of B-B24, wherein the exogenous TCR comprises a signal sequence, a first and second 2A sequence, and a TCR polypeptide sequence.
• B26 The foregoing method of B-B25, wherein the exogenous TCR recognizes a cancer antigen.
• B27. The foregoing method of B26, wherein the cancer antigen is a neoantigen.
• B33 The foregoing method of B-B32, wherein the recombining comprises cleavage of the endogenous locus by a nuclease; and recombination of the HR template nucleic acid sequence into the endogenous locus by homology directed repair.
• nuclease is a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) family nuclease, or derivative thereof.
• CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
• B36 The foregoing method of B-B35, wherein the process further comprises culturing the cell.
• B37 The foregoing method of B36, wherein the culturing is conducted in the presence of at least one cytokine.
• B38 The foregoing method of B36 or B37, wherein the culturing is conducted in the presence of IL2, IL7, IL15, or any combination thereof.
• B40 The foregoing method of B-B39, further comprising a gene modification to enhance cell persistence and/or enhances memory cell differentiation.
• B42 The foregoing method of B-B40, wherein the cell is a patient-derived cell.
• B43 The foregoing method of B-B40, wherein the cell is a lymphocyte.
• B45 The foregoing method of B-B40, wherein the cell is a young T cell.
• B46 The foregoing method of B45, wherein the cell is CD45RA+, CD62L+, CD28+, CD95-, CCR7+, and CD27+.
• B47 The foregoing method of B45, wherein the cell is CD45RA+, CD62L+, CD28+, CD95+, CD27+, CCR7+.
• B48 The foregoing method of B45, wherein the cell is CD45RO+, CD62L+, CD28+, CD95+, CCR7+, CD27+, CD127+.
• B49 The foregoing method of B-B48, wherein killing activity of the cell is increased between about 10% to about 500% as compared to killing activity of a cell that does not have the CD8 gene sequence.
• B50 The foregoing method of B-B49, wherein proliferation of the cell upon binding of the TCR to the antigen is increased between about 10% to about 500% as compared to proliferation of a cell that does not have the CD8 gene sequence.
• B51 The foregoing method of B-B50, wherein secretion of pro-inflammatory cytokine upon binding of the TCR to the antigen by the cell is increased between about 10% to about 500% as compared to secretion by a cell that does not have the CD8 gene sequence.
• B52 The foregoing method of B-B51, wherein LCK affinity of the cell is increased between about 10% to about 500% as compared to LCK affinity of a cell that does not have the CD8 gene sequence.
• B53 The foregoing method of B-B52, wherein persistence of the cell is increased between about 10% to about 500% as compared to persistence of a cell that does not have the CD8 gene sequence.
• B54 The foregoing method of B-B53, wherein tumor infiltration ability of the cell is increased between about 10% to about 500% as compared to tumor infiltration ability of a cell that does not have the CD8 gene sequence.
• B56 The foregoing method of B-B54, wherein the TCR gene encodes a CD8- independent TCR.
• B57 The foregoing method of B-B56, wherein the CD8 gene sequence is encoded by a CD8 Construct 1, a CD8 Construct 2, a CD8 Construct 3, or a CD8 Construct 4.
• B58 The foregoing method of B-B56, wherein the CD8 gene sequence comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain; or a CD8a extracellular domain, CD8a transmembrane domain, CD4 intracellular domain.
• the CD8 gene sequence comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a transmembrane domain, and a CD8a intracellular domain;
• the CD8 gene sequence comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a O ⁇ 8b signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembrane domain (SEQ ID NO: 146), and a O ⁇ 8b intracellular domain (SEQ ID NO: 147); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (
• the presently disclosed subject matter provides for a cell modified by the method of B-B57.
• composition comprising an effective amount of a cell of A-A46 or a cell of C.
• composition is a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient.
• composition of D or Dl wherein the composition is administered to a patient in need thereof for the treatment of cancer.
• composition of D-D2 wherein the composition comprises a cryopreservation agent.
• composition of D-D3, wherein the composition comprises serum albumin.
• D5 The foregoing composition of D-D4, wherein the composition comprises Plasma-Lyte A, HSA, and CryoStor CS10.
• the presently disclosed subject matter provides for a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of a cell of A-A46, a cell of claim C, or a composition of D-D5. El .
• a non-myeloablative lymphodepletion regimen is administered to the subject.
• E4 The foregoing method of E2, wherein 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.
• 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
• liquid tumor is selected from the group consisting of follicular lymphoma, leukemia, and multiple myeloma.
• kits comprising a cell of A-A46, reagents for performing the method of B- B57, a cell of C, or a composition of D-D5.
• kit further comprises written instructions for treating a cancer.
• the presently disclosed subject matter provides for a cell, comprising: an exogenous T cell receptor (TCR); and an exogenous CD8, comprising: a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a CD8P extracellular domain, a CD8P transmembrane domain, and a CD8P intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8P intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR T cell receptor
• the presently disclosed subject matter provides for a cell, comprising: an exogenous T cell receptor (TCR); and an exogenous CD8, comprising: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a CD8P signal peptide (SEQ ID NO: 144), a CD8P extracellular domain (SEQ ID NO: 145), a CD8P transmembrane domain (SEQ ID NO: 146), and a O ⁇ 8b intracellular domain (TCR); and an exogenous CD
• the presently disclosed subject matter provides for a method of modifying a cell, the method comprising: introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises: first and second homology arms homologous to first and second target nucleic acid sequences; a TCR gene sequence positioned between the first and second homology arms; a CD8 gene sequence positioned between the first and the second homology arms; and recombining the HR template nucleic acid into an endogenous locus of the cell, wherein the CD8 gene sequence comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a O ⁇ 8b extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain; a CD8a extracellular domain
• the presently disclosed subject matter provides for a method of modifying a cell, the method comprising: introducing into the cell a homologous recombination (HR) template nucleic acid sequence, wherein the HR template comprises: first and second homology arms homologous to first and second target nucleic acid sequences; a TCR gene sequence positioned between the first and second homology arms; a CD8 gene sequence positioned between the first and the second homology arms; and recombining the HR template nucleic acid into an endogenous locus of the cell, wherein the CD8 gene sequence comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 142); a CD8a
• the presently disclosed subject matter provides for a composition comprising a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a O ⁇ 8b extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a O ⁇ 8b intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR T cell receptor
• the presently disclosed subject matter provides for a composition comprising a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a O ⁇ 8b signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembrane domain (SEQ ID NO: 139), a CD
• the presently disclosed subject matter provides for a method of treating cancer in a subject in need thereof, the method comprising administering a therapeutically effective amount of a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a extracellular domain, a CD8a transmembrane domain, and a CD8a intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, a CD8a intracellular domain, a O ⁇ 8b extracellular domain, a O ⁇ 8b transmembrane domain, and a O ⁇ 8b intracellular domain; a CD8a extracellular domain, a CD8a transmembrane domain, and a O ⁇ 8b intracellular domain; or a CD8a extracellular domain, a CD8a transmembrane domain, and a CD4 intracellular domain.
• TCR exogenous T cell receptor
• CD8a extracellular domain a CD8a trans
• a method of treating cancer in a subject in need thereof comprising administering a therapeutically effective amount of a cell, wherein the cell comprises an exogenous T cell receptor (TCR) and an exogenous CD8, wherein the exogenous CD8 comprises: a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), and a CD8a intracellular domain (SEQ ID NO: 142); a CD8a signal peptide (SEQ ID NO: 139), a CD8a extracellular domain (SEQ ID NO: 140), a CD8a transmembrane domain (SEQ ID NO: 141), a CD8a intracellular domain (SEQ ID NO: 142), a O ⁇ 8b signal peptide (SEQ ID NO: 144), a O ⁇ 8b extracellular domain (SEQ ID NO: 145), a O ⁇ 8b transmembran
• Neoepitope-specific TCRs identified by the imPACT Isolation Technology described in PCT/US2020/17887 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 Figures 1A-1C). The single-step non-viral precision genome engineering resulted in the seamless replacement of the endogenous TCR with the patient’ s neoepitope- specific TCR, expressed by the endogenous promoter. The TCR expressed on the surface is entirely native in sequence.
• TLA Targeted Locus Amplification
• constructs containing genes of interest were inserted into endogenous loci. This was accomplished with the use of homologous repair templates containing the coding sequence of the gene of interest flanked by left and right HR arms. In addition to the HR arms, the gene of interest was sandwiched between 2A peptides, a protease cleavage site that is upstream of the 2A peptide to remove the 2A peptide from the upstream translated gene of interest, and signal sequences ( Figure IB). Once integrated into the genome, the gene of interested expression gene cassette was transcribed as single messenger RNA.
• flanking regions were unlinked from the gene of interest by the self-cleaving 2 A peptide and the protease cleavage site was cleaved for the removal of the 2A peptide upstream from the translated gene of interest ( Figure 1C).
• a gly-ser-gly (GSG) linker was inserted before each 2A peptide to further enhance the separation of the gene of interest from the other elements in the expression cassette.
• P2A peptides were superior to other 2A peptides for Cell Products because of its efficient cleavage. Accordingly, two (2) P2A peptides and codon divergence were used to express the gene of interest without introducing any exogenous epitopes from 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 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.
• NeoTCRs were integrated into the TCRa 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 TCRP 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 with linear templates.
• the target TCRa locus (Ca) is shown along with the plasmid HR template, and the resulting edited sequence and downstream mRNA/protein products in Figures IB and 1C.
• the target TCRa locus endogenous TRAC
• its CRISPR Cas9 target site horizontal stripe, cleavage site designated by arrow
• Figures 1A-1C The circular plasmid HR template with the polynucleotide encoding the NeoTCR is located between left and right homology arms (“LHA” and“RHA” respectively).
• LHA left and right homology arms
• the region of the TRAC introduced by the HR template that was codon optimized is shown (vertical stripe).
• the TCRP constant domain was derived from TRBC2, which is indicated as being functionally equivalent to TRBC1.
• the HR template of the NeoTCR expression gene cassette includes two flanking homology arms to direct insertion into the TCRa genomic locus targeted by the CRISPR Cas9 nuclease RNP with the TCRa guide RNA. These homology arms (LHA and RHA) flank the neoE-specific TCR sequences of the NeoTCR expression gene cassette. While the protease cleavage site used in this example was a furin protease cleavage site, any appropriate protease cleavage site known to one of skill in the art could be used. Similarly, while HGH was the signal sequence chosen for this example, any signal sequence known to one of skill in the art could be selected based on the desired trafficking and used.
• the NeoTCR expression gene cassette is transcribed as a single messenger RNA from the endogenous TCRa promoter, which still includes a portion of the endogenous TCRa polypeptide from that individual T cell ( Figure 1C).
• the NeoTCR sequences are unlinked from the endogenous, CRISPR- disrupted TCRa polypeptide by self-cleavage at a P2A peptide ( Figure 1C).
• NeoTCRa and NeoTCRp polypeptides are also unlinked from each other through cleavage by the endogenous cellular human furin protease and a second self-cleaving P2A sequence motifs included in the NeoTCR expression gene cassette ( Figure 1C).
• the NeoTCRa and NeoTCRp polypeptides are separately targeted by signal leader sequences (derived from the human growth hormone, HGH) to the endoplasmic reticulum for multimer assembly and trafficking of the NeoTCR protein complexes to the T cell surface.
• the inclusion of the furin protease cleavage site facilitates the removal of the 2A sequence from the upstream TCRP chain to reduce potential interference with TCRP function.
• Inclusion of a gly-ser-gly linker before each 2A (not shown) further enhances the separation of the three polypeptides.
• TRAC exon 1 vertical stripe
• NeoTCR Products In addition to NeoTCR Products, this method can be used for any CD8 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.
• TLA Targeted Locus Amplification
• 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 (using Miltenyi antibodies and isolation column) were used fresh or cryopreserved in 1% human serum albumin (Gemini), 49% plasmalyte (Baxter), and 50% CS10 (Sigma).
• T cells were electroporated with i) a plasmid for the production of a NeoTCR Product (see, e.g, Figure IB) or ii) a CD8 Construct 1 (e.g, consisting of the coding sequence of CD8a flanked by P2A sites upstream of the neoTCR beta and alpha sequences and gRNA-Cas9 RNPs targeting the TCR alpha and beta loci; see, e.g, Figure 2A).
• An exemplary expression construct of CD8 Construct 1 is shown in Figure 11 A.
• T cells were electroporated using the Lonza X-unit in 100 pL cuvettes and program EO-115. T cells are expanded in culture medium supplemented with 12.5 ng/mL IL7 + 12.5 ng/mL IL15. Supplemented medium was exchanged every 2-3 days until the end of study, 13 days after activation.
• 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.
• 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-CD8p, 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 analyzed with either FCS Express or FlowJo.
• Cytometric Bead Array 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.
• wash buffer PBS supplemented with 1% BSA and 0.05% 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 IX penicillin- streptomycin solution. T cells were plated onto the comPACT coated plate at 100 pL/well and incubated at 37°C, 5% C02. After 24h the supernatant was collected, and the cytokine concentrations were analyzed using the BD Cytometric Bead Array (CBA) Human Thl/Th2 Cytokine Kit II (Catalog No. 551809) following the manufacturer’s protocol.
• CBA Cytometric Bead Array
• 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 IFNy secretion over a range of comPACT concentrations.
• 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-CD8a, anti-CD8p, 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-IFNy, 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.
• e450 proliferation dye eBioscience
• HLA-matched cell lines were pulsed with the cognate neoantigen peptide or mismatched peptide for lh 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 48h 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.
• CD8 Product 1 An expression construct consisting of the coding sequence (CDS) of CD8a flanked by P2A sites upstream of the neoTCR beta and alpha sequences is synthesized. Briefly, the CDS of human CD8a is synthesized with a GSG-linker and P2A site upstream and flanked with restriction sites. The neoTCR expression vector of interest and the synthesized CD8a construct were incubated with restriction enzymes and ligated together to create the final HDR construct. The CD8 Construct 1 was electroporated along with gRNA-Cas9 RNPs targeting the TCRa and b loci.
• CDS coding sequence
• Model neoTCRs known to bind dextramer among CD8 T cells but not CD4 T cells were used to demonstrate that expression of the CD8a transgene enables these TCRs to bind dextramer among CD4 T cells.
• CD8a engineered CD4 T cells were stained with anti-CD8a antibodies and surface expression of the transgene is confirmed by flow cytometry as described above.
• NeoTCRs known to bind dextramer among CD8 T cells only e.g, TCR 097 were used to demonstrate that expression of the CD8a transgene enables these TCRs to bind dextramer among CD4 T cells. See, Figures 13A, 13B, 14, 15A, and 15B.
• CD4 T cells engineered to express the CD8a transgene were double positive for CD4 and CD8a.
• CD8 T cells were also engineered to express the CD8a transgene and characterized as described above.
• Relative CD8a gene expression was also quantified via RT-qPCR and compared to control non-engineered CD8 T cells.
• CD8 T cells expressing the CD8a transgene had higher than endogenous levels of CD8a expression. Effect of CD8 expression on T cell proliferation upon encounter of cognate antigen. Edited T cells were stained with a proliferation dye as described above. After staining, T cells were stimulated with a range of concentrations of cognate comPACT proteins. 48-72 hours later, T cells were harvested and stained with anti-CD4, anti-CD8, and anti-2A peptide as described above.
• NeoTCR-expressing T cells lacking the CD8a transgene were used as a negative control.
• NeoTCR CD4 T cells expressing the CD8a transgene proliferated in response to lower concentrations of cognate comPACT than CD4 T cells lacking CD8a expression.
• NeoTCR Products and CD8 Product 1 were be stimulated with various concentrations of cognate comPACT for 5 hours in the presence of brefeldin A. After stimulation, T cells were stained with anti-CD4 and anti-CD8a. Cells were be permeabilized and stained with anti-P2A peptide, anti-IFNy, anti-TNF, and anti- IL2.
• NeoTCR CD4 T cells expressing the CD8a transgene produced effector cytokines in response to lower concentrations of cognate comPACT than neoTCR CD4 T cells lacking CD8a expression.
• CD8a expression on killing activity upon encounter of cognate antigen.
• edited CD4 and CD8 T cells were cultured with HLA-matched target cells pulsed with cognate peptide as described above.
• CD4 and CD8 T cells were edited separately to evaluate the ability of CD4 T cells expressing CD8a to kill target cells.
• NeoTCR CD4 T cells expressing the CD8a transgene killed a greater fraction of target cells presenting cognate peptide than neoTCR CD4 T cells lacking CD8a expression.
• CD4 T cells engineered to express CD8a lack CD8P expression.
• CD8P has a higher affinity for LCK (Irie et ah, 1998, J. Immunol, 161(1), 183-191). Therefore, T cells were edited to co-express CD8P with CD8a (i.e., a CD8 Product 2).
• An additional construct containing CD8P flanked by P2A sites, CD8a flanked by P2A sites, followed by the TRB and TRA alleles as previously described is generated.
• CD4 and CD8 T cells expressing CD8a and CD8P are evaluated using the same assays described above.
• An exemplary expression construct with the CD8a and CD8 b sequences is shown in Figure 11B.
• NeoTCR CD4 T cells expressing the CD8a and OI ) 8b transgenes proliferated in response to lower concentrations of cognate comPACT than CD4 T cells expressing CD8a transgene alone.
• NeoTCR CD4 T cells expressing the CD8a and OI ) 8b transgenes also produced effector cytokines in response to lower concentrations of cognate comPACT than neoTCR CD4 T cells expressing the CD8a transgene alone.
• neoTCR CD4 T cells expressing the CD8a and CD8P transgenes killed a greater fraction of target cells presenting cognate peptide than neoTCR CD4 T cells expressing CD8a transgene alone.
• chimeric proteins made up of the coding sequences for the extracellular and transmembrane domains of CD8a linked to the intracellular domain of OI ) 8b were generated.
• An exemplary expression construct with the extracellular and transmembrane domains of CD8a linked to the intracellular domain of CD8P sequences is (i.e., a CD8 Product 3) shown in Figure 11C.
• CD4 has an even higher affinity for LCK than CD8 (Irie et ah, 1998). Therefore, a second chimeric protein was generated containing the coding sequences for the extracellular and transmembrane domains of CD8a linked to the intracellular domain of CD4.
• An exemplary expression construct with the extracellular and transmembrane domains of CD8a linked to the intracellular domain of CD4 sequences (i.e., a CD8 Product 4) is shown in Figure 11D.
• CD4 and CD8 T cells expressing the CD8 Products 3 and 4 were evaluated using the same assays described above.
• NeoTCR CD4 T cells expressing the CD8a-CD8P-ID transgene proliferated in response to lower concentrations of cognate comPACT than CD4 T cells expressing CD8a transgene alone.
• NeoTCR CD4 T cells expressing the CD8a-CD8P-ID transgene produced effector cytokines in response to lower concentrations of cognate comPACT than neoTCR CD4 T cells expressing the CD8a transgene alone.
• NeoTCR CD4 T cells expressing the CD8a-CD8p-ID transgene killed a greater fraction of target cells presenting cognate peptide than neoTCR CD4 T cells expressing CD8a-CD8P-ID transgene.
• NeoTCR CD4 T cells expressing the CD8a-CD4-ID transgene proliferated in response to lower concentrations of cognate comPACT than neoTCR CD4 T cells expressing CD8a-CD8P-ID transgene.
• NeoTCR CD4 T cells expressing the CD8a-CD4 transgene produced effector cytokines in response to lower concentrations of cognate comPACT than neoTCR CD4 T cells expressing the CD8a-CD8P-ID transgene.
• NeoTCR CD4 T cells expressing the CD8a-CD4-ID transgene killed a greater fraction of target cells presenting cognate peptide than neoTCR CD4 T cells expressing CD8a-CD8P-ID transgene.
• NeoTCR CD8 T cells expressing the CD8a-CD4-ID transgene proliferated in response to lower concentrations of cognate comPACT than neoTCR CD8 T cells lacking the transgene.
• NeoTCR CD8 T cells expressing the CD8a-CD4 transgene produced effector cytokines in response to lower concentrations of cognate comPACT than neoTCR CD8 T cells lacking the transgene.
• NeoTCR CD8 T cells expressing the CD8a-CD4-ID transgene killed a greater fraction of target cells presenting cognate peptide than neoTCR CD8 T cells lacking the transgene.
• Example 5 CD8 Products have increased sensitivity to neoE-HLA target recognition and trigger pro-inflammatory and cytotoxic function
• MHC-I neoTCRs were cloned from neoE-specific T cells captured from the blood of a patient with colorectal cancer. Healthy donor CD8 and CD4 T cells were precision genome engineered to express the cloned MHC-I neoTCRs alone or to include engineering of ectopic CD8 co-receptors in the gene-edited T cells. Flow cytometric analysis was used to evaluate surface expression of neoTCRs and ectopic CD8 co-receptors (i.e., the CD8 and CD4 components of the CD8 Constructs 1-4), respectively.
• CD8-dependent neoTCRs was observed.
• CD 107a and intracellular IFNy staining revealed 10- 100-fold increases in the sensitivity of MHC-I neoTCR-induced effector functions by CD4 T cells, with no effect on specificity. No change in functionality or sensitivity was seen on CD8 T cells by the expression of additional CD8 co-receptor.
• CD8a homodimer (CD8 Construct 1)
• CD8a-P2A-CD8p (CD 8 Construct 2)
• CD8a with CD8P intracellular domain (CD8 Construct 3)
• CD8a homodimer with CD4 intracellular domain (CD8 Construct 4)
• CD8 Constructs and resulting CD8 Products were designed to allow for varying degrees of LCK affinity.
• CD8 Product 1 was shown to have the lowest LCK affinity, followed by CD8 Product 2, CD8 Product 3, and CD8 Product 4 (in that order with CD8 Product 4 having the highest LCK affinity.
• this product was used in cell killing assays to exemplify the increased cell killing ability of CD8 Products 1-4 compared to NeoTCR Products.
• CD4+ T cells were engineered as described herein to express the CD8 Product 4 (with TCR097 as the NeoTCR in the product) described in Figured 2D and 3D.
• SW620 cell lines that were engineered to heterologously express the R20Q mutation (the cognate antigen to TCR097).
• the CD8 Product 4 expressing NeoTCR097 was combined with the SW620 heterologous cells.
• the CD8 Product 4 provided substantially better killing of the cognate antigen expressing SW620 cells than the NeoTCR Product also expressing the TCR097.
• the experiment shown in Figure 13A was done with an E:T ratio of 1 : 1 and as shown in the graph, the NeoTCR Product expressing TCR097 did not show any efficacy at killing of the cognate antigen expressing SW620 cells.
• the experiment shown in Figure 13B was done with an E:T ratio of 2: 1 and while the NeoTCR Product expressing TCR097 showed some ability to kill the cognate antigen expressing SW620 cells, it was clear from the experiment that the CD8 Product 4 expressing the TCR097 had superior efficacy.
• the high expression of the cognate antigen in the homozygous SW620 cells is not physiologically relevant and this experiment serves to highlight the ability to rescue NeoTCR Products with low affinity TCRs that cannot effectively engage with and kill tumor cells by further engineering them to also include a CD8a homodimer with CD4 intracellular domain (z.e., a CD8 Product 4).
• CD8 T cells were also transfected to express the NeoTCR097 and a CD8a homodimer with CD4 intracellular domain (z.e., a CD8 Product 4 using CD8 T cells instead of CD4 T cells).
• the CD8 Product 4 provided substantially better killing of the SW620 cells than the NeoTCR Product when the products were made from CD4 T cells.
• the CD8 Product 4 and NeoTCR Product were made from CD8 T cells (the bottom graphs in Figures 15A and 15B) the ability of the NeoTCR Product was rescued because of the endogenous CD8 expression in the CD8 T cells.
• Example 6 CD8 Products have increased CD4 T cell sensitivity while maintaining NeoTCR sensitivity
• CD8 Products 1, 2, 3, and 4 were tested to determine surface expression of CD8a. It was shown that each of CD8 Products 1, 2, 3, and 4 exhibited normal CD8a surface expression. Representative data from CD8 Product 4 is shown in Figure 16.
• CD8 Constructs affected CD4 T cell sensitivity and specificity for the cognate antigen of the expressed NeoTCR in the CD8 Products. Sensitivity experiments were performed and it was shown that CD8 Products 1- 4 exhibited an increased CD4 T cell sensitivity ( Figure 17A). Specificity experiments were also performed on CD8 Products 1-4. CD8 Products 1, 2, 3, and 4 were made with NeoTCR097. Experiments were performed to test the CD8 Products 1, 2, 3, and 4 (expressing NeoTCR097) to assess the specificity of these products to the cognate antigen to NeoTCR097.
• CD8 Products 1, 2, 3, and 4 (expressing NeoTCR097) were specific for the cognate antigen to NeoTCR097 and showed no activity when exposed to a mismatched antigen. The specificity was determined by INFy and CD 107 production which are evidence of T cell activation. Thus, the CD8 Products described herein have an increased sensitivity to CD4 T cells and maintain their specificity to cognate antigen to the expressed NeoTCR compared to NeoTCR Products expressing the same NeoTCR.
• NeoTCR Products 1, 2, 3, and 4 surprisingly increased the sensitivity of CD8-dependent (e.g., NeoTCR097) and CD8-independent (e.g., NeoTCR089) NeoTCRs. Accordingly, it was shown that the CD8 Constructs 1, 2, 3, and 4 can improve NeoTCR engagement and T cell killing of tumor cells with cognate NeoTCR antigens for all NeoTCRs regardless of whether they are CD8-dependent or CD8- independent.

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