Human T-cell Receptor Research Articles

Invariant VD and DJ Motifs Define a Novel Class of Human Antibodies and TCRs Prototyped by antigen receptors of Dual-Expresser Lymphocytes

ABSTRACT Introduction Dual-expressing lymphocytes (DEs) are unique immune cells that express both B cell receptors (BCRs, surface antibody) and T cell receptors (TCRs). In type 1 diabetes, DE antibodies are predominated by one antibody (x-mAb), an IgM monoclonal antibody with a germline-encoded CDR3 that recognizes self-reactive TCRs. We explored if x-mAb and its interacting TCRs have distinct structural features. Methods Using bioinformatics, we compared x-mAb and its most common interacting TCRαβ to billions of antigen receptor sequences to determine if they were unique or randomly generated. Results X-mAb represents a unique class of human antibodies with a conserved CDR3 sequence (CARx1-4DTAMVYYFYDW), consisting of a fixed DJH motif (DTAMVYYFDYW) paired with various VH genes. A public TCRβ clonotype (CASSPGTEAFF) associated with x-mAb on DEs features two invariant segments, VβD (CASSPGT) and DJβ (PGTEAFF), key to two large families of public TCRβ clonotypes—CASSPGT-Jβx and CASSPGT-Jβx—formed by recombining the VβD motif with Jβ genes and the DJβ motif with Vβ genes. B cells also use CASSPGT as a VHD motif for public IGH clonotypes (CASSPGT—Jβx). Discussion DEs, unlike conventional T and B cells, use invariant motifs to create public antibodies and TCRs, a trait previously seen only in cartilaginous fish.

Structure of a fully assembled γδ T cell antigen receptor

T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express—that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands1. Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood2,3, the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR–CD3δγε2ζ2 complex bound by anti-CD3ε antibody Fab fragments4,5. The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR2,3,6, the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.

Human T-cell receptor triggering requires inactivation of Lim kinase-1 by Slingshot-1 phosphatase

Actin dynamics control early T-cell receptor (TCR) signalling during T-cell activation. However, the precise regulation of initial actin rearrangements is not completely understood. Here, we have investigated the regulatory role of the phosphatase Slingshot-1 (SSH1) in this process. Our data show that SSH1 rapidly polarises to nascent cognate synaptic contacts and later relocalises to peripheral F-actin networks organised at the mature immunological synapse. Knockdown of SSH1 expression by CRISPR/Cas9-mediated genome editing or small interfering RNA reveal a regulatory role for SSH1 in CD3ε conformational change, allowing Nck binding and proper downstream signalling and immunological synapse organisation. TCR triggering induces SSH1-mediated activation of actin dynamics through a mechanism mediated by Limk-1 inactivation. These data suggest that during early TCR activation, SSH1 is required for rapid F-actin rearrangements that mediate initial conformational changes of the TCR, integrin organisation and proximal signalling events for proper synapse organisation. Therefore, the SSH1 and Limk-1 axis is a key regulatory element for full T cell activation.

Cancer Immunotherapies Ignited by a Thorough Machine Learning-Based Selection of Neoantigens.

Identification of neoantigens, derived from somatic DNA alterations, emerges as a promising strategy for cancer immunotherapies. However, not all somatic mutations result in immunogenicity, hence, efficient tools to predict the immunogenicity of neoepitopes are needed. A pipeline is presented that provides a comprehensive solution for the identification of neoepitopes based on genomic sequencing data. The pipeline consists of a data pre-processing step and three machine learning predictive steps. The pre-processing step analyzes genomic data for different types of alterations, produces a list of all possible antigens, and determines the human leukocyte antigen (HLA) type and T-cell receptor (TCR) repertoire. The first predictive step performs a classification into antigens and neoantigens, selecting neoantigens for further consideration. The next step predicts the strength of binding between neoantigens and available major histocompatibility complexes of class I (MHC-I). The third step is engaged to predict the likelihood of inducing an immune response. Neoepitopes satisfying all three predictive stages are assumed to be potent candidates to ensure immunogenicity. The predictive pipeline is used in two regimes: selecting neoantigens from patients' sequencing data and generating novel neoantigen candidates. Two different techniques - Monte Carlo and Reinforcement Learning - are implemented to facilitate the generativeregime.

Structures of human γδ T cell receptor–CD3 complex

Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology1–3. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex2. The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy4. Here we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR–CD3 complexes5,6, revealing two distinct assembly mechanisms that depend on Vγ usage. The Vγ9Vδ2 TCR–CD3 complex is monomeric, with considerable conformational flexibility in the TCRγ–TCRδ extracellular domain and connecting peptides. The length of the connecting peptides regulates the ligand association and T cell activation. A cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signalling. The Vγ5Vδ1 TCR–CD3 complex displays a dimeric architecture, whereby two protomers nestle back to back through the Vγ5 domains of the TCR extracellular domains. Our biochemical and biophysical assays further corroborate the dimeric structure. Importantly, the dimeric form of the Vγ5Vδ1 TCR is essential for T cell activation. These findings reveal organizing principles of the γδ TCR–CD3 complex, providing insights into the unique properties of γδ TCR and facilitating immunotherapeutic interventions.

Selection, engineering, and in vivo testing of a human leukocyte antigen-independent T-cell receptor recognizing human mesothelin.

Canonical α/β T-cell receptors (TCRs) bind to human leukocyte antigen (HLA) displaying antigenic peptides to elicit T cell-mediated cytotoxicity. TCR-engineered T-cell immunotherapies targeting cancer-specific peptide-HLA complexes (pHLA) are generating exciting clinical responses, but owing to HLA restriction they are only able to target a subset of antigen-positive patients. More recently, evidence has been published indicating that naturally occurring α/β TCRs can target cell surface proteins other than pHLA, which would address the challenges of HLA restriction. In this proof-of-concept study, we sought to identify and engineer so-called HLA-independent TCRs (HiTs) against the tumor-associated antigen mesothelin. Using phage display, we identified a HiT that bound well to mesothelin, which when expressed in primary T cells, caused activation and cytotoxicity. We subsequently engineered this HiT to modulate the T-cell response to varying levels of mesothelin on the cell surface. The isolated HiT shows cytotoxic activity and demonstrates killing of both mesothelin-expressing cell lines and patient-derived xenograft models. Additionally, we demonstrated that HiT-transduced T cells do not require CD4 or CD8 co-receptors and, unlike a TCR fusion construct, are not inhibited by soluble mesothelin. Finally, we showed that HiT-transduced T cells are highly efficacious in vivo, completely eradicating xenografted human solid tumors. HiTs can be isolated from fully human TCR-displaying phage libraries against cell surface-expressed antigens. HiTs are able to fully activate primary T cells both in vivo and in vitro. HiTs may enable the efficacy seen with pHLA-targeting TCRs in solid tumors to be translated to cell surface antigens.

Abstract 7042: Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis

Abstract The therapeutic potential of T cell therapies for treating solid tumors can be limited by intrinsic T cell exhaustion mechanisms and the suppressive tumor microenvironment. To better understand these challenges and identify genetic perturbations to enhance T cell functions, we developed in vivo exhaustion models and performed pooled CRISPR/Cas9-based screens with detailed characterization of T cell states through single cell RNA-sequencing (scRNA-seq). In vivo Xenograft exhaustion models were developed in the format of T cell receptor (TCR) T cells, with tumor cell lines expressing TCR-specific antigen (NY-ESO-1) respectively. Individual perturbations were introduced into T cells via non-viral editing and pooled before transferred into mice with established tumors of various sizes that provided continuous antigen exposure to drive exhaustion, while providing sufficient number of T cells from tumor and spleen tissues for scRNA-seq. The pooled CRISPR in vivo screens in human TCR T cells enabled us to evaluate T cell phenotypes resulting from gain-of-function, loss-of-function, or combinations of these modifications across a wide array of target genes. We identified known and previously uncharacterized combinatorial perturbations that were enriched or depleted and were associated with distinct transcriptional phenotypes over the course of chronic stimulation. This approach allows us to bridge the gaps in our understanding of how T cells can be reprogrammed to overcome exhaustion and function more effectively in the challenging environment of solid tumors. Citation Format: Dina Polyak, Jessica Fuhriman, Josephine Susanto, Allyson Merrell, Mandi Simon, Catherine Oh, Andrew Cordazo, David DeTomasso, Carla Tocchini, Vibhavari Sail, Eric Cui, Jeff Milush, Levi Gray-Rupp, Brendan Galvin, Christopher Murriel, Grace Zheng, Angela C. Boroughs, Pratiksha Thakore, Soyoung Oh, Jake Freimer, Bob Chen, Celine Eidenschenk, Emily Wheeler, Jacob Levine, Jan-Christian Huetter, Jill Schartner, Katie Geiger-Schuller, Orit Rozenblatt-Rosen, Sascha Rutz, Ira Mellman, W. Nicholas Haining. Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis [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 7042.

Abstract 5486: Spatial profiling reveals unique immune-transcriptomic features of tertiary lymphoid structures in melanoma

Abstract Background:Previous studies have shown that intratumoral immune aggregates called tertiary lymphoid structures (TLS) are associated with exceptional response to immune checkpoint blockade (ICB) in several cancer types. However, the specific mechanisms through which TLS contribute to ICB-response remain poorly characterized in part due to technical limitations with isolating TLS. Here, we use the NanoString GeoMx digital spatial profiler to interrogate TLS with deep spatial and transcriptional resolution and identify cellular and molecular features of response-associated TLS in melanoma. Methods:Twelve neoadjuvant ICB-treated high-risk resectable melanoma patients [NCT02519322] with formalin-fixed paraffin embedded (FFPE) surgical resections were included in this study. Major pathologic response (MPR) defined as <10% viable tumor at time of surgery was used to evaluate response (R – responder; NR – non-responder). TLS were sampled (via H&E) using 1mm core punches and assembled into a tissue microarray (TMA). The TLS TMA was probed using the human whole transcriptome atlas (huWTA) and the human T-cell receptor (huTCR) atlas. Melanoma (S100B) and immune markers (CD45 and CD20) were used to guide region-of-interest (ROI) selection of classical TLS. Differential gene expression was calculated using a linear mixed model and corrected with Benjamini-Hochberg. Immune deconvolution was performed using CIBERSORTx with FDR cutoff of < 0.25. Results:Fifty percent (6/12) of patients included in this study demonstrated MPR following treatment with neoadjuvant ICB. Principal component analysis of huWTA probes revealed distinct transcriptional states of R TLS vs NR TLS, with PC1 strongly correlating with response status (r=0.88, p<0.0001). Differential immune analysis showed that R TLS harbored more CD8+ T-cells (p<0.001), NK cells (p=0.004), γδ T-cells (p=0.017) and memory B-cells (p=0.026) and preferentially upregulated inflammatory genes such as pattern recognition receptors (TLR8 and KLRC2) and immune-stimulatory markers (CD27 and CD103). Immune-repertoire analysis revealed a trend towards increased TCR diversity in R TLS (p = 0.3) and distinct TCR signatures in R TLS underscored by elevated expression of TRDJ4 (p<0.001), TRGJ1/2(p<0.001), TRGV4(p<0.001) and TRAV1-2(p=0.018) genes amongst others. Conclusions:These findings demonstrate that, although melanomas from both R and NR patients contain TLS, the immune-phenotype of R TLS is more cytotoxic and characterized by a more diverse TLS-resident T-cell population. These findings present new insights into the therapeutic underpinnings of TLS in cancer and will inform future investigations evaluating their formation/function in solid tumors. Citation Format: Manoj Chelvanambi, Brenda Melendez, Elise F. Nassif, Rossana N. Lazcano, Matthew J. Lastrapes, Bharat S. Bhushan, Sarah B. Johnson, Khalida Wani, Davis R. Ingram, Y David Seo, Beth A. Helmink, Michael G. White, Russell G. Witt, Laurence P. Diggs, Golnaz Morad, Monika Zelazowska, Somnath Paul, Florentia Dimitriou, Ashish V. Damania, Matthew C. Wong, Neeta Somaiah, Nadim J. Ajami, Emily Z. Keung, Wolf H. Fridman, James P. Allison, Padmanee Sharma, Kevin M. McBride, Tina Cascone, Christina L. Roland, Alexander J. Lazar, Jennifer A. Wargo. Spatial profiling reveals unique immune-transcriptomic features of tertiary lymphoid structures in melanoma [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 5486.

Abstract 1173: T cell receptor diversity in buffy coat samples from subsets of breast and ovarian cancer patients

Abstract Background: Immunotherapy, mainly by the use of immune checkpoint inhibitors (ICI), has been established as a standard option for both, solid tumors and hematological malignancies. Unfortunately, this success has only been replicated in a subset of patients (pts) with gynecological cancers. In ovarian cancer (OC), response rates to ICI monotherapy were low and in breast cancer (BC), only the subgroup of triple-negative BC (TNBC) pts showed an improved outcome by the addition of ICI. One reason for limited success of immunotherapy might be an impaired immune system. In this regard, monitoring the T cell receptor (TCR) repertoire could provide key insights into adaptive immune responses to ultimately understand disease initiation, progression and treatment response. Here we elucidated TCR alpha, beta, gamma and delta in buffy coats of pts with non-metastatic OC as well as non-metastatic and metastatic TNBC and compared the results with healthy donors (HDs). Methods: RNA was isolated from buffy coat samples of 20 HDs, 10 treatment-naïve primary OC pts, 14 treatment-naïve, non-metastatic TNBC pts (participating in the phase II neomono trial) and 19 pts with metastatic TNBC by a modified QIAamp RNA Blood Mini protocol. A survey of the TCR diversity and mapping of common and unique TCRs was done using the QIAseq Targeted RNA Panel Human TCR panel for all known T-cell receptors (alpha, beta, gamma, delta). Results: Regardless of the cancer entity, a significant reduction in TCR diversity was observed compared to HDs with the greatest differences observed in the delta receptors. When OC samples were compared with HDs, the difference in diversity was highly significant for all TCR subtypes (TCRalpha: p=0.013; TCRbeta: p=0.008; TCRgamma: 0.008; TCRdelta: 0.006). Similar results were obtained for non-metastatic TNBC (TCRalpha: p=0.0002; TCRbeta: p=0.0001; TCRgamma: p=0.002; TCRdelta: p=0.002) as well as metastatic TNBC patients (TCRalpha: p=0.001; TCRbeta: p=0.001; TCRgamma: p=0.005; TCRdelta: p=0.003) when their TCR diversity was compared to HDs. Interestingly, no significant differences in diversity were obtained when treatment-naïve non-metastatic TNBC pts were compared with heavily pretreated metastatic TNBC pts. The lowest diversity was found in BC pts compared to the OC pts. Conclusion: We have initiated a survey of the TCR diversity in TNBC and OC patients. Further evaluations will include the correlation of these findings with clinical characteristics and outcome. Whether the reduced TCR diversity represents T cell exhaustion or T cell specialization cannot yet be deduced from the results. Nevertheless, the addition of a TCR diversity score could provide an additional metric which may help provide patient guidance when integrated into a multi-modal molecular test. Citation Format: Corinna Keup, Cornelia Kolberg-Liedtke, Song Tian, Samuel J. Rulli, Siegfried Hauch, Paul Buderath, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir-Bauer. T cell receptor diversity in buffy coat samples from subsets of breast and ovarian cancer patients [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 1173.

Lymph Node-Targeted Vaccine Boosting of TCR T-cell Therapy Enhances Antitumor Function and Eradicates Solid Tumors.

T-cell receptor (TCR)-modified T-cell therapies have shown promise against solid tumors, but overall therapeutic benefits have been modest due in part to suboptimal T-cell persistence and activation in vivo, alongside potential tumor antigen escape. In this study, we demonstrate an approach to enhance the in vivo persistence and function of TCR T cells through combination with Amphiphile (AMP) vaccination including cognate TCR T peptides. AMP modification improves lymph node targeting of conjugated tumor immunogens and adjuvants, thereby coordinating a robust T cell-activating endogenous immune response. AMP vaccine combination with TCR T-cell therapy led to complete eradication and durable responses against established murine solid tumors refractory to TCR T-cell monotherapy. Enhanced antitumor efficacy was correlated with simultaneous in vivo invigoration of adoptively transferred TCR T cells and in situ expansion of the endogenous antitumor T-cell repertoire. Long-term protection against tumor recurrence in AMP-vaccinated mice was associated with antigen spreading to additional tumor-associated antigens not targeted by vaccination. AMP vaccination further correlated with pro-inflammatory lymph node transcriptional reprogramming and increased antigen presenting-cell maturation, resulting in TCR T-cell expansion and functional enhancement in lymph nodes and solid tumor parenchyma without lymphodepletion. In vitro evaluation of AMP peptides with matched human TCR T cells targeting NY-ESO-1, mutant KRAS, and HPV16 E7 illustrated the clinical potential of AMP vaccination to enhance human TCR T-cell proliferation, activation, and antitumor activity. Taken together, these studies provide rationale and evidence to support clinical evaluation of combining AMP vaccination with TCR T-cell therapies to augment antitumor activity.

Abstract A003: Preliminary safety results from a phase I study of autologous transgenic T cells expressing high affinity mesothelin-specific T cell receptor (TCR) (FH-TCR TMSLN) in patients (pts) with metastatic pancreatic ductal adenocarcinoma (mPDA)

Abstract Background: We previously demonstrated murine CD8+ T cells engineered to express a high affinity MSLN-specific TCR exhibit efficacy in the KPC mouse model, particularly with serial infusions, and thus developed a human TCR for expression in autologous T cells for targeting MSLN, which is overexpressed by 80% of PDAs. In this first-in-human phase I trial, we are determining safety, preliminary efficacy, as well as persistence, activation, localization, and functional capacity of autologous FH-TCR-TMSLN (T) cells in refractory, MSLN+ mPDA. Methods: Eligible pts have ECOG PS 0-1, ≥1 prior therapy for mPDA, life expectancy ≥12 weeks, MSLN 2+ expression in ≥30% tumor cells by IHC, HLA-A*2:01, no HLA-B*13:02. Pts undergo leukapheresis, and 3-4 weeks later receive the first T cell infusion. Three T-cell infusions, if sufficient T cells can be manufactured, are being administered every 21 days (d) at 3 dose level cohorts: 1 × 109, 3.3 × 109 and 1 × 1010 T cells, with a 3+3 design. Dose limiting toxicities (DLTs) are assessed during the 21d after each T cell dose. Only pts who receive ≥75% of the assigned T cell dose are DLT evaluable, but all pts are evaluable for safety. Lymphodepleting chemotherapy (LDC) with fludarabine/cyclophosphamide is administered prior to the last T cell infusion (cohorts 1-2) or prior to the first T cell infusion (cohort 3). Primary endpoints are safety and DLTs. Secondary endpoints are response rate, progression-free and overall survival. Exploratory endpoints include TCR-TMSLN cells in tumor biopsies and blood as biomarkers. Results: Between Dec 2021 to July 2023, 7 pts were enrolled, and 6 pts treated (n=3 at dose at level 1, n=3 at dose level 2), 4 women, median age 60 years (range 51-70), median 3 prior systemic therapies. All pts underwent research-related tumor biopsies at baseline, and 2-3 weeks post first T cell infusion, and 2 pts had biopsies after the last T-cell infusion. Treatment exposure was median 3 (range 1-3) T cell infusions. No DLTs occurred among 6 pts treated at dose levels 1 × 109 and 3.3 × 109 T cells. Treatment related adverse events (TRAE) thought at least possibly related to T cells infusions were fever [n=2 grade (gr) 1, n=1 gr 2], and gr 2 chills, cytokine release syndrome (CRS), dizziness, fatigue, hypertension, hypotension, nausea, acute generalized exanthematous pustulosis (AGEP) rash, and sinus tachycardia (n=1 each). TRAE due to LDC were transient leukopenia (n=2 gr 4, n=1 gr 3, n=2 gr 2), neutropenia (n=4 gr 4, n=1 gr 2), lymphopenia (n=3 gr 4), dysgeusia (n=2 gr 2), anemia (n=1 gr 3) and fatigue (n=1 gr 2). One patient had a serious adverse event with gr 2 CRS and gr 2 AGEP, which resolved. Due to anticipated difficulty attaining sufficient T cells doses for three high dose infusions, we amended the protocol to allow treatment with at least one T cell infusion, with the first dose preceded by LDC at the 1 × 1010 T cells dose level. Conclusions: FH-TCR-TMSLN cells are well tolerated with no on-target toxicity, and the study is open to accrual (NCT04809766). Citation Format: Elena G. Chiorean, Aude Chapuis, Andrew Coveler, Cecilia Yeung, Ted Gooley, David B. Zhen, Gentry King, Stacey Cohen, Lindsay Hannan, Rachael Safyan, Anthony Germani, Susan Ra, Jennifer Casserd, Tom Schmitt, Philip Greenberg. Preliminary safety results from a phase I study of autologous transgenic T cells expressing high affinity mesothelin-specific T cell receptor (TCR) (FH-TCR TMSLN) in patients (pts) with metastatic pancreatic ductal adenocarcinoma (mPDA) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A003.

Longitudinal change trend of the TCR repertoire reveals the immune response intensity of the inactivated COVID-19 vaccine

Evidence concerning the individual differences in neutralizing antibody responses after receiving the COVID-19 vaccine remains lacking. In this study, we collected the serum and Peripheral blood mononuclear cells(PBMC) of 16 subjects who had never suffered from COVID-19 before during the course of two vaccine doses. Microneutralization assay is used to determine the immune response intensity of vaccine subjects. we revealed the change trend of TCR diversity using T cell receptor (TCR) sequencing. Then, we analyzed the correlation between HLA class II allele frequencies and the intensity of immune response. Finally, we identified several CDR3 sequences related to the intensity of the immune response. We analyzed the differences in D50 (DD50) between different time points, and found that there were two patterns in the change trend of TCR diversity, and the increased diversity group has stronger immune response. The inactivated vaccine is different from the mRNA vaccine against the spike protein, resulting in differences in TCR repertoire response patterns and antibody responses, which are related to HLA-DRB1 * 09:01. The presence of specific CDR3 sequences in the increased diversity group, rather than gene usage of the VJ gene, determines the intensity and persistence of neutralizing antibody titers. Finally, We identified the different response patterns of the human TCR repertoire to inactivated vaccines. The pattern with increased diversity is more likely to appear strong and more lasting immune response.

NLGN4X TCR transgenic T cells to treat gliomas.

Neuroligin 4 X-linked (NLGN4X) harbors a human leukocyte antigen (HLA)-A*02-restricted tumor-associated antigen, overexpressed in human gliomas, that was found to induce specific cytotoxic T cell responses following multi-peptide vaccination in patients with newly diagnosed glioblastoma. T cell receptor (TCR) discovery was performed using droplet-based single-cell TCR sequencing of NLGN4X-tetramer-sorted T cells postvaccination. The identified TCR was delivered to Jurkat T cells and primary human T cells (NLGN4X-TCR-T). Functional profiling of NLGN4X-TCR-T was performed by flow cytometry and cytotoxicity assays. Therapeutic efficacy of intracerebroventricular NLGN4X-TCR-T was assessed in NOD scid gamma (NSG) major histocompatibility complex (MHC) I/II knockout (KO) (NSG MHC I/II KO) mice bearing NLGN4X-expressing experimental gliomas. An HLA-A*02-restricted vaccine-induced T cell receptor specifically binding NLGN4X131-139 was applied for preclinical therapeutic use. Reactivity, cytotoxicity, and polyfunctionality of this NLGN4X-specific TCR are demonstrated in various cellular models. Intracerebroventricular administration of NLGN4X-TCR-T prolongs survival and leads to an objective response rate of 44.4% in experimental glioma-bearing NSG MHC I/II KO mice compared to 0.0% in control groups. NLGN4X-TCR-T demonstrate efficacy in a preclinical glioblastoma model. On a global scale, we provide the first evidence for the therapeutic retrieval of vaccine-induced human TCRs for the off-the-shelf treatment of glioblastoma patients.Keywords cell therapy | glioblastoma | T cell receptor | tumor antigen.

P06.12.A NLGN4X-SPECIFIC TCR T CELLS TARGETING EXPERIMENTAL GLIOMAS

Abstract BACKGROUND A human leukocyte antigen (HLA)-A*02-restricted tumor associated antigen in the neuroligin 4 X-linked (NLGN4X) protein was found to be specifically overexpressed in human gliomas. Individualized multipeptide vaccination targeted NLGN4X and induced specific cytotoxic T cells responses in patients with newly diagnosed glioblastoma. MATERIAL AND METHODS Post vaccination NLGN4X-tetramer-sorted T cells were subjected to single cell T cell receptor (TCR) sequencing for TCR discovery. The identified TCR was delivered to human T cells (NLGN4X-TCR-T) and functional profiling was performed by flow cytometry and in vitro cytotoxicity assays. NOD scid gamma (NSG) major histocompatibility complex (MHC) I/II knockout (KO) (NSG MHC I/II KO) mice were challenged with NLGN4X-expressing experimental gliomas and treated with intracerebroventricular injection of NLGN4X-TCR-T to assess its therapeutic potential. RESULTS We apply for the first time for therapeutic use of an HLA-A*02 restricted vaccine-induced TCR that binds to the NLGN4X antigen. We show the cytotoxic and polyfunctional phenotype of NLGN4X-TCR-T in various cellular models. Intracerebroventricular delivery of NLGN4X-TCR-T prolongs survival and leads to objective radiographic responses in experimental gliomas-bearing NSG MHC I/II KO mice. CONCLUSION NLGN4X-TCR-T demonstrates efficacy in a preclinical experimental glioblastoma model. On a global scale, we provide first evidence for the therapeutic retrieval of vaccine-induced human TCRs for the off-the-shelf treatment of glioblastoma patients.

Abstract 2752: Targeting intracellular tumor antigens using fully human TCR mimic antibodies derived from HLA transgenic RenMiceTM

Abstract Therapeutic antibodies have ushered in a new age of cancer immunotherapy. Historically, these therapies have targeted a limited subset of soluble and cell surface tumor-associated antigens (TAAs). T cell receptors (TCRs) on cytotoxic CD8+ T cells recognize peptide antigens bound to major histocompatibility class I (MHC-I) proteins, called HLA-A/B/C in humans. By this pathway, antigen is regularly sampled from the intracellular peptidome, processed, and presented to cytotoxic T cells. Expanding TCR-based recognition of soluble, intracellular TAAs presented on the surface of malignant cells by this mechanism is a propitious therapeutic strategy. Here we describe a novel platform for generating T cell receptor mimic (TCRm) antibodies using our humanized immunoglobulin (RenMabTM) mice engineered to express HLA. TCRm antibodies have the same binding properties as endogenous TCRs and recognize processed, HLA-bound peptides including intracellular tumor-associated antigens, viral oncoproteins, and cancer-testis antigen (CTA). TCRm antibodies bind peptide-HLA with high specificity and up to nanomolar affinity. Our optimized immunization protocols and high-throughput screening methods allow for one-step TCRm antibody generation. TCRm antibodies can also be used to assemble bispecific T cell engaging antibodies (BiTEs) to enhance tumor targeting of cytotoxic T cells. Biocytogen’s TCRm antibodies are a flexible and powerful tool for cancer immunotherapy. By enabling TCR-mediated recognition of an unrestricted repertoire of cancer neoantigens, TCRm antibodies may find broad clinical application. Citation Format: Jun Du, Taolin Liu, Wanbo Tang, Yue Zhang, Limin Zhao, Xin Jiao, Chao Sun, Pengfei Du, Yuqi Zhang, Baihong Liu, Qingcong Lin, Yi Yang. Targeting intracellular tumor antigens using fully human TCR mimic antibodies derived from HLA transgenic RenMiceTM [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 2752.

Archaic humans have contributed to large-scale variation in modern human T cell receptor genes

Human Tcell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.

Generation of TGFβR2(-1) neoantigen-specific HLA-DR4-restricted T cell receptors for cancer therapy

BackgroundAdoptive transfer of patient’s T cells, engineered to express a T cell receptor (TCR) with defined novel antigen specificity, is a convenient form of cancer therapy. In most cases, major...

Genetic associations of human leukocyte antigen alleles in cutaneous delayed drug hypersensitivity reactions: An updated review

Abstract Cutaneous delayed drug hypersensitivity reactions (DHRs) are common iatrogenic events with potentially life-threatening consequences. Delayed DHRs encompass diverse phenotypes and can be classified by their distinct T-cell responses to drug antigens. Interaction between the immune receptors, human leukocyte antigen (HLA) and T-cell receptor (TCR), and the complementary antigenic peptide is required for the development of delayed DHRs. These idiosyncratic interactions can be elicited by the formation of antigenic drug-protein adducts (hapten hypothesis) or from direct interactions of drugs with the immune receptors (pharmacological interaction of drugs with immune receptors concept, altered peptide repertoire model, and altered TCR model). In addition, viral infections may play a role by providing co-stimulatory signals or enhancing TCR/HLA expression on T-cells. The associations of HLA allele polymorphisms and DHRs are phenotype and ethnicityspecific. The discovery of genetic polymorphisms associated with DHRs has provided a strategy to prevent and diagnose potentially life-threatening reactions. Recently, advances in next-generation sequencing technologies, such as the incorporation of whole-exome or whole-genome sequencing, enabled the comprehensive detection of susceptibility loci. Several HLA associations have shown clinical utility and cost-effectiveness, such as HLA-B*15:02 (carbamazepine-induced Stevens–Johnson syndrome/toxic epidermal necrolysis in Han Chinese), HLA-B*58:01 (allopurinol-induced severe cutaneous adverse reactions in Han Chinese), HLA-B*57:01 (abacavir hypersensitivity reactions in Caucasians), and HLA-B*13:01 (dapsone-induced drug reaction with eosinophilia and systemic symptoms in Han Chinese). Herein, we summarize the current knowledge of the pathogenesis, antigen presentation models, and HLA associations of cutaneous delayed DHRs.

Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires.

Here, we describe the identification of two T-cell receptors (TRs) containing TRDV genes in their TRA chains, the first one in human and the second one in mouse. First, using 5'RACE on a mixed lymphocyte-tumor cell culture (MLTC), we identified TRDV1 5'-untranslated region (UTR) and complete coding sequence rearranged productively to TRAJ24. Single-cell TR RNA sequencing (RNA-seq) of the MLTC, conducted to identify additional clonotypes, revealed that the analysis software detected the hybrid TRDV-TRAJ TRA (TRA) chain but excluded it from the final results. In a separate project, we performed TR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Here, the predominant clonotype contained a TRA chain with a TRDV2-2-TRAJ49 rearrangement. Again, the hybrid TRA chain was not reported in the final results. Transfection of both TR cDNAs resulted in cell surface localization of TR together with CD3, suggesting a productive protein in both cases. Tumor recognition of the Homo sapiens (Homsap) TRDV1-containing TR could be demonstrated by IFN Gamma ELISA ELISpot kit, whereas the Mus musculus (Musmus) TR did not recognize a tumor-derived cell line. To determine whether the TRDV-containing TRA chains we detected were rare events or whether TRDV genes are commonly incorporated into TRA chains, we queried the NCBI Sequence Read Archive for TR single-cell RNA-seq data and analyzed 21 human and 23 murine datasets. We found that especially Homsap TRDV1, Musmus TRDV1, and to some extent Musmus TRDV2-2 are more commonly incorporated into TRA chains than several TRAV genes, making those TRDV genes a relevant contribution to TRA diversity. TRDV-containing TRA chains are currently excluded from the final results of V-(D)-J dataset analyses with the CellRanger software. We provide a work-around to avoid exclusion of those hybrid TRA chains from the final analysis results.

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

BackgroundCynomolgus macaque (Macaca fascicularis) is an attractive animal model for the study of human disease and is extensively used in biomedical research. Cynomolgus macaques share behavioral, physiological, and genomic traits with humans and recapitulate human disease manifestations not observed in other animal species. To improve the use of the cynomolgus macaque model to investigate immune responses, we defined and characterized the T cell receptor (TCR) repertoire.ResultWe identified and analyzed the alpha (TRA), beta (TRB), gamma (TRG), and delta (TRD) TCR loci of the cynomolgus macaque. The expressed repertoire was determined using 22 unique lung samples from Mycobacterium tuberculosis infected cynomolgus macaques by single cell RNA sequencing. Expressed TCR alpha (TRAV) and beta (TRBV) variable region genes were enriched and identified using gene specific primers, which allowed their functional status to be determined. Analysis of the primers used for cynomolgus macaque TCR variable region gene enrichment showed they could also be used to amplify rhesus macaque (M. mulatta) variable region genes.ConclusionThe genomic organization of the cynomolgus macaque has great similarity with the rhesus macaque and they shared > 90% sequence similarity with the human TCR repertoire. The identification of the TCR repertoire facilitates analysis of T cell immunity in cynomolgus macaques.