Tumor-reactive T-cell Receptor Research Articles

Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms.

A central challenge in developing personalized cancer cell immunotherapy is the identification of tumor-reactive T cell receptors (TCRs). By exploiting the distinct transcriptomic profile of tumor-reactive T cells relative to bystander cells, we build and benchmark TRTpred, an antigen-agnostic in silico predictor of tumor-reactive TCRs. We integrate TRTpred with an avidity predictor to derive a combinatorial algorithm of clinically relevant TCRs for personalized T cell therapy and benchmark it in patient-derived xenografts.

Abstract 53: T-cell receptor repertoire changes associated with clinical response in patients with B-cell non-Hodgkin’s lymphoma receiving CD19 CAR-T therapy

Abstract Background: Although CAR T-cell therapy has achieved remarkable response rates in adult patients (pts) with relapsed and refractory B-cell non-Hodgkin’s lymphoma (NHL), 20-30% of pts still have primary refractory disease, and 30-40% of pts relapse, often within 6 months of therapy. Given that durable clinical response can be achieved without CAR T cell persistence, we hypothesized that durable remission is correlated with the expansion of tumor-reactive T-cell receptor (TCR) clones following CAR T-cell infusion. To assess this, we examined the TCR repertoire of adult pts with B-NHL who received CD19 CAR T-cell (axi-cel) therapy to identify correlates of clinical response. Methods: Single-cell (sc) RNA sequencing (seq) and scTCR-seq were performed on peripheral blood mononuclear cells from B-NHL pts before lymphodepletion chemotherapy (pre), at peak CAR-T expansion (peak), and one month following CAR-T (M1). scRNAseq and scTCR-seq data were processed using CellRanger v7.0.1, which were then analyzed using Immunarch (v0.9.0) for TCR clonality and sample diversity. Diversity was assessed using the Gini coefficient to indicate clone size inequality (0 = maximum diversity). TCR diversity and phenotype of expanded and emerged TCR clones post CAR-T were compared across clinical response categories: CR (complete remission for at least 6 months), PD1 (primary refractory), and PD2 (relapsed after partial or complete response). Results: We analyzed 107,035 T cells from 77 serial samples of 32 pts (16 CR, 4 PD1, 12 PD2) and 5 healthy controls. Compared to pts with PD1 and PD2, pts with CR had a larger Gini coefficient for TCR clones at M1 relative to Pre and Peak. The Gini coefficient was the largest for tumor recirculating CD8 T effector memory (Tem) and activated CD8 peripheral memory (Tpm) cells at M1 for pts with CR. Examining the repertoire of emerged and expanded TCR clones at Peak and M1 from Pre, pts with PD2, compared to pts with CR, had a higher percentage of activated CD8 T peripheral memory (Tpm) and T regulatory cells (Treg) among the emerged clones and activated CD8 Tpm among the expanded clones. Patients with PD1, relative to patients with CR, had more proliferating and non-activated CD8 Tpm among the expanded and emerged clones. Conclusion: NHL pts with CR after CAR-T had more robust clonal expansion of T cells, particularly tumor recirculating CD8 Tem and activated CD8 Tpm, compared to pts with relapsed or refractory disease. In contrast, pts with relapsed or refractory disease had an expansion of TCR clones with a larger proportion of CD8 Tpm and Tregs. Endogenous tumor-reactive TCR expansion may help predict favorable clinical response following CAR T-cell therapy. Citation Format: Aiman J. Faruqi, Panwen Wang, Radhika Bansal, Andre De Menezes Silva Corraes, Henan Zhang, Zuoyi Shao, Kevin Regan, Eider Moreno Cortes, Arushi Khurana, Nora Bennani, Yucai Wang, Paul Hampel, Jonas Paludo, Patrick Johnston, Hemant Murthy, Madiha Iqbal, Stephen Ansell, Javier Munoz, Allison Rosenthal, Mohamed Kharfan Dabaja, Januario E. Castro, Saad Kenderian, Haidong Dong, Ying Li, Yi Lin. T-cell receptor repertoire changes associated with clinical response in patients with B-cell non-Hodgkin’s lymphoma receiving CD19 CAR-T therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 53.

Abstract 14: Identification of tumor-reactive T cell receptors through functional single cell interaction analyses for personalized T cell therapy

Abstract Innovative immunotherapy approaches such as adoptive transfer of chimeric antigen receptor (CAR) T cells or tumor infiltrating lymphocytes (TILs) have shown great success in the treatment of solid tumors and hematological malignancies. Although treatment of multiple myeloma with CAR T cells can induce deep responses, relapses frequently occur due to antigen escape and limited CAR T cell persistence. TCR-engineered T cells may show prolonged persistence in vivo and could mediate sustained antitumor effects. A further benefit of TCR transgenic T cells is the ability to target intracellular antigens that are inaccessible to CAR T cells, expanding the range of potential targets for immunotherapy. In our project, we propose to identify T cell receptors (TCRs) specifically targeting autologous myeloma cells. Tumor-reactive T cells were identified using the Bruker Cellular Analysis Lightning® platform, allowing simultaneous functional analysis of up to 1500 individual T cell/target cell interactions on a chip. Reactive T cells were identified upon detection of secreted cytokines (IFNγ, TNFα, IL2) and measurement of 4-1BB (CD137) surface expression. Tumor-reactive T cells showing various cytokine secretion patterns and 4-1BB expression profiles were detected in each myeloma patient (on average 11.9 T cells out of 1243 cells tested per assay run). Individual tumor-reactive T cells have been isolated and their TCRs were sequenced. TCR sequences of tumor-reactive T cells were mapped to single-cell RNA sequencing data of T cells from the same patiens to reveal a gene expression signature of myeloma-reactive T cells. TCR genes of reactive T cells were cloned and overexpressed in autologous T cells for functional validation and analysis of tumor derived neoepitope specificity. In summary, we present a pipeline allowing identification of myeloma-recognizing T cells and recovery of bona fide tumor-reactive TCRs eligible for patient-individualized T cell therapy. Citation Format: Tim Robin Wagner, Niklas Kehl, Simon Steiger, Michael Kilian, Bruno Schönfelder, Tamara Boschert, Katharina Lindner, Patrick Schmidt, Karsten Rippe, Hartmut Goldschmidt, Marc-Steffen Raab, Michael Platten, Mirco Friedrich, Stefan B. Eichmüller. Identification of tumor-reactive T cell receptors through functional single cell interaction analyses for personalized T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 14.

Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy.

The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.

T-Cell-Based Platform for Functional Screening of T-Cell Receptors Identified in Single-Cell RNA Sequencing Data Sets of Tumor-Infiltrating T-Cells.

The advent of single-cell RNA sequencing (scRNAseq) has enabled in-depth gene expression analysis of several thousand cells isolated from tissues. We recently reported the application of scRNAseq toward the dissection of the tumor-infiltrating T-cell repertoire in human pancreatic cancer samples. In this study, we demonstrated that combined whole transcriptome and T-cell receptor (TCR) sequencing provides an effective way to identify tumor-reactive TCR clonotypes on the basis of gene expression signatures. An important aspect in this respect was the experimental validation of TCR-mediated anti-tumor reactivity by means of an in vitro functional assay, which is the subject of the present protocol. This assay involves the transient transfection of mRNA gene constructs encoding TCRα/β pairs into a well-defined human T-cell line, followed by co-cultivation with the tumor cells of interest and detection of T-cell activation by flow cytometry. Due to the high transfectability and the low background reactivity of the mock-transfected T-cell line to a wide variety of tumor cells, this assay offers a highly robust and versatile platform for the functional screening of large numbers of TCR clonotypes as identified in scRNAseq data sets. Whereas the assay was initially developed to test TCRs of human origin, it was more recently also applied successfully for the screening of TCRs of murine origin. Key features • Efficient functional screening of-and discrimination between-TCRs isolated from tumor-reactive vs. bystander T-cell clones. • Applicable to TCRs from CD8+ and CD4+ tumor-infiltrating T-cells originating from patient-derived tumor samples and syngeneic mouse tumor models. • Rapid flow cytometric detection of T-cell activation by means of TNFα and CD107a expression after a 5 h T-cell/tumor cell co-cultivation.

Tumor Reactive T Cells Reside in the Bone Marrow and Are Associated with Clinical Response to Hematological Malignancies

T cell receptors (TCRs) play a crucial role in orchestrating cellular immunity in both health and disease, particularly in the context of cancer. Although immunotherapy and stem cell transplantation have shown promising clinical responses in hematological malignancies, these have not been linked to the presence of endogenous tumor reactive T cells. Moreover, the specificities and phenotypes of such tumor recognizing TCRs in these largely low immunogenic entities are unknown. In this study, we addressed this gap by developing an approach to map TCR specificities and transcriptional phenotypes of human bone marrow-resident T cells directly ex vivo, focusing on patients who were treatment-naïve at the time of biopsy. This allowed us to generalize our findings beyond immune checkpoint inhibitor-treated patients, a limitation of previous studies in solid cancers. To discover T cells that specifically recognize cancer cells or viral epitopes, we developed a multiplexed profiling approach using microfluidic reaction chambers, optical cytokine detection and TCR sequencing of patient-derived primary T cells. We were able to confidently map TCR recognition of 25,957 bone marrow-resident T cells from n=20 hematological cancer patients. Based on the acquired functional data and reverse phenotyping of screened TCRs to their original cell state in situ, we built a bone marrow T cell atlas charting >300,000 expression profiles in human bone marrow-resident T cells, their TCR specificities as well as their longitudinal clonal dynamics upon therapeutic perturbations in n=40 patients with newly diagnosed multiple myeloma (MM) and acute myeloid leukemia (AML). Our approach detected tumor-reactive T cell clones in the bone marrow of all screened individuals with varying frequency (1-5% of T cells), which were largely found to display a CD8+ effector-memory or progenitor-exhausted phenotype. In contrast, non-tumor reactive clones were either CD4+ or enriched for viral specificities. We identified a conserved signature of anti-tumor reactivity across patients. This signature included the ITGB1 gene, which encodes CD29 and was uniformly expressed in tumor reactive T cells. Importantly, ITGB1 expression was specifically restricted to tumor reactive, compared to virus-specific or bystander T cells. In two independent mouse tumor models, we found that CD29 protein was significantly upregulated on homed T cells carrying tumor reactive TCRs compared to non-reactive TCRs. A causal link between tumor reactive T cells and clinical response to hematological cancers would be strengthened by finding that these cells specifically recognize autologous cancer epitopes and clonally expand as part of a clinical anti-tumor response. We therefore cloned patient-individualized TCR libraries and performed immunoprecipitation of MHC class I : peptide complexes from cancer cells. We validated TCR binding against ~1-20 epitopes per patient, which were mostly derived from cancer/testis antigens (CTAs) and novel open reading frames (nORFs). Finally, we classified tumor reactive TCRs in three clinical cohorts: Notably, we observed selective expansion of tumor reactive TCRs upon autologous stem cell transplantation, which was associated with deep clinical response in newly diagnosed MM patients. Conversely, the failure of tumor reactive TCRs to clonally expand on-treatment underlined clinical non-response to bispecific BCMAxCD3 antibody therapy (MM) or combination therapy with immune checkpoint inhibitors and Azacytidine (AML). We show here that, unexpectedly, clinically relevant endogenous anti-tumor reactivity lies in a rare subset of bone marrow-resident T cells. The recurrent detection of these immunotherapy-responsive TCRs in patients with MM or AML revealed the selective clonal expansion of tumor-reactive TCRs following autologous stem cell transplantation. We describe a conserved gene signature of tumor reactivity that diverges from lymphocytes infiltrating solid tumors and includes CD29 as an indicator of antigen-specific T cell homing. Our findings facilitate the antigen-agnostic identification of tumor-reactive TCRs with potential for future patient-individualized cell therapies and suggest the relevance of immune responses against alternative epitopes, such as cancer/testis antigens, in hematological malignancies with low mutational loads.

A costimulatory chimeric antigen receptor targeting TROP2 enhances the cytotoxicity of NK cells expressing a T cell receptor reactive to human papillomavirus type 16 E7

Immune cells modified to express a tumor-reactive T cell receptor (TCR) have shown limited efficacy as stand-alone therapy against solid tumors. Genital and oropharyngeal carcinomas induced by human papillomavirus (HPV) type 16 express constitutively its E6 and E7 oncoproteins, which makes them convenient targets for adoptive cell immunotherapy. However, viral antigen presentation by tumor cells is low and limits the anti-tumor efficacy of CD8+ T cells. To enhance the functionality of immune effector cells, we have devised a strategy combining a costimulatory chimeric antigen receptor (CAR) with a TCR. We used a clinically tested TCR specific to E7 (E7-TCR) of HPV16 and a newly constructed CAR targeting the trophoblast cell surface antigen 2 (TROP2), which carried the intracellular costimulatory domains CD28 and 4-1BB, but was devoid of the CD3ζ domain. Flow cytometry analyses showed a notable upregulation of activation markers and of cytolytic molecule release by NK-92 cells genetically engineered to express CD3, CD8 and both E7-TCR and TROP2-CAR, after co-incubation with HPV16+ cervical cancer cells. Furthermore, the E7-TCR/TROP2-CAR NK-92 cells demonstrated enhanced antigen-specific activation and augmented cytotoxicity against tumor cells compared with NK-92 cells expressing the E7-TCR alone. A costimulatory TROP2-CAR can synergistically cooperate with the E7-TCR in NK cells thereby enhancing their signaling strength and antigen-specific cytotoxicity. This approach might improve the outcome of adoptive cell immunotherapies for HPV16+ cancer patients that are currently under investigation.

Cell surface marker-based capture of neoantigen-reactive CD8+ T-cell receptors from metastatic tumor digests

BackgroundCellular immunotherapies using autologous tumor-infiltrating lymphocytes (TIL) can induce durable regression of epithelial cancers in selected patients with treatment-refractory metastatic disease. As the genetic engineering of T cells with tumor-reactive...

Abstract 4071: Identification of myeloma-specific T cell receptors by functional single cell interaction analyses

Abstract Innovative immunotherapy approaches such as adoptive transfer of chimeric antigen receptor (CAR) T cells or tumor infiltrating lymphocytes (TILs) have shown great success in the treatment of solid tumors and hematological malignancies. Although treatment of multiple myeloma with CAR T cells can induce deep responses, relapses frequently occur due to antigen escape and limited CAR T cell persistence. TCR-engineered T cells may mediate sustained antitumor effects upon recognition of intracellular targets, thereby significantly increasing the range of relevant target antigens. In our project, we propose to identify T cell receptors (TCRs) specifically targeting autologous myeloma cells. Tumor-reactive T cells were identified using the Berkeley Lights Lightning platform, allowing simultaneous functional analysis of up to 1500 individual T cell/target cell interactions per run. Reactive T cells have been identified upon detection of secreted chemokines (IFNγ, TNFα, IL-2) and by measurement of CD137 surface expression. Tumor-reactive T cells showing various cytokine secretion patterns and CD137 expression profiles could be detected in each myeloma patient (7 to 26 of approx.1200 cells tested per patient). Individual tumor reactive T cells have been isolated for TCR sequencing. Recovered TCR genes will be cloned and overexpressed in autologous T cells for functional validation and analysis of tumor derived neoepitope specificity. In summary, we present a pipeline allowing identification of myeloma-recognizing T cells and recovery of bona fide tumor-reactive TCRs eligible for patient-individualized T cell therapy. Citation Format: Tim R. Wagner, Eren Boğa, Patrick Schmidt, Wolfram Osen, Michael Platten, Hartmut Goldschmidt, Marc S. Raab, Mirco J. Friedrich, Stefan B. Eichmüller. Identification of myeloma-specific T cell receptors by functional single cell interaction analyses. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4071.

TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs

T cell receptor (TCR) technologies, including repertoire analyses and Tcell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from Tcell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.

Global analysis of HLA-A2 restricted MAGE-A3 tumor antigen epitopes and corresponding TCRs in non-small cell lung cancer.

Background: Advanced non-small cell lung cancer (NSCLC) is the most common type of lung cancer with poor prognosis. Adoptive cell therapy using engineered T-cell receptors (TCRs) targeting cancer-testis antigens, such as Melanoma-associated antigen 3 (MAGE-A3), is a potential approach for the treatment of NSCLC. However, systematic analysis of T cell immune responses to MAGE-A3 antigen and corresponding antigen-specific TCR is still lacking. Methods: In this study, we comprehensively screened HLA-A2 restricted MAGE-A3 tumor epitopes and characterized the corresponding TCRs using in vitro artificial antigen presentation cells (APC) system, single-cell transcriptome and TCR V(D)J sequencing, and machine-learning. Furthermore, the tumor-reactive TCRs with killing potency was screened and verified. Results: We identified the HLA-A2 restricted T cell epitopes from MAGE-A3 that could effectively induce the activation and cytotoxicity of CD8+ T cells using artificial APC in vitro. A cohort of HLA-A2+ NSCLC donors demonstrated that the number of epitope specific CD8+ T cells increased in NSCLC than healthy controls when measured with tetramer derived from the candidate MAGE-A3 epitopes, especially epitope Mp4 (MAGE-A3: 160-169, LVFGIELMEV). Statistical and machine-learning based analyses demonstrated that the MAGE-A3-Mp4 epitope-specific CD8+ T cell clones were mostly in effector and proliferating state. Importantly, T cells artificially expressing the MAGE-A3-Mp4 specific TCRs exhibited strong MAGE-A3+ tumor cell recognition and killing effect. Cross-reactivity risk analysis of the candidates TCRs showed high binding stability to MAGE-A3-Mp4 epitope and low risk of cross-reaction. Conclusions: This work identified candidate TCRs potentially suitable for TCR-T design targeting HLA-A2 restricted MAGE-A3 tumor antigen.

Signatures of recent activation identify a circulating T cell compartment containing tumor-specific antigen receptors with high avidity.

T cell receptor (TCR) avidity is assumed to be a major determinant of the spatiotemporal fate and protective capacity of tumor-specific T cells. However, monitoring polyclonal T cell responses with known TCR avidities in vivo over space and time remains challenging. Here, we investigated the fate and functionality of tumor neoantigen-specific T cells with TCRs of distinct avidities in a well-established, reductionist preclinical tumor model and human patients with melanoma. To this end, we used polyclonal T cell transfers with in-depth characterized TCRs together with flow cytometric phenotyping in mice inoculated with MC38 OVA tumors. Transfer of T cells from retrogenic mice harboring TCRs with high avidity resulted in best tumor protection. Unexpectedly, we found that both high- and low-avidity T cells are similarly abundant within the tumor and adopt concordant phenotypic signs of exhaustion. Outside the tumor, high-avidity TCR T cells were not generally overrepresented but, instead, selectively enriched in T cell populations with intermediate PD-1 protein expression. Single-cell sequencing of neoantigen-specific T cells from two patients with melanoma-combined with transgenic reexpression of identified TCRs by CRISPR-Cas9-mediated orthotopic TCR replacement-revealed high-functionality TCRs to be enriched in T cells with RNA signatures of recent activation. Furthermore, of 130 surface protein candidates, PD-1 surface expression was most consistently enriched in functional TCRs. Together, our findings show that tumor-reactive TCRs with high protective capacity circulating in peripheral blood are characterized by a signature of recent activation.

Abstract 2762: Single-cell analysis of circulating neoantigen-reactive CD8+ T cells allows isolation of novel tumor reactive TCRs

Abstract Adoptive cell transfer of gene-engineered lymphocytes expressing T cell receptors (TCRs) targeting tumor antigens has shown promising clinical efficacy for the treatment of advanced cancer patients. For personalized treatment and to minimize “off-target” effects, neoantigens have become an attractive class of targets. While Tumor-Infiltrating Lymphocytes (TILs) have served as the main source of neoantigen-reactive TCRs (NeoTCRs), this strategy requires the patient to undergo surgery to obtain tumor samples. Circulating T cells are an alternative source for neoantigen-reactive T cells; however, the frequency of NeoTCRs in the blood is extremely low. Several approaches have been developed aiming to enrich these cells or isolate their TCRs by cell-sorting of cells expressing activation or exhaustion markers. Yet, the expression of these nonspecific markers by bystander T cells hampers the efficiency of these methods. Here, we sought to study the transcriptional and protein markers of circulating neoantigen-reactive CD8+ T cells by Single-Cell RNA Sequencing (scRNA-Seq) coupled with TCR-Seq and Cellular Indexing of Transcriptome and Epitope by Sequencing (CITE-Seq) from apheresis. To this end, we FACS-enriched neoantigen-reactive T cells from blood samples from 3 patients using pHLA tetramers of neoantigens previously discovered in autologous TIL samples. To be able to study the differences in the phenotype of these cells and other subsets of CD8+ cells in the blood, including viral-targeting T cells, we mixed tetramerpos and tetramerneg cells prior to sequencing. Projecting NeoTCRs onto phenotypic clusters showed a distinct population of these clones with upregulation of CD45RO, HLA-DR and -DP, and exhaustion markers (CD39, CD103, PD-1, etc.). To circumvent the limitation of tetramers (HLA tetramer availability, defined neoantigens and minimal epitopes) we FACS-sorted CD45RO+HLA-DRAhi-CD39+, -CD103+ single-positive, and -CD39+CD103+ double-positive cells, based on our CITE-Seq results, to enrich for neoantigen-reactive cells from 3 additional patients. Transcriptional analysis of all 6 patient samples allowed us to define a distinct gene-signature of circulating neoantigen-reactive CD8+ cells that showed an activated resident-memory-like phenotype. Moreover, using the surface markers that were identified in our analysis we FACS-sorted CD45RO+HLA-DRAhiCD39+CD103+ cells from blood samples into 96-well plates and performed single-cell TCR sequencing. We were able to detect NeoTCRs in 6 out of 8 patients, with frequencies ranging from 4-50% of the sorted cells. In summary, we were able to phenotype low-frequency neoantigen-reactive CD8+ T cells from blood samples and develop a simple sorting method that can bypass the need for invasive surgery, allowing isolation of TCRs that can be engineered into autologous lymphocytes to treat patients with metastatic cancer Citation Format: Rami Yoseph, Sri Krishna, Frank J. Lowery, Amy R. Copeland, Neilesh B. Parikh, Kyle Hitscherich, Paul F. Robbins, Steven A. Rosenberg. Single-cell analysis of circulating neoantigen-reactive CD8+ T cells allows isolation of novel tumor reactive TCRs [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 2762.

A novel linked TCR: MyD88 receptor improves anti-tumor responses while maintaining antigen specificity

Abstract The treatment of malignant tumors utilizing engineered T cell receptor (TCR) therapies in the clinic have demonstrated encouraging therapeutic potential in a subset of patients. Limitations to T cell-based therapies include down-regulation of tumor-antigen presentation by the tumor cells, poor TCR activation, and the immunosuppressive effects of the tumor microenvironment (TME). Attempts to ameliorate these issues by utilizing T cells engineered with tumor-reactive TCRs with increased affinity showed enhanced responses. However, affinity-modified TCRs are more promiscuous and can lead to off-target toxicity. We and others have demonstrated that activating MyD88 signaling (a key adapter protein in toll-like receptor signaling) in T cells enhances effector function and expansion while simultaneously reducing their propensity to enter an exhausted state. In these studies, we designed novel receptors in which the death and intermediate domains of MyD88 are fused to the TCR. T cells engineered to express this novel TCR:MyD88 receptor showed improved responses in a tumor-antigen dependent manner, as demonstrated by increased proliferation and expression of effector molecules, without reducing the specificity of the TCR. In mouse models, TCR:MyD88 T cells conferred improved anti-tumor responses against tumors expressing suboptimal levels of target antigen which was associated with increased T cell infiltration, reduced T cell exhaustion, and an altered TME. These results demonstrate the ability of TCR:MyD88 to improve current therapies without sacrificing the specificity of the TCR which we believe can be utilized to improve the outcome of patients suffering from advanced cancer while reducing toxicities. Supported by -US Department of Veteran Affairs -Leukemia Lymphoma Society -University of Colorado -Shoots Medical Center -NCI (R01CA207913)

Tuning T cell receptor sensitivity through catch bond engineering.

Adoptive cell therapy using engineered T cell receptors (TCRs) is a promising approach for targeting cancer antigens, but tumor-reactive TCRs are often weakly responsive to their target ligands, peptide-major histocompatibility complexes (pMHCs). Affinity-matured TCRs can enhance the efficacy of TCR-T cell therapy but can also cross-react with off-target antigens, resulting in organ immunopathology. We developed an alternative strategy to isolate TCR mutants that exhibited high activation signals coupled with low-affinity pMHC binding through the acquisition of catch bonds. Engineered analogs of a tumor antigen MAGE-A3-specific TCR maintained physiological affinities while exhibiting enhanced target killing potency and undetectable cross-reactivity, compared with a high-affinity clinically tested TCR that exhibited lethal cross-reactivity with a cardiac antigen. Catch bond engineering is a biophysically based strategy to tune high-sensitivity TCRs for T cell therapy with reduced potential for adverse cross-reactivity.

Pinpointing the tumor-specific T cells via TCR clusters.

Adoptive cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lysed tumor cells, but these approaches remain laborious, time-consuming, and functionally limited, hampering clinical development of ACT. Here, we demonstrate that homology cluster analysis of T cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs allowing to: (1) detect their presence within the pool of tumor-infiltrating lymphocytes (TILs); (2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; (3) investigate surface marker-based enrichment for tumor-targeting T cells in freshly isolated TILs (enrichment confirmed for CD4+ and CD8+ PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). We believe that this approach to the rapid assessment of tumor-specific TCR enrichment should accelerate T cell therapy development.

Rapid identification of tumor-reactive T-cell receptors by RNA preamplification-based single-cell sequencing

T-cell receptor (TCR)-transduced T (TCR-T) cell therapy has shown promising efficacy in the clinical treatment of malignant cancers. However, the populations covered by reported TCRs are still limited. Tumor infiltrating lymphocytes (TILs) are natural reservoirs of tumor-reactive T cells and TCRs. Approaches are required for the fast and cost-effective identification of tumor-reactive TCRs from TILs. The widely employed TCR identification approaches by the clonal expansion of TILs involve a TCR singularization process for the direct pairing of TCR Vα and the Vβ chain. However, the clonal expansion of T cells is well known to require extensive time and effort due to the involvement of T cell cultures. Several single-cell multiplexing PCR methods followed by Sanger sequencing have been developed, representing a cost-effective and fast approach for single-cell TCR identification. In this study, an RNA-based preamplification step was included in the single-cell TCR sequencing, which can reduce the multiplexing PCR amplification to one round. Moreover, the cDNA product of RNA preamplification is derived from the whole genome mRNA, instead of TCR mRNA only by multiplexing primers-based DNA preamplification, which is valuable for many other analyses (e.g., phenotypic analysis) of the tumor-reactive T cells that can be correlated with the identified TCRs. The feasibility for both single α chain and dual α chain TILs of this approach highlights its potential value as a rapid and cost-effective sequencing strategy for the development of TCR-T therapies for solid cancers.

Isolation of TCR genes with tumor-killing activity from tumor-infiltrating and circulating lymphocytes in a tumor rejection cynomolgus macaque model

To develop effective adoptive cell transfer therapy using T cell receptor (TCR)-engineered T cells, it is critical to isolate tumor-reactive TCRs that have potent anti-tumor activity. In humans, tumor-infiltrating lymphocytes (TILs) have been reported to contain CD8+PD-1+ T cells that express tumor-reactive TCRs. Characterization of tumor reactivity of TILs from non-human primate tumors could improve anti-tumor activity of TCR-engineered T cells in preclinical research. In this study, we sought to isolate TCR genes from CD8+PD-1+ T cells among TILs in a cynomolgus macaque model of tumor transplantation in which the tumors were infiltrated with CD8+ T cells and were eventually rejected. We analyzed the repertoire of TCRα and β pairs obtained from single CD8+PD-1+ T cells in TILs and circulating lymphocytes and identified multiple TCR pairs with high frequency, suggesting that T cells expressing these recurrent TCRs were clonally expanded in response to tumor cells. We further showed that the recurrent TCRs exhibited cytotoxic activity to tumor cells in vitro and potent anti-tumor activity in mice transplanted with tumor cells. These results imply that this tumor transplantation macaque model recapitulates key features of human TILs and can serve as a platform toward preclinical studies of non-human primate tumor models.

167 High-efficiency capture of anti-tumor neoantigen-reactive T cell receptors from tumor digest

BackgroundAs cellular immunotherapies utilizing genetically engineered T cells become a more significant focus of clinical investigation, identification of patient-specific neoantigen-reactive T cell receptors (TCRs) in a practical and efficient manner is a top priority. Using high-dimensional single-cell analysis, we recently identified a common gene expression signature in anti-tumor, neoantigen-reactive tumor-infiltrating lymphocytes (TIL) from patients with metastatic cancer, which included high gene expression of cell-surface markers of exhaustion.1 Furthermore, analyses of intra-tumoral T cell populations have shown that neoantigen-specific TIL are enriched in subsets defined by cell-surface markers of exhaustion, likely secondary to oligoclonal expansion that occurs upon tumor antigen recognition in vivo.2–5 In this study we describe an efficient method to prospectively capture and reconstruct neoantigen-reactive T cell receptors from tumor digest based on co-expression of CD39, PD-1, and TIGIT.MethodsWe evaluated the ability of PD-1+, CD39+, and TIGIT+ TIL (TIL-TP) to enrich for neoantigen-reactivity by sorting, sequencing, and reconstructing high-frequency TCR alpha/beta pairs from tumor digest in 5 patients with metastatic epithelial cancers. We then tested the ability of PD-1/CD39/TIGIT co-expressing TILs to sustain reactivity to patient-specific tumor neoantigens following in vitro expansion under similar conditions to our current clinical trial protocols (figure 1).ResultsWe prospectively reconstructed TIL-TP TCRs to identify additional novel TCRs, with 35% of prospectively screened TCRs being neoantigen- or tumor-reactive. Including both previously known and newly predicted TCRs, TIL-TP demonstrated enrichment for neoantigen-reactivity in 4 of 5 patients, with a median of at least 26.8% of sequenced TIL-TP cells being neoantigen-reactive (range: 11.9 – 88.4%). TIL-TP TCR isolation demonstrated a high degree of correlation with single-cell transcriptomic approaches to identification of neoantigen-reactive TCRs, though TIL-TP TCRs represent a more cost-effective and widely available approach compared to those utilizing more advanced technologies. However, despite their substantial enrichment for neoantigen-reactive TCR clonotypes, the majority of TIL-TP populations failed to demonstrate neoantigen-reactivity following in vitro expansion and exhibited loss of neoantigen-reactive clones as well as functional impairment.Abstract 167 Figure 1ConclusionsTIL-TP serve as a highly efficient and reliable source of tumor-reactive TCRs. While direct utilization of these TIL-TP as a source for cellular therapy presents significant challenges, sorting for TIL-TP offers a streamlined approach using readily available and affordable technology to identify neoantigen-reactive TCRs that may be used to design TCR engineered cellular immunotherapies.ReferencesLowery, FJ, et al. Single cell mapping of tumor infiltrating lymphocytes enables neoantigen-reactive T cell identification in metastatic human cancer [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 127.Duhen, T. et al. Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors. Nat Commun 2018;9:2724, doi:10.1038/s41467-018-05072-0.Gros A, et al. PD-1 identifies the patient-specific CD8(+) tumor-reactive repertoire infiltrating human tumors. J Clin Invest 2014;124:2246–2259, doi:10.1172/JCI73639.Pasetto, A. et al. Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor. Cancer Immunol Res 2016;4:734–743, doi:10.1158/2326-6066.CIR-16-0001.Yossef, R. et al. Enhanced detection of neoantigen-reactive T cells targeting unique and shared oncogenes for personalized cancer immunotherapy. JCI Insight 2018;3: doi:10.1172/jci.insight.122467.

TCR function analysis using a novel system reveals the multiple unconventional tumor-reactive T cells in human breast cancer-infiltrating lymphocytes.

Tumor-infiltrating lymphocytes (TILs) are a potent source for obtaining tumor-reactive T cell receptors (TCRs). Although comprehensive methods to analyze the TCR repertoire in TILs have been reported, the evaluation system for TCR-reactivity to endogenously expressed antigen in tumor cells remains laborious and time consuming. Consequently, very limited numbers of TCRs in TILs have been analyzed for their reactivity to tumor cells. In this study, we developed an efficient evaluation system for TCR function designated c-FIT (comprehensive functional investigation of TCRs) to analyze TCR reactivity. The c-FIT system enabled us to analyze up to 90 TCRs for their reactivity to tumor cells by a single assay within a month. Using c-FIT, we analyzed 70 TCRs of CD8+ TILs derived from two breast cancer patients and obtained 23 TCRs that reacted to tumor cells. Surprisingly, although two TCRs were HLA class I-restricted, the remaining 21 TCRs were non-HLA-restricted. Thus, c-FIT can be applied for monitoring multiple conventional and unconventional antigen-specific killer T cells in TILs, leading to the development of new designs for more effective T-cell-based immunotherapies.