Functional Avidity Research Articles

NK Receptor Signaling Lowers TCR Activation Threshold, Enhancing Selective Recognition of Cancer Cells by TAA-Specific CTLs.

Cytotoxic CD8+ T lymphocyte (CTL) recognition of non-mutated tumor-associated antigens (TAA), present on cancer cells and also in healthy tissues, is an important element of cancer immunity, but the mechanism of its selectivity for cancer cells and opportunities for its enhancement remain elusive. In this study, we found that CTL expression of the NK receptors (NKR) DNAM1 and NKG2D was associated with the effector status of CD8+ tumor-infiltrating lymphocytes and long-term survival of patients with melanoma. Using MART1 and NY-ESO-1 as model TAAs, we demonstrated that DNAM1 and NKG2D regulate T-cell receptor (TCR) functional avidity and set the threshold for TCR activation of human TAA-specific CTLs. Superior co-stimulatory effects of DNAM1 over CD28 involved enhanced TCR signaling, CTL killer function, and polyfunctionality. Double transduction of human CTLs with TAA-specific TCR and NKRs resulted in strongly enhanced antigen sensitivity, without a reduction in antigen specificity and selectivity of killer function. In addition, the elevation of NKR ligand expression on cancer cells due to chemotherapy also increased CTL recognition of cancer cells expressing low levels of TAAs. Our data help explain the ability of self-antigens to mediate tumor rejection in the absence of autoimmunity and support the development of dual-targeting adoptive T-cell therapies that use NKRs to enhance the potency and selectivity of recognition of TAA-expressing cancer cells.

Identification of an HLA-A*11:01-restricted neoepitope of mutant PIK3CA and its specific T cell receptors for cancer immunotherapy targeting hotspot driver mutations

Hotspot driver mutations presented by human leukocyte antigens might be recognized by anti-tumor T cells. Based on their advantages of tumor-specificity and immunogenicity, neoantigens derived from hotspot mutations, such as PIK3CAH1047L, may serve as emerging targets for cancer immunotherapies. NetMHCpan V4.1 was utilized for predicting neoepitopes of PIK3CA hotspot mutation. Using in vitro stimulation, antigen-specific T cells targeting the HLA-A*11:01-restricted PIK3CA mutation were isolated from healthy donor-derived peripheral blood mononuclear cells. T cell receptors (TCRs) were cloned using single-cell PCR and sequencing. Their functionality was assessed through T cell activation markers, cytokine production and cytotoxic response to cancer cell lines pulsed with peptides or transduced genes of mutant PIK3CA. Immunogenic mutant antigens from PIK3CA and their corresponding CD8+ T cells were identified. These PIK3CA mutation-specific CD8+ T cells were subsequently enriched, and their TCRs were isolated. The TCR clones exhibited mutation-specific and HLA-restricted reactivity, demonstrating varying degrees of functional avidity. Identified TCR genes were transferred into CD8+ Jurkat cells and primary T cells deficient of endogenous TCRs. TCR-expressing cells demonstrated specific recognition and reactivity against the PIK3CAH1047L peptide presented by HLA-A*11:01-expressing K562 cells. Furthermore, mutation-specific TCR-T cells demonstrated an elevation in cytokine production and profound cytotoxic effects against HLA-A*11:01+ malignant cell lines harboring PIK3CAH1047L. Our data demonstrate the immunogenicity of an HLA-A*11:01-restricted PIK3CA hotspot mutation and its targeting therapeutic potential, together with promising candidates of TCR-T cell therapy.

Lineage tracing reveals heterogeneity within tumor-reactive CD8 T cells in mismatch repair-proficient (MMR-p) CRC

Abstract While CRC develop in the colon and rectum, little is known about the relationship between tissue resident memory (TRM) CD8 T cells and newly recruited tumor-reactive T cells. We compared the phenotype of CD8 T cells from paired adjacent normal colon (NC) and tumor by flow cytometry and observed a higher T cell infiltration in the tumor with an enrichment in CD8 T cells. Interestingly, a subset of CD103+ CD8 T cells in NC expressed CD39, a phenotype reminiscent of tumor-reactive T cells, but those cells lacked PD-1 and Ki-67. To better understand the relationship between T cells from NC and tumor and to uncover the differentiation path of tumor-reactive CD8 T cells, we performed scRNA-seq and scTCR-seq together with CITE-seq on paired NC and tumor from five patients. We confirmed that DP CD8 T cells from NC were distinct from tumor-infiltrating DP CD8 T cells (DP CD8 TILs). In contrast, the latter represented an heterogenous population with cells at different stages of differentiation as illustrated by the detection of cells sharing the same TCRs in multiple cell clusters. To further appreciate the differentiation path of neoantigen-reactive CD8 TILs, we performed neoantigen discovery on three of the five patients. We are now evaluating whether T cell differentiation and activation are linked to functional avidity and cellular location in the tumor. This work provides essential information regarding the differentiation of tumor-reactive CD8 TILs in MMR-p CRC tumors.

CARs derived from broadly neutralizing, human monoclonal antibodies identified by single B cell sorting target hepatitis B virus-positive cells.

To design new CARs targeting hepatitis B virus (HBV), we isolated human monoclonal antibodies recognizing the HBV envelope proteins from single B cells of a patient with a resolved infection. HBV-specific memory B cells were isolated by incubating peripheral blood mononuclear cells with biotinylated hepatitis B surface antigen (HBsAg), followed by single-cell flow cytometry-based sorting of live, CD19+ IgG+ HBsAg+ cells. Amplification and sequencing of immunoglobulin genes from single memory B cells identified variable heavy and light chain sequences. Corresponding immunoglobulin chains were cloned into IgG1 expression vectors and expressed in mammalian cells. Two antibodies named 4D06 and 4D08 were found to be highly specific for HBsAg, recognized a conformational and a linear epitope, respectively, and showed broad reactivity and neutralization capacity against all major HBV genotypes. 4D06 and 4D08 variable chain fragments were cloned into a 2nd generation CAR format with CD28 and CD3zeta intracellular signaling domains. The new CAR constructs displayed a high functional avidity when expressed on primary human T cells. CAR-grafted T cells proved to be polyfunctional regarding cytokine secretion and killed HBV-positive target cells. Interestingly, background activation of the 4D08-CAR recognizing a linear instead of a conformational epitope was consistently low. In a preclinical model of chronic HBV infection, murine T cells grafted with the 4D06 and the 4D08 CAR showed on target activity indicated by a transient increase in serum transaminases, and a lower number of HBV-positive hepatocytes in the mice treated. This study demonstrates an efficient and fast approach to identifying pathogen-specific monoclonal human antibodies from small donor cell numbers for the subsequent generation of new CARs.

Abstract 6332: Evaluating the relationship of affinity, functional avidity, and in vivo potency in KIR-CAR T cells

Abstract Chimeric antigen receptors (CARs) targeting CD19 demonstrate remarkable clinical outcomes in patients (pts) with B-cell malignancies. Importantly, all four FDA-approved CD3ζ-based CAR T cell therapies use the same FMC63-derived single-chain variable fragment (scFv) to target CD19+ tumors. Although response rates are high in diffuse large B cell lymphoma, only ~40% of pts achieve durable, long-term remissions. Improved CAR T cell therapies are therefore needed. We have previously shown that a novel killer immunoglobulin receptor (KIR)-based CAR expressed in T cells as a multichain receptor with DAP12 (KIR-CAR T) has enhanced anti-tumor activity in several preclinical solid tumor models suggesting that this platform may show better activity in lymphoma. Some recent studies report that lower-affinity CD19 binders compared to the benchmark FMC63-scFv yield equivalent or increased anti-tumor activity of CAR T in pts, raising the question of optimal affinity for a KIR-based CAR. In this study, we aimed to evaluate the relationship of affinity, functional avidity, and in vivo potency of CD19 binders in a KIR-based CAR T cell. Using a highly-diverse 40-billion member canine scFv phage display library, we generated 19 unique human CD19-specific binders that compete with FMC63 binder supporting a similar binding epitope. Different KIR-CAR T cells were generated, and relative affinities were compared via binding to a recombinant (rec) CD19 protein. We found that although CAR receptor expression was similarly expressed, the concentration of soluble rec CD19 protein required to saturate the surface CAR varied more than 2-log among the different scFv binders suggesting a range of affinities relative to FMC63. We selected several scFvs with lower, and equivalent CD19 binding MFI compared to the FMC63-scFv and found that all scFvs could mediate similarly robust in vitro potency. In vivo anti-tumor efficacy was next assessed using the NSG xenograft mouse model of B-cell leukemia NALM6 cells. Interestingly, despite their comparable in vitro functions, some binders with relatively similar binding MFI failed to control the tumors. In contrast, two binders with an ~30-fold apparent affinity relative to FMC63 exhibited robust anti-tumor activity comparable to the benchmark scFv. These preliminary data suggest that the in vivo functional activity of chimeric KIR-based immunoreceptors is insensitive to binder affinity over a wide range of affinities. The failure of some scFvs with comparable affinity and binding epitope suggest that other, yet to be characterized attributes of the binder may be critical for optimal function. Further characterization of these binders is being conducted to understand the relationship between affinity, functional avidity, antigen density, and in vivo potency. This study paves the way for developing an improved CD19-specific KIR-CAR T cell therapy for treating pts with B-cell malignancies. Citation Format: Jun Xu, Selene Nunez-Cruz, John M. Leferovich, Gayathri Gulendran, Chune Zhang, Nora D. Yucel, Megan C. Blair, William S. Stanley, Laura A. Johnson, Don L. Siegel, Michael C. Milone. Evaluating the relationship of affinity, functional avidity, and in vivo potency in KIR-CAR T cells [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 6332.

Abstract 8: Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors

Abstract Background: T cell receptor-engineered T cell (TCR-T) therapy has been studied as a high potential approach for cancer treatment. Beyond cell-surface tumor antigens, TCR-Ts can recognize HLA-presented intracellular epitopes which allows them to address a wide range of cancer-specific targets. Existing TCR-T therapies focus on a limited number of epitopes, many of which are restricted to HLA allele HLA-A*02:01. Identification of novel anti-tumor TCRs covering a broad range of HLA alleles is necessary to address unmet clinical needs. Natural T cells undergo thymic selection and present a favorable safety profile for mining such anti-tumor TCRs for therapeutic development. However, discovery of natural anti-tumor TCRs has been challenging due to i) the absence of high-throughput methods for identifying tumor-reactive TCRs in limited quantity human samples and ii) lack of sensitivity in detecting low frequency, naturally occurring tumor-reactive T cells. Methods: We developed TargetScape® as a part of our Deep Immunomics platform for efficient discovery of natural tumor-specific TCRs in healthy donors and cancer patients. Cells from blood and tissue samples were stained with metal-barcoded peptide-MHC tetramers, containing 500+ tumor-specific antigens, alongside metal-conjugated antibodies, allowing rapid identification and high dimensional phenotypic analysis of CD8+ T cells at the millions of cells scale. Single-cell sequencing revealed paired TCR sequences. Selected TCRs were introduced into luminescent Jurkat reporter cells for validation screening with peptide-pulsed targets and the relevant HLA restriction. TCRs of interest were further integrated into primary T cells and evaluated for their effector function. Results: We utilize our sensitive, high-throughput TargetScape® platform to detect and characterize putative cancer-specific TCRs from blood and tissue samples in frequencies as low as ~0.003% of total CD8+ cells. We have functionally validated over 100 TargetScape® derived TCRs with luminescent Jurkat reporters. Validated TCRs cover high prevalence HLA alleles and target a broad range of cancer antigen classes, including tumor associated antigens (TAA), Human endogenous retroviruses (HERVs), shared splice variants, and frameshift mutations. Several natural TCRs demonstrate recognition of low concentrations of peptide, indicating high functional avidity. Further evaluations of specificity and activity of TCRs of interest transduced into primary T cells are currently in progress. Conclusions: Our Deep Immunomics platform allows us to identify and confirm activity of novel, naturally-derived TCR candidates against therapeutically relevant cancer antigens presented on six common HLA alleles. These findings validate our discovery workflow leading to a portfolio of potential clinically relevant candidates that are currently under preclinical development. Citation Format: Hannah Fields, Juliana Velez Lujan, Kan Xing Wu, Natalie Epstein, Nazihah Beevi, Florence Chioh, Nicholas Tan, Neeraja Kulkarni, Noella Mukobo, Srikanthi R, Yovita Purwanti, Evan Newell, Alessandra Nardin, Michael Fehlings, Katja Fink, Daniel MacLeod. Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors [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 8.

Enhanced T cell receptor specificity through framework engineering.

Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.

Structural basis for self-discrimination by neoantigen-specific TCRs

T cell receptors (TCR) are pivotal in mediating tumour cell cytolysis via recognition of mutation-derived tumour neoantigens (neoAgs) presented by major histocompatibility class-I (MHC-I). Understanding the factors governing the emergence of neoAg from somatic mutations is a major focus of current research. However, the structural and cellular determinants controlling TCR recognition of neoAgs remain poorly understood. This study describes the multi-level analysis of a model neoAg from the B16F10 murine melanoma, H2-Db/Hsf2 p.K72N68-76, as well as its cognate TCR 47BE7. Through cellular, molecular and structural studies we demonstrate that the p.K72N mutation enhances H2-Db binding, thereby improving cell surface presentation and stabilizing the TCR 47BE7 epitope. Furthermore, TCR 47BE7 exhibited high functional avidity and selectivity, attributable to a broad, stringent, binding interface enabling recognition of native B16F10 despite low antigen density. Our findings provide insight into the generation of anchor-residue modified neoAg, and emphasize the value of molecular and structural investigations of neoAg in diverse MHC-I contexts for advancing the understanding of neoAg immunogenicity.

An EBV-related CD4 TCR immunotherapy inhibits tumor growth in an HLA-DP5+ nasopharyngeal cancer mouse model.

Adoptive transfer of T cell receptor-engineered T cells (TCR-T) is a promising strategy for immunotherapy against solid tumors. However, the potential of CD4+ T cells in mediating tumor regression has been neglected. Nasopharyngeal cancer is consistently associated with EBV. Here, to evaluate the therapeutic potential of CD4 TCR-T in nasopharyngeal cancer, we screened for CD4 TCRs recognizing EBV nuclear antigen 1 (EBNA1) presented by HLA-DP5. Using mass spectrometry, we identified EBNA1567-581, a peptide naturally processed and presented by HLA-DP5. We isolated TCR135, a CD4 TCR with high functional avidity, that can function in both CD4+ and CD8+ T cells and recognizes HLA-DP5-restricted EBNA1567-581. TCR135-transduced T cells functioned in two ways: directly killing HLA-DP5+EBNA1+ tumor cells after recognizing EBNA1 presented by tumor cells and indirectly killing HLA-DP5-negative tumor cells after recognizing EBNA1 presented by antigen-presenting cells. TCR135-transduced T cells preferentially infiltrated into the tumor microenvironment and significantly inhibited tumor growth in xenograft nasopharyngeal tumor models. Additionally, we found that 62% of nasopharyngeal cancer patients showed 50%-100% expression of HLA-DP on tumor cells, indicating that nasopharyngeal cancer is well suited for CD4 TCR-T therapy. These findings suggest that TCR135 may provide a new strategy for EBV-related nasopharyngeal cancer immunotherapy in HLA-DP5+ patients.

CD3 downregulation identifies high-avidity, multipotent SARS-CoV-2 vaccine- and recall antigen-specific Th cells with distinct metabolism.

Functional avidity is supposed to critically shape the quality of immune responses, thereby influencing host protection against infectious agents including SARS-CoV-2. Here we show that after human SARS-CoV-2 vaccination, a large portion of high-avidity spike-specific CD4+ T cells lost CD3 expression after in vitro activation. The CD3- subset was enriched for cytokine-positive cells, including elevated per-cell expression levels, and showed increased polyfunctionality. Assessment of key metabolic pathways by flow cytometry revealed that superior functionality was accompanied by a shift toward fatty acid synthesis at the expense of their oxidation, whereas glucose transport and glycolysis were similarly regulated in SARS-CoV-2-specific CD3- and CD3+ subsets. As opposed to their CD3+ counterparts, frequencies of vaccine-specific CD3- T cells positively correlated with both the size of the naive CD4+ T cell pool and vaccine-specific IgG levels. Moreover, their frequencies negatively correlated with advancing age and were impaired in patients under immunosuppressive therapy. Typical recall antigen-reactive T cells showed a comparable segregation into functionally and metabolically distinct CD3+ and CD3- subsets but were quantitatively maintained upon aging, likely due to earlier recruitment in life. In summary, our data identify CD3- T helper cells as correlates of high-quality immune responses that are impaired in at-risk populations.

Discovery of U2AF1 neoantigens in myeloid neoplasms

BackgroundMyelodysplastic syndromes (MDS) arise from somatic mutations acquired in hematopoietic stem and progenitor cells, causing cytopenias and predisposing to transformation into secondary acute myeloid leukemia (sAML). Recurrent mutations in spliceosome...

Increased SARS-CoV-2 reactive low avidity T cells producing inflammatory cytokines in pediatric post-acute COVID-19 sequelae (PASC).

A proportion of the convalescent SARS-CoV-2 pediatric population presents nonspecific symptoms, mental health problems, and a reduction in quality of life similar to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID-19 symptomatic. However, data regarding its clinical manifestation and immune mechanisms are currently scarce. In this study, we perform a comprehensive clinical and immunological profiling of 17 convalescent COVID-19 children with post-acute COVID-19 sequelae (PASC) manifestation and 13 convalescent children without PASC manifestation. A detailed medical history, blood and instrumental tests, and physical examination were obtained from all patients. SARS-CoV-2 reactive T-cell response was analyzed via multiparametric flow cytometry and the humoral immunity was addressed via pseudovirus neutralization and ELISA assay. The most common PASC symptoms were shortness of breath/exercise intolerance, paresthesia, smell/taste disturbance, chest pain, dyspnea, headache, and lack of concentration. Blood count and clinical chemistry showed no statistical differences among the study groups. We detected higher frequencies of spike (S) reactive CD4+ and CD8+ T cells among the PASC study group, characterized by TNFα and IFNγ production and low functional avidity. CRP levels are positively correlated with IFNγ producing reactive CD8+ T cells. Our data might indicate a possible involvement of a persistent cellular inflammatory response triggered by SARS-CoV-2 in the development of the observed sequelae in pediatric PASC. These results may have implications on future therapeutic and prevention strategies.

CD3 downregulation identifies high-avidity human CD8 T cells.

CD8 T cells recognize infected and cancerous cells via their T-cell receptor (TCR), which binds peptide-MHC complexes on the target cell. The affinity of the interaction between the TCR and peptide-MHC contributes to the antigen sensitivity, or functional avidity, of the CD8 T cell. In response to peptide-MHC stimulation, the TCR-CD3 complex and CD8 co-receptor are downmodulated. We quantified CD3 and CD8 downmodulation following stimulation of human CD8 T cells with CMV, EBV, and HIV peptides spanning eight MHC restrictions, observing a strong correlation between the levels of CD3 and CD8 downmodulation and functional avidity, regardless of peptide viral origin. In TCR-transduced T cells targeting a tumor-associated antigen, changes in TCR-peptide affinity were sufficient to modify CD3 and CD8 downmodulation. Correlation analysis and generalized linear modeling indicated that CD3 downmodulation was the stronger correlate of avidity. CD3 downmodulation, simply measured using flow cytometry, can be used to identify high-avidity CD8 T cells in a clinical context.

Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors

The success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy donors. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCR biophysicochemical properties, we derive and apply an in silico model predicting TCR structural avidity and validate the enrichment in high avidity T cells in patients’ tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.

Low avidity circulating SARS-CoV-2 reactive CD8+ T cells with proinflammatory TEMRA phenotype are associated with post-acute sequelae of COVID-19.

The role of adaptive SARS-CoV-2 specific immunity in post-acute sequelae of COVID-19 (PASC) is not well explored, although a growing population of convalescent COVID-19 patients with manifestation of PASC is observed. We analyzed the SARS-CoV-2-specific immune response, via pseudovirus neutralizing assay and multiparametric flow cytometry in 40 post-acute sequelae of COVID-19 patients with non-specific PASC manifestation and 15 COVID-19 convalescent healthy donors. Although frequencies of SARS-CoV-2-reactive CD4+ T cells were similar between the studied cohorts, a stronger SARS-CoV-2 reactive CD8+ T cell response, characterized by IFNγ production and predominant TEMRA phenotype but low functional TCR avidity was detected in PASC patients compared to controls. Of interest, high avidity SARS-CoV-2-reactive CD4+ and CD8+ T cells were comparable between the groups demonstrating sufficient cellular antiviral response in PASC. In line with the cellular immunity, neutralizing capacity in PASC patients was not inferior compared to controls. In conclusion, our data suggest that PASC may be driven by an inflammatory response triggered by an expanded population of low avidity SARS-CoV-2 reactive pro-inflammatory CD8+ T cells. These pro-inflammatory T cells with TEMRA phenotype are known to be activated by a low or even without TCR stimulation and lead to a tissue damage. Further studies including animal models are required for a better understanding of underlying immunopathogensis. Summary: A CD8+ driven persistent inflammatory response triggered by SARS-CoV-2 may be responsible for the observed sequelae in PASC patients.

Abstract A009: AFNT-111: A novel TCR-engineered T cell therapy targeting the oncogenic driver KRAS G12V

Abstract Mutations in the RAS family are highly prevalent in human cancers, including up to 35% of non-small cell lung, 45% of colorectal, and 95% of pancreatic cancers. Kirsten rat sarcoma viral oncogene homologue (KRAS) is the most frequently mutated RAS oncogene and patients with KRAS mutations have poor responses to standard treatment regimens. Therefore, successful KRAS-targeted therapies represent a high unmet need. The AFNT-111 cellular therapy consists of autologous CD8+ and CD4+ T cells expressing a high affinity TCR specific for the prevalent KRASG12V mutation presented by HLA-A*11:01, one of the most common HLA alleles worldwide. AFNT-111 is engineered to express the CD8α/β coreceptor, enabling a coordinated CD4+/CD8+ tumor response to induce robust T cell activity and persistence while minimizing T cell exhaustion. Lentiviral vector was used to transduce primary healthy human CD4+ and CD8+ T cells with the KRASG12V-specific human TCR and CD8α/β coreceptor. Engineered T cells were assessed against exogenous KRASG12V peptide as well as a panel of tumor cell lines endogenously expressing KRASG12V and probed for in vitro activation, proliferation, cytotoxicity and cytokine secretion. In parallel, in vitro safety studies were performed to evaluate autoantigen cross-reactivity and alloreactivity. In vivo efficacy studies were conducted using established human KRASG12V xenografts in NSG mice. AFNT-111 demonstrated potent functional avidity towards the KRASG12V peptide with no reactivity against KRASWT. Several naturally expressing KRASG12V human tumor cell lines led to significant AFNT-111 T cell activation and proliferation, as well as potent cytotoxicity. The addition of the CD8α/β coreceptor revealed a coordinated and synergistic cytotoxic CD4+ and CD8+ T cell response, enhancing activation of the AFNT-111 cell product. Robust cytotoxicity was associated with increased T cell secretion of IFNγ and TNFα. Durable in vivo anti-tumor efficacy was observed in three established mouse xenograft tumor models. XScan studies using amino acid substitutions of the index KRASG12V peptide revealed a restrictive TCR recognition motif. Further, potentially cross-reactive human self-peptides matching this motif were tested and no significant cross-reactivities were identified. To test alloreactivity, a large lymphoblastoid cell line library was assessed with no alloreactive responses detected. A streamlined manufacturing process has also been developed in which CD4+/CD8+ T cell ratios are controlled, with the final AFNT-111 product retaining a high degree of stem-like properties. AFNT-111 preclinical data demonstrate a highly potent and specific TCR-engineered T cell product that is cytotoxic to KRASG12V-expressing tumor cells both in vitro and in vivo. Cross-reactivity and alloreactivity assessments establish a potentially favorable safety profile of AFNT-111, supporting clinical translation. First-in-human clinical studies will focus on advanced or metastatic pancreatic, colorectal, and lung cancer indications. Citation Format: Michele Hoffmann, Xingyue He, Cheryl Black, Joshua Francis, James Parsons, Christian Roy, Jinsheng Liang, Hongjing Qu, Martin Campbell, Tomasz Sewastianik, Jessica Webb, Aude Chapuis, Thomas Schmitt, Philip Greenberg, Damien Hallet, Markus Vallaster, Piotr Pierog, Gary Shapiro, Hubert Lam, Loic Vincent. AFNT-111: A novel TCR-engineered T cell therapy targeting the oncogenic driver KRAS G12V [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A009.

Abstract PR08: TCR1020 specific for KRAS G12V restricted to HLA-A*11:01 exhibits potent and precise antigen specificity for clinical development

Abstract Background: KRAS mutations drive tumorigenesis in adenocarcinomas of the lung (30-40%), colon (40-50%) and pancreas (>90%). Recent clinical evidence demonstrates potent and durable anti-tumor activity of adoptively transferred KRAS-specific T cells in select patients with KRAS-mutated advanced solid tumors. We have defined mutant KRAS (mKRAS) epitopes restricted to high prevalence HLA class I alleles and validated this oncoprotein as an immunological target amenable to T cell receptor (TCR)-based therapeutic approaches. Here, we describe the pre-clinical development of TCR1020, a human TCRab specific for KRAS G12V restricted to HLA-A*11:01. Methods: In vitro stimulation assays were used to generate CD8+ T cell responses specific for a decamer epitope of KRAS G12V (VVVGAVGVGK) using blood specimens collected from A*11:01+ healthy donors. TCR1020 was identified by TCRab RNA sequencing of flow cytometrically sorted peptide/HLA multimer+ CD8 T cells. Transgenic expression of TCR1020 was attained via lentiviral transduction of reporter cell lines and gene-edited (TCRabnull) primary T cells. TCR1020 antigen specificity, affinity and cross-reactivity was assessed using in vitro coculture, limiting peptide dilution, and combinatorial peptide scanning assays. TCR1020 reactivity to G12V/A*11:01+ cell lines was assessed using in vitro cytokine release and cytotoxicity assays, as well as mouse xenograft tumor models. Results: TCR1020 exhibits specificity to the cognate KRAS G12V epitope with cross-reactivity to G12C but not wild-type KRAS. TCR1020 has a measured functional avidity (EC50) of 262 pM. TCR1020-redirected primary CD8+ T cells promote cytolysis of A*11:01+ tumor cell lines of lung, colonic or pancreatic origin harboring endogenous KRAS G12V mutations. The adoptive transfer of TCR1020-engineered primary CD8+ T cells exhibits potent in vivo antitumor activity in mouse xenograft tumor models of metastatic cancer. TCR1020 demonstrates CD8 co-receptor independence, and CD4+ T cells expressing TCR1020 express cytokines and lyse G12V/A*11:01+ tumor cell lines. In-depth characterization of the TCR1020 peptide recognition motif using alanine/glycine scanning libraries reveals a unique antigen binding motif with 5 critical amino acid residues excluding peptide/HLA anchor residues. Combinatorial peptide library scanning identifies five A*11:01-restricted peptide candidates within the human proteome with potential cross-reactivity to TCR1020, none of which activate TCR1020-engineered T cells over a wide range of concentrations. TCR1020 exhibits no evidence of reactivity against cell lines derived from healthy human tissues nor alloreactivity against a panel of lymphoblastoid cell lines encompassing a wide array of HLA class I alleles. Conclusion: TCR1020 exhibits high potency and exquisite antigen cognate specificity, and it is under clinical development for the treatment of A*11:01+ patients with KRAS G12V+ advanced solid tumors. Citation Format: Adham S. Bear, Rebecca B. Nadler, John Scholler, Robert H. Vonderheide, Gerald P. Linette, Beatriz M. Carreno. TCR1020 specific for KRAS G12V restricted to HLA-A*11:01 exhibits potent and precise antigen specificity for clinical development [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr PR08.

Selection of highly responsive T cell receptors by an analysis combining the expression of multiple markers.

The clinical success of T cell receptor (TCR) gene-transduced T (TCR-T) cell therapy is expected as one of the next-generation immunotherapies for cancer, in which the selection of TCRs with high functional avidity (high-functional TCRs) is important. One widely used approach to select high-functional TCRs is a comparison of the EC50 values of TCRs, which involves laborious experiments. Therefore, the establishment of a simpler method to select high-functional TCRs is desired. We herein attempted to establish a simple method to select high-functional TCRs based on the expression of T cell activation markers using the mouse T cell line BW5147.3 (BW). We examined relationships between the EC50 values of TCRs in interleukin-2 production and the expression levels of TCR activation markers on BW cells. In TCR-expressing BW cells stimulated with antigenic peptides, the CD69, CD137, and PD-1 expression was differentially induced by various doses of peptides. An analysis of TCRs derived from the tumor-infiltrating lymphocytes of murine melanoma and peripheral blood T cells of hepatocellular carcinoma patients treated with a peptide vaccination revealed that an analysis combining CD69, CD137, and PD-1 expression levels in BW cells stimulated with a single dose of an antigenic peptide selected high-functional TCRs with functional avidity assessed by EC50 values. Our method facilitates the section of high-functional TCRs among tumor-reacting TCRs, which will promote TCR-T cell therapy. The stimulation of BW cells expressing objective TCRs with a single dose of antigenic peptides and analysis combining the expression of CD69, CD137, and PD-1 allows us to select highly responsive TCRs.

Establishment of a novel NFAT-GFP reporter platform useful for the functional avidity maturation of HLA class II-restricted TCRs

CD4+ T cells that recognize antigenic peptides presented on HLA class II are essential for inducing an optimal anti-tumor immune response, and adoptive transfer of tumor antigen-specific TCR-transduced CD4+ T cells with high responsiveness against tumor is a promising strategy for cancer treatment. Whereas a precise evaluation method of functional avidity, an indicator of T cell responsiveness against tumors, has been established for HLA class I-restricted TCRs, it remains unestablished for HLA class II-restricted TCRs. In this study, we generated a novel platform cell line, CD4-2D3, in which GFP reporter was expressed by NFAT activation via TCR signaling, for correctly evaluating functional avidity of HLA class II-restricted TCRs. Furthermore, using this platform cell line, we succeeded in maturating functional avidity of an HLA class II-restricted TCR specific for a WT1-derived helper peptide by substituting amino acids in complementarity determining region 3 (CDR3) of the TCR. Importantly, we demonstrated that transduction of an avidity-maturated TCR conferred strong cytotoxicity against WT1-expressing leukemia cells on CD4+ T cells, compared to that of its original TCR. Thus, CD4-2D3 cell line should be useful not only to evaluate TCR functional avidity in HLA class II-restricted TCRs but also to screen appropriate TCRs for clinical applications such as cancer immunotherapy.

Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor diversity

T cells play a crucial role in combatting SARS-CoV-2 and forming long-term memory responses to this coronavirus. The emergence of SARS-CoV-2 variants that can evade T cell immunity has raised concerns about vaccine efficacy and the risk of reinfection. Some SARS-CoV-2T cell epitopes elicit clonally restricted CD8+ T cell responses characterized by T cell receptors (TCRs) that lack structural diversity. Mutations in such epitopes can lead to loss of recognition by most T cells specific for that epitope, facilitating viral escape. Here, we studied an HLA-A2-restricted spike protein epitope (RLQ) that elicits CD8+ T cell responses in COVID-19 convalescent patients characterized by highly diverse TCRs. We previously reported the structure of an RLQ-specific TCR (RLQ3) with greatly reduced recognition of the most common natural variant of the RLQ epitope (T1006I). Opposite to RLQ3, TCR RLQ7 recognizes T1006I with even higher functional avidity than the WT epitope. To explain the ability of RLQ7, but not RLQ3, to tolerate the T1006I mutation, we determined structures of RLQ7 bound to RLQ-HLA-A2 and T1006I-HLA-A2. These complexes show that there are multiple structural solutions to recognizing RLQ and thereby generating a clonally diverse T cell response to this epitope that assures protection against viral escape and T cell clonal loss.