Non-viral precision T cell receptor replacement for personalized cell therapy

T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1-3. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.

Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy

Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells1-14. The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8+ T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.

Abstract 2829: Non-viral precision genome engineering enables personalized adoptive neoTCR T cell therapy for cancer including multiple additional edits that improve the activity of neoTCR T cells by enhancing CD4 T cell antigen sensitivity and conferring resistance to TGFβ

Personalized autologous TCR-T cell therapies targeting neoepitopes (neoE) derived from tumor-specific mutations are a compelling approach for the treatment of patients with solid tumors. Using the ultra-sensitive imPACT Isolation Technology®, antigen-experienced, neoE-specific CD8 T cells are captured from the blood of patients with solid cancers followed by cloning of the cognate, neoE-specific, MHC class I-restricted T cell receptors (neoTCRs). DNA-mediated (non-viral) precision genome engineering technology is then used to engineer autologous CD8 and CD4 T cells to express the neoTCR. We have further built upon this platform to modify neoTCR-T cells to address potential sources for tumor immune evasion.

The versatility of this single-step gene editing platform is demonstrated here by the presentation of a neoTCR T cell product with knockout of endogenous TCRα and TCRβ and the simultaneous expression of a neoTCR with CD8 co-receptor (CD8coR) from the same expression cassette along with knockout of TGFβ receptor 2 (TGFBR2). We have previously shown that CD8coR expression augments the activity of CD4 T cells engineered to express MHC class I restricted neoTCRs, by increasing CD4 neoTCR T cell helper and effector function. TGFβ is known to promote tumor growth, metastasis, and epithelial to mesenchymal transition (EMT) and to inhibit effector immune responses while promoting fibrosis and the differentiation of inhibitory cell types such as regulatory T cells. TGFβ is expressed by many tumor types and high TGFβ expression is associated with worse prognosis for several cancer subtypes including colorectal, lung and glioblastoma. TGFBR2 is a critical mediator of TGFβ signaling, resulting in potent, inhibitory effects on T cell function.

Our data show that simultaneous ablation of TGFBR2 signaling and expression of CD8coR was achieved with high efficiency, resulting in fully functional CD8 and CD4 neoTCR-T cells. Deletion of TGFBR2 with or without CD8coR expression, together with the expression of a neoE-targeted TCR preserved T cell effector function in the presence of inhibitory concentrations of TGFβ. Importantly, the combination of TGFBR2 knockout and CD8coR expression resulted in additive benefits, providing proof-of-concept for modifying two orthogonal features to improve neoTCR T cell function. Altogether, these results demonstrate the applicability of this versatile, precision genome engineering platform technology to yield enhanced, next-generation neoTCR-T cell therapies to expand the potential for clinical benefit in persons with solid cancers.

Citation Format: Charles W. Tran, Kayla Lee, Bhamini Purandare, James Byers, Michael M. Dubreuil, William Lu, Michal Mass, Kyle Jacoby, Stefanie J. Mandl, Barbara Sennino. Non-viral precision genome engineering enables personalized adoptive neoTCR T cell therapy for cancer including multiple additional edits that improve the activity of neoTCR T cells by enhancing CD4 T cell antigen sensitivity and conferring resistance to TGFβ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2829.

Targeting CD73 with AB680 (Quemliclustat), a Novel and Potent Small-Molecule CD73 Inhibitor, Restores Immune Functionality and Facilitates Antitumor Immunity

T cells play a critical role in the control of cancer. The development of immune checkpoint blockers (ICB) aimed at enhancing antitumor T-cell responses has revolutionized cancer treatment. However, durable clinical benefit is observed in only a subset of patients, prompting research efforts to focus on strategies that target multiple inhibitory signals within the tumor microenvironment (TME) to limit tumor evasion and improve patient outcomes. Adenosine has emerged as a potent immune suppressant within the TME, and CD73 is the major enzyme responsible for its extracellular production. CD73 can be co-opted within the TME to impair T-cell-mediated antitumor immunity and promote tumor growth. To target this pathway and block the formation of adenosine, we designed a novel, selective, and potent class of small-molecule inhibitors of CD73, including AB680 (quemliclustat), which is currently being tested in patients with cancer. AB680 effectively restored T-cell proliferation, cytokine secretion, and cytotoxicity that were dampened by the formation of immunosuppressive adenosine by CD73. Furthermore, in an allogeneic mixed lymphocyte reaction where CD73-derived adenosine had a dominant suppressive effect in the presence of PD-1 blockade, AB680 restored T-cell activation and function. Finally, in a preclinical mouse model of melanoma, AB680 inhibited CD73 in the TME and increased the antitumor activity of PD-1 blockade. Collectively, these data provide a rationale for the inhibition of CD73 with AB680 in combination with ICB, such as anti-PD-1, to improve cancer patient outcomes.

Abstract 1526: Single-step precision genome engineering platform enables versatile generation of personalized (neoTCR) adoptive cell therapy T cells with supplementary anti-tumor attributes

Personalized autologous TCR-T cell therapies targeting neoE-specific neoepitopes (NeoE) derived from tumor-exclusive mutations are a compelling approach for the treatment of patients with solid tumors. Using the ultra-sensitive imPACT Isolation Technology®, antigen-experienced neoE-specific CD8 T cells are captured from the blood of patients with solid cancers followed by cloning of the cognate neoepitope-specific HLA class I-restricted T cell receptors (HLA-I neoTCRs). Using DNA-mediated (non-viral) precision genome engineering technology, fresh CD8 and CD4 T cells from the same patient with cancer are engineered to express the HLA-I neoTCR. We have further innovated this platform of precision genome engineering to confer neoTCR-T cells with supplementary gene edits to address the array of potential sources for tumor immune evasion. Two examples of the versatility of this single step gene editing platform are described in this study: 1) concurrent expression of a CD8 co-receptor (CD8coR) to augment activity of CD4 T cells engineered with lower affinity HLA-I neoTCRs; and 2) simultaneous disruption of TET2 expression in T cells, which has previously been reported to positively affect T cell differentiation and persistence. The data shows that these simultaneous supplemental gene modifications were achieved with high efficiency, resulting in fully functional CD8 and CD4 neoTCR-T cells. Surface expression of CD8coR together with the neoE-targeted TCR increased T cell effector function and antigen-specific tumor cell killing. NeoTCR-T cells with concomitant deletion of TET2-expression exhibited enhanced cytotoxicity against neoantigen-expressing tumor cells. Together, these results demonstrate the applicability of this versatile precision genome engineering platform technology to yield enhanced next generation neoTCR-T cell therapies to expand the potential for clinical benefit in treating persons with solid cancers.

Citation Format: Michael M. Dubreuil, Charles W. Tran, Bhamini Purandare, William Lu, James Byers, Michal Mass, Kyle Jacoby, Barbara Sennino, Alex Franzusoff, Stefanie J. Mandl. Single-step precision genome engineering platform enables versatile generation of personalized (neoTCR) adoptive cell therapy T cells with supplementary anti-tumor attributes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1526.

Abstract 2177: Tumor neoantigen profiling with validated patient-specific TCR characterization to improve neoepitope prediction

PACT Pharma has developed an ultra-sensitive approach to validate predicted neoantigens and the cognate T cell receptors (neoTCRs) from tumor specific somatic mutations by capturing neoantigen-specific T cells from peripheral blood. This process is used in clinical trials (NCT03970382) of personalized neoTCR-T therapy for persons with solid cancers.

Using the state of the art prediction pipeline and screening process, more than one hundred twenty neoantigens were predicted from 5 type of solid cancers that were validated by characterizing cognate T cells and their close to 200 unique TCRs captured from the blood of the same individual. These validated neoepitopes of 8 to 11 amino acids represent broad HLA class I coverage with >30 alleles to date. Our analysis revealed that mutations can occur in all positions within the epitopes. Epitope immunogenicity is potentially affected by different mechanisms including mutation position, agretopicity, as well as HLA interacting positions and/or by interactions between mutated residues and its cognate TCRs. It was observed that these validated neoepitopes comprise broad ranges of predicted HLA binding affinities, stability, and neoantigen expression levels. The analysis presented here offers insights to enable machine learning to advance rules for epitope selection and prioritization that may be important for immunological approaches to address a broad range of diseases, including cancer.

Citation Format: Zheng Pan, Olivier Dalmas, Songming Peng, Kyle Jacoby, Barbara Sennino, Yan Ma, Chad Smith, Amin Momin, Allison Xu, Katharine Heeringa, Jonathan Johnston, Duo An, Boi Quach, William Lu, Diana Nguyen, Andrew Conroy, Bhamini Purandare, Eva Huang, Eric Stawiski, Alex Franzusoff, Stefanie Mandl. Tumor neoantigen profiling with validated patient-specific TCR characterization to improve neoepitope prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2177.

Abstract 2192: Non-viral genome engineering method allows highly efficient, single-step removal and precise insertion of multiple large genes

Recent advances in gene editing have enabled the targeted engineering of primary cells to insert entire transgenes without the use of viral vectors. Using these methods, novel genes can be inserted in a seamless manner into the specified genomic locus, realizing the goal of precise targeted genomic modifications. Non-viral modification of primary cells holds potential to significantly reduce costs and time needed for the generation of therapeutic cell products. It has also allowed the generation of personalized cell therapies involving patient-specific manufacturing of DNA constructs, such as for the developed of patient-derived, neoepitope-specific TCR-T cells.

Proof-of-concept experiments have shown that non-viral genome engineering methods can integrate small genetic elements such as GFP, while the delivery of larger therapeutically relevant payloads at high efficiency has previously been challenging. Here we describe a proprietary single-step, DNA-mediated method developed for seamlessly engineering fully natural neoepitope-specific TCRs (neoTCR) into the endogenous TCR locus of primary human T cells at high efficiencies (i.e. >50% gene editing efficiency). This method allows the delivery of the two genes comprising the neoTCR without the need for selection necessitated by less efficient approaches.

To further evaluate this approach, fresh human donor T cells were engineered to express the patient-specific neoTCR plus two additional gene products, CD8α and CD8β (i.e. precise genome engineering of four ectopic genes). The data shows that these modifications were made at high efficiency, resulting in fully functional CD8 and CD4 T cells. Surface expression of CD8 coreceptor together with the neoE-targeted TCR increased T cell signaling sensitivity of the engineered neoTCR-T cells by 10-100 fold.

The potential for off-target cleavage or unexpected genomic outcomes was assessed using multiple methods, including a newly developed primary T cell GUIDE-seq assay. Despite multi-locus editing, no evidence of off-target insertion or unexpected genomic rearrangements were observed.

In summary, these results demonstrate the applicability of a single step, highly efficient method for manufacturing fresh human T cells into neoTCR-T cell therapies, engineered with multiple functionalities. This proprietary precision genome engineering technology supports the on-going Phase 1 clinical trial of personalized autologous, NeoTCR-P1 engineered T cell therapies for patients with solid tumors (NCT03970382).

Citation Format: Kyle Jacoby, William Lu, Diana Nguyen, Barbara Sennino, Andrew Conroy, Bhamini Purandare, Alex Franzusoff, Stefanie Mandl. Non-viral genome engineering method allows highly efficient, single-step removal and precise insertion of multiple large genes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2192.

Abstract NG11: Landscape analysis of neoepitope-specific T-cell responses to immunotherapy

In infectious disease, polyclonal T cell responses against immunodominant epitopes drive successful immune responses. In cancer, neoepitopes (neoE) derived from non-synonymous mutations, similarly to the immunodominant epitopes in viral infections, are potentially highly immunogenic because the T cells recognizing these antigens are not subjected to the mechanisms of tolerance. Indeed, early studies support that neoE derived from non-synonymous mutations are the primary target of T cell responses induced by immune checkpoint blockade therapy and have been successfully targeted by adoptively transferred T cell therapies (ACT) in multiple cancer histologies. However, there is limited knowledge on the immunodominance and evolution of neoE's, or the clonality of the T cell responses against these neoE. Furthermore, little is known regarding the correlation between the presence and expansion of neoE-specific T cells and the clinical response to immunotherapy in patients. To characterize the neoE-specific T cell responses induced after immunotherapy, we collected peripheral blood mononuclear cells (PBMCs) over time (longitudinally) and established expanded tumor infiltrating lymphocyte cultures (TILs) and autologous tumor cell lines from the patient's tumor biopsies. We performed whole exome and RNA sequencing of the tumor and normal tissue controls for the computational prediction and ranking of patient-specific neoEs. We then generated a library of capture reagents consisting of the patient HLA class I molecules loaded with predicted neoE (Peng et al. AACR 2019) and isolated neoE-specific T cells from the patients' PBMC or TIL samples. Once isolated, the paired neoE-specific TCR alpha and beta chains (neoTCR) were obtained by single cell sequencing. For functional characterization of the neoTCRs, healthy donor primary human T cells were modified to express the neoTCR using CRISPR-based, non-viral precision genome engineering by replacing the endogenous TCR with the respective neoTCR (Jacoby et al., AACR 2019, Sennino et al., AACR 2019). These gene-edited T cells were then used in co-culture experiments with the patient autologous cell lines. We analyzed T cell responses in three patients (PT1, PT2, and PT3) with metastatic melanoma receiving immunotherapy. PT1 had a fast and durable anti-tumor response to anti-PD-1 therapy. Sequencing identified 2556 somatic coding mutations. A library of 243 neoE-specific pMHC capture reagents across 3 HLA types, HLA-A*03:01, A*24:01, and C*12:03 was generated and used for screening of PBMCs or TILs derived from multiple longitudinal time points. Several hundred neoE-specific T cells were isolated. Importantly, this neoE-specific T cell response was comprised of 17 different neoE-specific T cells clones targeting only 5 different HLA-neoE complexes supporting the immunodominance hypothesis. On the other hand, PT2 and PT3 showed marginal responses to immunotherapy. Patient two progressed after being treated with anti-PD1. This patient had 24 somatic coding mutations. Seventeen neoE-HLA reagents across 3 HLAs, B*35:03, C*12:03, and C*08:01 were generated and used to capture neoE-specific T cells from TILs and PBMCs. While 14 different TCRs targeting 7 HLA-neoE complexes were identified from expanded TILs, no neoE-reactive T cells were captured from the peripheral blood. PT3 presented with progressive disease after being treated with local TVEC. This patient had 61 somatic coding mutations; 78 neoE-specific pHLA capture reagents covering HLA-A*02:01, A*03:01, B*07:02, C*05:01, and C*07:02 were generated and used to screen for neoE-specific T cells in the patient's TIL and PBMCs. In contrast to PT2, 2 different neoTCRs targeting the same HLA-neoE complexes were isolated from PBMCs, but none from TILs. To further characterize the T cell responses from patients that responded or did not respond to immunotherapy, we generated 18 separate T cell products, each expressing a different neoTCR isolated from PT1, PT2 and PT3. For PT1, we characterized 14 different neoTCRs specific for neoE's in the mutated IL8, PUM1 and TPP2 genes. All 14 T cell products displayed specific cytotoxicity against the matched autologous melanoma cell line established from a biopsy of patient one (50-75% tumor growth inhibition compared to melanoma cell line growth in co-culture with a mismatched control TCR, 96 hour assay using a product to target ratio (P:T) of 1:1, p < 0.000001 for each comparison). No cytotoxic effect against an unmatched human melanoma cell line was observed. Furthermore, neoE TCR T cells upregulated 4-1BB and OX-40, secreted IFNγ, IL-2, TNFα, and IL6, and induced T cell proliferation and degranulation. Again, no unspecific T cell activation was observed when T cells were co-cultured with unmatched targets. Interestingly, precision genome engineered T cell products expressing neoTCRs identified from patients that did not respond to therapy (PT2 and PT3), also potently killed autologous tumor cells. Four neoTCRs were studied (2 TCR for PT2 and 2 TCRs for PT3), and three of them showed specific cytotoxicity against the matched autologous melanoma cell line (50-100% tumor growth inhibition compared to melanoma cell line growth in co-culture with a mismatched control TCR, 96 hour assay using P:T 5:1, p < 0.05 for each comparison). Additionally, upon co-culture with the matched melanoma cell line, but not against an unmatched melanoma cell line control, neoE TCR T cells upregulated 4-1BB and OX-40, secreted IFNγ, IL-2, TNFα, and IL6, and induced T cell proliferation and degranulation. These data demonstrate that even patients that did not respond to immunotherapy harbor neoTCRs that, when expressed in ‘fresh' T cells, are able to kill the autologous tumor cell lines. Using newly developed techniques to isolate and capture neoE-specific single T cells, as well as non-viral gene editing, we isolated and characterized neoE-specific T cells that can recognize the cancer cells and induce an anti-tumor response. We also studied the neoE immunodominance and TCR clonality over time of the natural T cell repertoire that induce anti-tumor responses to ICB therapy. Our results show that in a patient with a good response to anti-PD-1, there is a polyclonal response that targets a limited number of neoE-HLA complexes (2% of the neoE tested in the case of patient one) highlighting the immunodominance of these epitopes. Interestingly, different T cell clonotypes targeting the same mutations evolve over time, suggesting functional differences amongst the TCRs. In addition, our results demonstrate that even patients that did not respond to these therapies harbor neoE-specific T cells, as we were able to isolate neoE-specific T cells that recognized and killed patient-derived cancer cells. This suggests that even in patients that do not respond to immunotherapy, neoE-specific TCRs can be isolated and could be potentially used for personalized ACT. Finally, our results also show how non-viral precision genome engineering can successfully redirect T cells to neoE-expressing tumors, enabling the personalized ACT.

Citation Format: Cristina Puig-Saus, Barbara Sennino, Bhamini Purandare, Duo An, Boi Quach, Songming Peng, Huiming Xia, Sidi Zhao, Zheng Pan, Yan Ma, Justin Saco, Sameeha Jilani, Christine Shieh, Katharine Heeringa, Olivier Dalmas, Robert Moot, Diana Nguyen, William Lu, Kyle Jacoby, Andrew Conroy, Jasreet Hundal, Malachi Griffith, Stefanie Mandl, Alex Franzusoff, Antoni Ribas. Landscape analysis of neoepitope-specific T-cell responses to immunotherapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr NG11.

Abstract 1435: An ultra-sensitive and high-throughput technology (imPACT) for the identification and isolation of intrinsic and emergent neoepitope-specific T cells from the peripheral blood and TILs of cancer patients

T cells capable of targeting neoepitopes (neoE) from tumor-specific mutations hold the potential to uniquely recognize and kill tumor cells. However, most cancer patients fail to mount a sufficient intrinsic T cell immune response to translate into clinical benefit. PACT Pharma has developed an ultra-sensitive and high-throughput technology (imPACT) for identifying and isolating neoE-specific T cells from peripheral blood. Whole exome sequencing of tumors and computational prediction identify patient-specific neoepitopes resulting from tumor-specific mutations. We then interrogate patient blood for neoE-specific T cells using human leukocyte antigen (HLA) protein-based reagents comprising a spectrum of human HLAs, thus enabling the evaluation of >99% of all individuals with cancer. We have identified and isolated neoE-specific T cells from the peripheral blood of >80% treatment-naive patients with bladder and colorectal cancers, melanoma and other solid tumors. Primary human T cells engineered with T cell receptor sequences (TCRs) cloned from the imPACT-isolated T cells gain the ability to kill cognate neoE-presenting tumor cells, thereby also confirming the specificity of the isolated TCR sequences to bind to the neoE target. This approach is also amenable to the longitudinal analysis of patients undergoing treatment for their cancers, to characterize the neoE-specific T cell populations likely to confer clinical benefit. In summary, the imPACT technology efficiently discovers potentially meaningful intrinsic neoE-specific TCRs from patients, enabling the development of personalized neoTCR-T cell therapies for the eradication of solid tumors.

Citation Format: Songming Peng, Boi Quach, Duo An, Salemiz Sandoval, Robert Bao, Zheng Pan, Michael Bethune, Olivier Dalmas, Michael Yi, Corey Meadows, Katherine Heeringa, Linlin Guo, Benjamin yuen, John Sorfleet, Kyle Jacoby, Robert Moot, William Lu, Diana Nguyen, Barbara Sennino, Andrew Conroy, Bhamini Purandare, Adam Litterman, Stefanie Mandl, Alex Franzusoff. An ultra-sensitive and high-throughput technology (imPACT) for the identification and isolation of intrinsic and emergent neoepitope-specific T cells from the peripheral blood and TILs of cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1435.

Abstract 4783: Highly efficient, non-viral precision genome engineering for the generation of personalized neoepitope-specific adoptive T cell therapies

Methods used to engineer cells for adoptive cell therapies (ACT) utilizing receptors that are constant across many patients (CAR or shared Ag TCRs) typically rely on Lenti-, retro-, or adeno-associated virus to deliver specificity-altering sequences to T cells. However, for personalized therapies such as the generation of neoepitope-specific TCR T cell therapies, use of viral vectors is not feasible due to long manufacturing timelines and prohibitive per-patient costs. PACT Pharma has developed a highly efficient, DNA-mediated (non-viral) proprietary precision genome engineering approach to engineer neoepitope-specific primary human T cells. This method can be widely utilized to generate T cells at research scale, as well as for ex vivo manufacturing.

Briefly, genomes of individual primary human CD8 and CD4 T cells are engineered with site-specific nucleases in a single-step transfection process to yield efficient, targeted replacement of the endogenous TCR with the therapeutic neoTCR sequences. In this way, the expression of the endogenous TCR is abolished ensuring natural expression and regulation of the inserted neoTCR. The precision of neoTCR-T cell genome engineering was evaluated by Targeted Locus Amplification (TLA) for off-target integration hot spots or translocations, and by next generation sequencing based off-target cleavage assays and found to lack evidence of unintended outcomes.

Engineered neoepitope-specific T cells are highly functional as demonstrated by antigen-specific proliferation, killing and cytokine production. Phenotype and detailed functional characterization of PACTs neoTCR-P1 T cells were performed and are described in a separate abstract.

PACT’s precision genome engineering approach enables highly efficient generation of bespoke NeoTCR T cells for personalized adoptive cell therapy for patients with solid tumors. Furthermore, PACT precision genome 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.

Citation Format: Kyle Jacoby, Robert Moot, William Lu, Diana Nguyen, Barbara Sennino, Andrew Conroy, Bhamini Purandare, Adam J. Litterman, Fabrizia Urbinati, Susan P. Foy, Theresa Hunter, Albert Tai, Michael T. Bethune, Songming Peng, Olivier Dalmas, Alex Franzusoff, Stefanie J. Mandl. Highly efficient, non-viral precision genome engineering for the generation of personalized neoepitope-specific adoptive T cell therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4783.

Inhibition of DNA methylation enhances HLA-G expression in human mesenchymal stem cells

Mesenchymal stem cells (MSCs) are immunosuppressive multipotent cells under investigation for potential therapeutic applications in regenerative medicine and prevention of graft-versus-host disease. Human leukocyte antigen (HLA)-G contributes to the immunomodulatory properties of MSCs. HLA-G expression in MSCs is very low and diminishes during in vitro expansion. Epigenetic regulation activates HLA-G expression in some cancer cell lines but not in MSCs. In the present study, adipose- and bone marrow-derived MSCs were exposed to the DNA demethylating agent 5-aza-2-deoxycytidine (5-aza-dC) and histone deacetylase inhibitor valproic acid (VPA) and HLA-G mRNA levels assessed using semi-quantitative reverse-transcription PCR. Exposure to 5-aza-dC resulted in HLA-G1 and -G3 upregulation in both early and late passage MSCs. VPA treatment did not induce HLA-G expression in both bone marrow and adipose derived MSCs. Our results provide the first evidence that HLA-G3 could be expressed in MSCs and that methylation-mediated repression is partly responsible for the observed low levels of HLA-G expression in MSCs. Our findings provide insight that treatment of MSCs with specific epigenetic regulatory modulators may improve their immunoregulatory capability for therapeutic applications.

Temporal HLA profiling and immunomodulatory effects of human adult bone marrow- and adipose-derived mesenchymal stem cells

AIM

To investigate the temporal HLA expression profile and immunomodulatory function of mesenchymal stem cells (MSCs) during in vitro expansion.

MATERIALS & METHODS

Adult bone marrow-derived MSCs (BMSCs) and adipose-derived MSCs (AMSCs) were cultured and HLA class I and II mRNA expression were investigated during serial expansion using semiquantitative reverse-transcription PCR. The immunomodulatory properties of MSCs were monitored using peripheral blood mononuclear cell (PBMC) proliferation and cytotoxicity assays.

RESULTS

Semiquantitative reverse-transcription PCR revealed that classical HLA class I molecules were highly expressed in MSCs and remained relatively stable during extended culture. Variable expression levels of HLA class II molecules were detected in both BMSCs and AMSCs across passages. AMSCs were more resistant to PBMC-mediated cytotoxicity and suppressed PBMC proliferation more than BMSCs, although the effect was diminished with increasing passage.

CONCLUSION

These findings provide insight regarding the relationship between MSC passage number and MSC immunosuppressive properties and suggest that AMSCs hold advantages over BMSCs for immunomodulatory therapeutic purposes.

β2-Microglobulin-free HLA-G activates natural killer cells by increasing cytotoxicity and proinflammatory cytokine production

Human leukocyte antigen-G (HLA-G) is a nonclassical HLA class-I molecule and plays a role in tissue specific immunoregulation. Many studies have addressed functional aspects of β2-microglobulin (β2m)-associated HLA-G1. β2m-free HLA-G has been found in human placental cytotrophoblasts and pancreatic β cells although its function remains unclear. In the present study, we investigated the function of β2m-free HLA-G by transfecting HLA-G1 and -G3 into human β2m deficient rat pancreatic β cell carcinoma (BRIN-BD11) cells. RT-PCR and western blots studies confirmed high expression of HLA-G1 and -G3 in -G1 and -G3 transfectants, respectively. HLA-G1 and -G3 were detected mainly in intracellular compartments of BRIN-BD11 transductants by confocal fluorescent microscopy and flow cytometry. Functional analysis revealed that β2m-free HLA-G promoted xenogeneic cytotoxic lysis of BRIN-BD11 cells by natural killer (NK) cells and increased production of IL-1β, TNF-α, and IFN-γ. Stimulation of cytotoxic lysis was impaired by blocking the MAPK and DNA-PKcs pathways in NK cells. Importantly, treatment with 33mAb, a KLR2DL4 receptor agonist, induced NK-mediated cytotoxic lysis of BRIN-BD11 cells transfected with a mock vector. Our data suggest that β2m-free HLA-G activates NK cells via engagement of KLR2DL4 receptors.