To redirect T cells against tumor cells, T cells can be engineered ex vivo to express cancer-antigen specific T cell receptors (TCRs), generating products known as TCR-engineered T cells (TCR T). Unlike chimeric antigen receptors (CARs), TCRs recognize HLA-presented peptides derived from proteins of all cellular compartments. The use of TCR T cells for adoptive cellular therapies (ACT) has gained increased attention, especially as efforts to treat solid cancers with ACTs have intensified. In this review, we describe the differing mechanisms of T cell antigen recognition and signal transduction mediated through CARs and TCRs. We describe the classes of cancer antigens recognized by current TCR T therapies and discuss both classical and emerging pre-clinical strategies for antigen-specific TCR discovery, enhancement, and validation. Finally, we review the current landscape of clinical trials for TCR T therapy and discuss what these current results indicate for the development of future engineered TCR approaches.

BackgroundSuccessful targeting of solid tumors such as breast cancer (BC) using chimeric antigen receptor (CAR) T cells has proven challenging, largely attributed to the immunosuppressive tumor microenvironment (TME). Myeloid-derived suppressor cells (MDSCs) inhibit CAR T cell function and persistence within the breast TME. To overcome this challenge, we have developed CAR T cells targeting tumor-associated mucin 1 (MUC1) with a novel chimeric costimulatory receptor that targets tumor necrosis factor–related apoptosis-inducing ligand receptor 2 (TR2) expressed on MDSCs.MethodsThe function of the TR2.41BB costimulatory receptor was assessed by exposing non-transduced (NT) and TR2.41BB transduced T cells to recombinant TR2, after which nuclear translocation of NFκB was measured by ELISA and western blot. The cytolytic activity of CAR.MUC1/TR2.41BB T cells was measured in a 5-hour cytotoxicity assay using MUC1+ tumor cells as targets in the presence or absence of MDSCs. In vivo antitumor activity was assessed using MDSC-enriched tumor-bearing mice treated with CAR T cells with or without TR2.41BB.ResultsNuclear translocation of NFκB in response to recombinant TR2 was detected only in TR2.41BB T cells. The presence of MDSCs diminished the cytotoxic potential of CAR.MUC1 T cells against MUC1+ BC cell lines by 25%. However, TR2.41BB expression on CAR.MUC1 T cells induced MDSC apoptosis, thereby restoring the cytotoxic activity of CAR.MUC1 T cells against MUC1+ BC lines. The presence of MDSCs resulted in an approximately twofold increase in tumor growth due to enhanced angiogenesis and fibroblast accumulation compared with mice with tumor alone. Treatment of these MDSC-enriched tumors with CAR.MUC1.TR2.41BB T cells led to superior tumor cell killing and significant reduction in tumor growth (24.54±8.55 mm3) compared with CAR.MUC1 (469.79±81.46 mm3) or TR2.41BB (434.86±64.25 mm3) T cells alone. CAR.MUC1.TR2.41BB T cells also demonstrated improved T cell proliferation and persistence at the tumor site, thereby preventing metastases. We observed similar results using CAR.HER2.TR2.41BB T cells in a HER2+ BC model.ConclusionsOur findings demonstrate that CAR T cells that coexpress the TR2.4-1BB receptor exhibit superior antitumor potential against breast tumors containing immunosuppressive and tumor promoting MDSCs, resulting in TME remodeling and improved T cell proliferation at the tumor site.

No abstract

1032 Background: Successful targeting of solid tumors such as breast cancer (BC) using CAR T cells (CARTs) has proven challenging, largely due to the immune suppressive tumor microenvironment (TME). Myeloid derived suppressor cells (MDSCs) inhibit CART’s function and persistence within the breast TME. We generated CAR T cells targeting tumor-expressed mucin 1 (MUC1) (Bajgain P et al, 2018) for BC. To potentiate expansion and persistence of MUC1 CARTs and modulate the suppressive TME, we developed a novel chimeric co-stimulatory receptor, TR2.4-1BB, encoding a ScFv derived from a TNF-related apoptosis-inducing ligand receptor 2 (TR2) mAb followed by a 4-1BB endodomain. We hypothesize that engagement with TR2 expressed on TME-resident MDSCs, will lead to both MDSC apoptosis and CART co-stimulation, promoting T cell persistence and expansion at tumor site. Methods: Function of the novel TR2.4-1BB receptor, was assessed by exposing non-transduced (NT) and TR2.4-1BB transduced T cells to recombinant TR2 and nuclear translocation of NFκB was measured by ELISA. Functionality of in vitro generated MDSCs was determined by the suppression assay. In vitro CART/costimulatory receptor T cell function was measured by cytotoxicity assays using MUC1+ tumor targets in presence or absence of MDSCs. In vivo anti-tumor activity was assessed using MDSC enriched tumor-bearing mice using calipers to assess tumor volume and bioluminescence imaging to track T cells. Results: Nuclear translocation of NFκB was detected only in TR2.4-1BB T cells. MDSCs significantly attenuated T cell proliferation by 50±5% and IFNγ production by half compared with T cells cultured alone. Additionally, presence of MDSCs, diminished cytotoxic potential of MUC1 CARTs against MUC1+ BC cell lines by 25%. However, TR2.4-1BB expression on CAR.MUC1 T cells induced MDSC apoptosis thereby restoring the cytotoxic activity of CAR.MUC1 against MUC1+ BC lines in presence of TR2.4-1BB (67±8.5%). There was an approximate two-fold increase in tumor growth due enhanced angiogenesis and fibroblast accumulation in mice receiving tumors + MDSCs compared to tumors alone. Treatment of these MDSC-enriched tumors with MUC1.TR2.4-1BB CARTs led to superior tumor cell killing and significant reduction in tumor growth (24.54±8.55 mm3) compared to CAR.MUC1 (469.79.9±81.46mm3) or TR2.4-1BB (434.86±64.25 mm3) T cells alone (Day 28 after T cell injection). The treatment also improved T cell proliferation and persistence at the tumor site. Thereby, leading to negligible metastasis demonstrating ability of CARTs to eliminate tumor and prevent dissemination. We observed similar results using HER2.TR2.4-1BB CARTs in a HER2+ BC model. Conclusions: Our findings demonstrate that CARTs co-expressing our novel TR2.4-1BB receptor have higher anti-tumor potential against BC tumors and infiltrating MDSCs, resulting in TME remodeling and improved T cell proliferation at the tumor site.

T cell receptor engineered T cell (TCR T) therapy has emerged as a promising therapeutic modality for solid cancer following recent trials demonstrating the safety and efficacy of TCR T therapies against some types of metastatic solid cancers. However, the broader application of TCR T towards many solid tumors, including metastatic breast cancer (MBC), has been limited by several factors, chiefly among them the current scarcity of tumor selective target antigens. Neoantigens, which are expressed exclusively in cancer cells, are currently underrepresented in TCR T development, being targeted in only about 7% of trials conducted to date, and thus represent a relatively untapped source of potentially safe and effective novel targets. Driver mutations in AKT1, ESR1, PIK3CA, and TP53 are common in patients with MBC, and could serve as ideal neoantigen targets for TCR T therapies. We hypothesized that we could generate MBC driver mutation-specific T cells from which we could isolate and clone neoantigen-specific TCRs to generate TCR T products for MBC. We identified 13 driver missense mutations that are among the most frequent in patients with MBC, which included AKT1 (E17K), ESR1 (K303R, Y537S, D538G), PIK3CA (E542K, E545K, H1047L, H1047R), and TP53 (R175H, R248Q, R248W, R273C, R273H), then designed peptide libraries consisting of 15-mer overlapping peptides that contain these mutations. To determine if these neopeptides could elicit T cell responses, we isolated T cells from 15 healthy donors and 11 MBC patients who expressed at least one of the targeted mutations and performed successive stimulations with neopeptide pulsed dendritic cells, then screened the resulting T cell lines for neoantigen specificity using an IFN-γ ELISpot assay. We observed neopeptide T cell responses in 8/16 lines generated from healthy donors and 7/11 lines generated from MBC patients, which were collectively directed against 11/13 of the targeted driver mutations. To isolate neoantigen-specific TCRs from one of these lines, we performed IFN-γ capture, limiting dilution, and 5’ RACE, and isolated an HLA-B*35 restricted TP53 R248W-specifc TCR. Gene transfer of this TCR conferred edited T cells with potent activity towards the TP53 R248W and not the TP53 WT peptide as assessed by ELISpot (1036 vs 46 SFU/1 × 105 cells, respectively) and chromium release cytoxicity assay targeting peptide pulsed autologous PHA blasts (37.5% vs 0% lysis at E:T 40:1, respectively). To increase the throughput of TCR discovery, we next used a single cell RNA sequencing based TCR discovery approach whereby we stimulated T cells from one of the generated lines with ESR1 WT or neopeptide and identified responsive T cell clones through upregulation of IFN-γ and/or TNF-α. This strategy has so far enabled us to identify and validate two ESR1 mutant-specific TCRs. This includes an HLA-C*01 restricted TCR that confers edited T cells with dual activity towards both ESR1 Y537S and D538G, but not WT peptide as determined by both ELISpot (2094, 3194, and 79 SFU, respectively) and chromium release cytotoxicity (31.3%, 77.8%, and 9.1% lysis, respectively), as well as an HLA-B*40 restricted TCR that confers high ESR1 Y537S specificity (5039 vs 138 SFU in response to ESR1 Y537S vs WT peptide, respectively). In summary, we have demonstrated responses of T cells derived from both healthy donors and MBC patients towards neopeptides derived from common MBC driver mutations. We have so far isolated neoantigen specific TCRs from two of the neoantigen-specific T cells lines, including TCRs specific towards TP53 R248W, ESR1 Y537S, dual ESR1 Y537S+D538G that are restricted to three different HLA alleles, and have successfully used these TCRs to generate TCR T products with high neoantigen activity. These results encourage further efforts to identify TCRs recognizing these MBC driver mutations, with our ultimate aim to translate neoantigen-targeted TCR T therapies to clinical trials of MBC. Citation Format: Paul Shafer, Wingchi K. Leung, Mae L. Woods, Carlos Rodriguez-Plata, Arushana Ali, Saisha Nalawade, Lauren M. Kelley, Jarrett Joubert, Anthony Manliguez, Spyridoula Vasileiou, Suzanne A. Fuqua, Premal Lulla, Cliona Rooney, Ann Leen, Valentina Hoyos. Engineered neoantigen-specific T cell receptors to treat metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-10-11.

Bone marrow failure is a significant complication of many chronic infections, which affect a third of the world's population. The inflammatory cytokine interferon-gamma (IFNy) contributes to bone marrow failure syndromes by activating hematopoietic stem cells (HSCs) and impairing their self-renewal. IFNy upregulation during many chronic infections such as tuberculosis, HIV and hepatitis B directly depletes hematopoietic stem cells (HSCs). The mechanisms by which IFNy drives the loss of quiescence and ultimate exhaustion of HSCs remain poorly understood, but may be related to changes in the interaction between HSCs and the bone marrow (BM) microenvironment, or BM niche. Current evidence suggests that quiescent HSCs reside predominantly in the vascular niche, where the production of stem cell factor (SCF) from endothelial cells and CXCL12 from perivascular CXCL12 abundant reticular (CAR) stromal cells are critical for maintaining their quiescence. The goal of our work was to determine whether IFNy signaling alters HSC interactions within the niche. We performed transcriptomic analysis of IFNy-stimulated HSCs and focused on changes in cell-surface expressed genes that may influence HSC-niche interactions. Our analysis revealed Bone Marrow Stromal Antigen 2 (BST2) as the only surface protein upregulated on HSCs upon 24-hour IFNy stimulation. To study the effects of BST2 on HSC-niche interactions, we performed intravital imaging using two reporter mouse models: CXCL12-GFP reporter mice in which CAR cells are labeled with GFP, and CXCL12-GFP Krt18-Cre LSL-tdTomato dual reporter mice in which CAR cells are labelled with GFP and HSCs are labeled with tdTomato. After exogenously labeling and transferring HSCs into CXCL12-GFP mice or endogenously labeling HSCs in the CXCL12-GFP Krt18-Cre LSL-tdTomato mice, we observed that HSCs stimulated with IFNy were significantly distanced from CAR cells compared to pre-treated controls. These findings are consistent with other reports that chemotherapeutic and inflammatory stress disrupts HSC interactions with the niche and promotes HSC migration. Conversely, we observed no change in HSC distancing from CAR cells after IFNy stimulation of IFNy-receptor deficient HSCs, suggesting that the observed HSC displacement was due to a cell autonomous mechanism. These changes were not due to a loss of CXCL12 receptor (CXCR4) expression or disrupted capacity of HSCs to migrate towards CXCL12. Interestingly, Intravital imaging using BST2-deficient HSCs revealed that BST2 KO HSCs do not re-localize from CAR cells during IFNy stimulation. Increased BST2 expression has been linked to the migration, adhesion and metastasis of various cancer cells and we explored whether it could serve a similar role in protein binding in HSCs. Using in vitro plate binding assays, we found that IFNy-treatment promoted increased HSC binding to E-selectin via BST2, as well as increased HSC homing to the bone marrow, a property that is dependent on E-selectin binding. Finally, to determine whether BST2 affects IFNy-dependent HSC activation we performed cell cycle analysis of WT and BST2 KO HSCs. We discovered that the loss of BST2 protects against HSC activation during Mycobacterium avium infection. Furthermore, HSC depletion during chronic infection was mitigated in BST2 KO mice. Our data identifies BST2 as a key protein that influences niche relocalization and activation in response to inflammatory stimulation. This study expands our understanding of factors that contribute to HSC activation and loss of quiescence. These findings could shed light on novel therapeutic interventions for patients who develop pancytopenia or bone marrow failure due to chronic inflammation. Disclosures No relevant conflicts of interest to declare.

Background: Molecularly targeted therapies are critical for improving cancer treatment. Since proteins are the targets of these therapies and functional effectors of genomic aberrations, proteogenomics data from the Clinical Proteomics Tumor Analysis Consortium (CPTAC) provides an unprecedented opportunity to characterize existing and future therapeutic targets for cancer treatment. Approach: CPTAC proteogenomics data from >1000 cancer patients spanning 10 cancer types was used to evaluate current and potential therapeutic targets curated from four databases. Cell line data from DepMap was further integrated to distinguish causations from associations. Computational pipelines were deployed to identify synthetic lethality for targeting tumor suppressor loss and to prioritize tumor associated antigens as immunotherapy targets. Results: We systematically collected 3050 druggable proteins and classified them into 5 tiers to facilitate different applications such as companion diagnostics, drug repurposing, and new therapy development. Many druggable proteins showed poor mRNA-protein correlation, including secreted proteins and proteins whose abundance was correlated with their interaction partners instead of cognate mRNA, highlighting the necessity of direct proteomic quantification of drug targets. 618 druggable proteins showed both overexpression in tumors compared to normal and significant dependency in CRISPR-Cas9 screens of cell lines of the same lineage. Notably, PAK1, a kinase targeted by investigational drugs, demonstrated both overexpression and dependency in all cancer types. A similar analysis of phosphoproteomics data focusing on known activating sites of druggable proteins further revealed targetable dependencies driven by protein hyperactivation. The phosphosite pS50 on PTPN1, a phosphatase targeted by experimental drugs, was increased in 7 cancer types and PTPN1 demonstrated dependency in related cancer cell lines. Based on tumor proteogenomic data and cell line CRISPR-Cas9 screen data, we identified synthetic lethality for difficult to target tumor suppressor losses, revealing TP53 mutations as a candidate biomarker to select breast cancer patients for CHEK1 inhibition, and endometrial cancer patients for treatment with doxorubicin. We identified 140 proteins whose expression was restricted in normal tissues but abnormal in tumors. Experimental analysis of peptides predicted to have high binding affinity to the most common allotype HLA-A02 for 7 prioritized proteins identified 21 peptides from 5 proteins with both strong binding affinity and immunogenicity which could be further investigated as immunotherapy targets. Conclusion: We generate a comprehensive resource of protein and peptide targets that covers multiple therapeutic modalities. This unique resource will pave the way for repurposing of currently available drugs and developing new drugs for cancer treatment. Citation Format: Jonathan T. Lei, Sara R. Savage, Xinpei Yi, Bo Wen, Hongwei Zhao, Lauren K. Somes, Paul W. Shafer, Yongchao Dou, Qiang Gao, Valentina Hoyos, Bing Zhang. Pan-cancer proteogenomics expands the landscape of therapeutic targets. [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 5726.