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 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.

Development of chimeric antigen receptors targeting T-cell malignancies using two structurally different anti-CD5 antigen binding domains in NK and CRISPR-edited T cell lines

Relapsed T-cell malignancies have poor outcomes when treated with chemotherapy, but survival after allogeneic bone marrow transplantation (BMT) approaches 50%. A limitation to BMT is the difficulty of achieving remission prior to transplant. Chimeric antigen receptor (CAR) T-cell therapy has shown successes in B-cell malignancies. This approach is difficult to adapt for the treatment of T-cell disease due to lack of a T-lymphoblast specific antigen and the fratricide of CAR T cells that occurs with T-cell antigen targeting. To circumvent this problem two approaches were investigated. First, a natural killer (NK) cell line, which does not express CD5, was used for CAR expression. Second, CRISPR-Cas9 genome editing technology was used to knockout CD5 expression in CD5-positive Jurkat T cells and in primary T cells, allowing for the use of CD5-negative T cells for CAR expression. Two structurally distinct anti-CD5 sequences were also tested, i) a traditional immunoglobulin-based single chain variable fragment (scFv) and ii) a lamprey-derived variable lymphocyte receptor (VLR), which we previously showed can be used for CAR-based recognition. Our results show i) both CARs yield comparable T-cell activation and NK cell-based cytotoxicity when targeting CD5-positive cells, ii) CD5-edited CAR-modified Jurkat T cells have reduced self-activation compared to that of CD5-positive CAR-modified T cells, iii) CD5-edited CAR-modified Jurkat T cells have increased activation in the presence of CD5-positive target cells compared to that of CD5-positive CAR-modified T cells, and iv) although modest effects were seen, a mouse model using the CAR-expressing NK cell line showed the scFv-CAR was superior to the VLR-CAR in delaying disease progression.

Genetic engineering of chimeric antigen receptors using lamprey derived variable lymphocyte receptors

Chimeric antigen receptors (CARs) are used to redirect effector cell specificity to selected cell surface antigens. Using CARs, antitumor activity can be initiated in patients with no prior tumor specific immunity. Although CARs have shown promising clinical results, the technology remains limited by the availability of specific cognate cell target antigens. To increase the repertoire of targetable tumor cell antigens we utilized the immune system of the sea lamprey to generate directed variable lymphocyte receptors (VLRs). VLRs serve as membrane bound and soluble immune effectors analogous but not homologous to immunoglobulins. They have a fundamentally different structure than immunoglobulin (Ig)-based antibodies while still demonstrating high degrees of specificity and affinity. To test the functionality of VLRs as the antigen recognition domain of CARs, two VLR-CARs were created. One contained a VLR specific for a murine B cell leukemia and the other contained a VLR specific for the human T cell surface antigen, CD5. The CAR design consisted of the VLR sequence, myc-epitope tag, CD28 transmembrane domain, and intracellular CD3ζ signaling domain. We demonstrate proof of concept, including gene transfer, biosynthesis, cell surface localization, and effector cell activation for multiple VLR-CAR designs. Therefore, VLRs provide an alternative means of CAR-based cancer recognition.

High-throughput screening identifies compounds that enhance lentiviral transduction

A difficulty in the field of gene therapy is the need to increase the susceptibility of hematopoietic stem cells (HSCs) to ex vivo genetic manipulation. To overcome this obstacle a high-throughput screen was performed to identify compounds that could enhance the transduction of target cells by lentiviral vectors. Of the 1280 compounds initially screened using the myeloid-erythroid-leukemic K562 cell line, 30 were identified as possible enhancers of viral transduction. Among the positive hits were known enhancers of transduction (camptothecin, etoposide and taxol), as well as the previously unidentified phorbol 12-myristate 13-acetate (PMA). The percentage of green fluorescent protein (GFP)-positive-expressing K562 cells was increased more than fourfold in the presence of PMA. In addition, the transduction of K562 cells with a lentiviral vector encoding fVIII was four times greater in the presence of PMA as determined by an increase in the levels of provirus in genetically modified cells. PMA did not enhance viral transduction of all cell types (for example, sca-1(+) mouse hematopoietic cells) but did enhance viral transduction of human bone marrow-derived CD34(+) cells. Notably, the percentage of GFP-positive CD34(+) cells was increased from 7% in the absence of PMA to greater than 22% in the presence of 1 nM PMA. PMA did not affect colony formation of CD34(+) cells or the expression of the hematopoietic markers CD34 and CD45. These data demonstrate that high-throughput screening can be used to identify compounds that increase the transduction efficiency of lentiviral vectors, identifying PMA as a potential enhancer of lentiviral HSC transduction.

Simplified prototyping of perfusable polystyrene microfluidics

Cell culture in microfluidic systems has primarily been conducted in devices comprised of polydimethylsiloxane (PDMS) or other elastomers. As polystyrene (PS) is the most characterized and commonly used substrate material for cell culture, microfluidic cell culture would ideally be conducted in PS-based microsystems that also enable tight control of perfusion and hydrodynamic conditions, which are especially important for culture of vascular cell types. Here, we report a simple method to prototype perfusable PS microfluidics for endothelial cell culture under flow that can be fabricated using standard lithography and wet laboratory equipment to enable stable perfusion at shear stresses up to 300 dyn/cm(2) and pumping pressures up to 26 kPa for at least 100 h. This technique can also be extended to fabricate perfusable hybrid PS-PDMS microfluidics of which one application is for increased efficiency of viral transduction in non-adherent suspension cells by leveraging the high surface area to volume ratio of microfluidics and adhesion molecules that are optimized for PS substrates. These biologically compatible microfluidic devices can be made more accessible to biological-based laboratories through the outsourcing of lithography to various available microfluidic foundries.

Phenotypic correction of hemophilia A in sheep by postnatal intraperitoneal transplantation of FVIII-expressing MSC

We recently re-established a line of sheep that accurately mimics the clinical symptoms and genetics of severe hemophilia A (HA). Here, we tested a novel, nonablative transplantation therapy in two pediatric HA animals. Paternal mesenchymal stem cells (MSC) were transduced with a porcine FVIII-encoding lentivector and transplanted via the intraperitoneal route without preconditioning. At the time of transplantation, these animals had received multiple human FVIII treatments for various spontaneous bleeds and had developed debilitating hemarthroses, which produced severe defects in posture and gait. Transplantation of transduced MSC resolved all existent hemarthroses, and spontaneous bleeds ceased. Damaged joints recovered fully; the animals regained normal posture and gait and resumed normal activity. Despite achieving factor-independence, a sharp rise in pre-existent Bethesda titers occurred following transplantation, decreasing the effectiveness and duration of therapy. Postmortem examination revealed widespread engraftment, with MSC present within the lung, liver, intestine, and thymus, but particularly within joints affected at the time of transplantation, suggesting MSC homed to sites of ongoing injury/inflammation to release FVIII, explaining the dramatic improvement in hemarthrotic joints. In summary, this novel, nonablative MSC transplantation was straightforward, safe, and converted life-threatening, debilitating HA to a moderate phenotype in a large animal model.

Functional aspects of factor VIII expression after transplantation of genetically-modified hematopoietic stem cells for hemophilia A

BACKGROUND

Major complications with respect to the development of gene therapy treatments for hemophilia A include low factor VIII (fVIII) expression and humoral immune responses resulting in inhibitory anti-fVIII antibodies. We previously achieved sustained curative fVIII activity levels in hemophilia A mice after nonmyeloablative transplantation of genetically-modified hematopoietic stem cells (HSCs) encoding a B-domain deleted porcine fVIII (BDDpfVIII) transgene with no evidence of an immune response.

METHODS

Mouse HSCs were transduced using MSCV-based recombinant virus encoding BDDpfVIII and transplanted into hemophilia A mice. Transplanted mice were followed for donor cell engraftment, fVIII expression and activity, and generation of anti-fVIII immune response.

RESULTS

We now show that: (i) the protein expressed by hematopoietic cells has a specific activity similar to that of purified protein; (ii) BDDpfVIII expressed from hematopoietic cells effectively induces thrombus formation, which is shown using a new method of in vivo analysis of fVIII function; (iii) naïve and pre-immunized mice receiving HSC gene therapy are nonresponsive to challenges with recombinant human fVIII; (iv) nonresponsiveness is not broken after stringent challenges with BDDpfVIII; and (v) T cells from these mice are unresponsive to BDDpfVIII presentation. Furthermore, stem cells isolated from donors with high titer anti-human fVIII antibodies show no defects in donor cell engraftment or the ability to express BDDpfVIII.

CONCLUSIONS

These results demonstrate that HSC gene therapy can be an effective alternative treatment for individuals with hemophilia A and may benefit patients by inducing immunological nonresponsiveness to fVIII replacement products.