TCR Repertoire Research Articles

Clinical Behavior, Mutational Profile and T-Cell Repertoire of High-Grade Neuroendocrine Tumors of the Head and Neck.

Neuroendocrine carcinomas (NECs) of the head and neck (HN) account for <1% of HN cancers (HNCs), with a 5-year overall survival (OS) <20%. This is a retrospective study of HN NECs diagnosed at our institution between 2005 and 2022. Immunohistochemistry and next-generation sequencing (NGS) were used to evaluate neuroendocrine markers, tumor mutational burden (TMB), mutational profiles and T-cell receptor repertoires. Eleven patients with high-grade HN NECs were identified (male:female ratio 6:5; median age 61 (Min-Max: 31-86)): nasoethmoidal (3), parotid gland (3), submaxillary gland (1), larynx (3) and base of tongue (1). Among n = 8 stage II/IVA/B, all received (chemo)radiotherapy with/without prior surgery or induction chemotherapy, with complete response in 7/8 (87.5%). Among n = 6 recurrent/metastatic patients, three received anti-PD1 (nivolumab (2), pembrolizumab (1)): two achieved partial responses lasting 24 and 10 months. After a median follow-up of 30 and 23.5 months since diagnosis and since recurrent/metastatic, median OS was not reached. Median TMB (n = 7) was 6.72 Mut/Mb. The most common pathogenic variants were TP53, HNF1A, SMARCB1, CDKN2A, PIK3CA, RB1 and MYC. There were 224 median TCR clones (n = 5 pts). In one patient, TCR clones increased from 59 to 1446 after nivolumab. HN NECs may achieve long-lasting survival with multimodality treatment. They harbor moderate-high TMBs and large TCR repertoires, which may explain responses to anti-PD1 agents in two patients and justify the study of immunotherapy in this disease.

Abstract CT086: H3.3-K27M neoantigen vaccine elicits CD4+ and CD8+ T cells immunity and improved prognosis against diffuse intrinsic pontine glioma

Abstract Background: Diffuse intrinsic pontine glioma (DIPG) harboring H3.3-K27M mutation is a malignant pediatric brain tumor with a &amp;gt;90% mortality rate within two years of diagnosis. Aiming to improve therapeutic outcomes, we herein describe a neoantigen peptide vaccine against H3.3-K27M which effectively triggers both CD8+ and CD4+ T cell responses. Methods: A neoantigen vaccine was designed to trigger T cell immunity against DIPGs harboring the H3.3-K27M mutation. ENACTING (NCT04749641) was then initiated as an open-label, single center, two-armed phase 1 trial to assess T cell immune responses and vaccine safety. The vaccine was administered intramuscularly with poly-ICLC adjuvant until tumor progression or untolerated toxicity. PBMCs before and after each vaccine treatment were collected for TCR repertoire analysis and immune response assessment. Results: As of November 2022, 10 patients have been treated. No grade 3-4 treatment-related adverse events have been observed, with fever (80%) and injection site pain (60%) being the most common AEs. On a per patient basis, vaccines induce a landscape change of TCR repertoire in patients’ PBMC after 4-6 times of dosing, indicating multiple dosing is required to trigger extensive T cell responses. T cell responses against neoantigens were detected and H3.3-K27M mutation-specific CD4+ and two CD8+ clones were validated. Among 9 efficacy-assessable patients, the one-year overall survival rate was 71.4%. The mPFS has reached 11.7 months and increasing. One patient reached complete response. As this trial remains ongoing, subgroup analysis will be reported in the future. Conclusion: The H3.3-K27M neoantigen vaccine was well tolerated and elicited mutation-specific CD4+ and CD8+ T cell responses in patients. Initial results from this ongoing study suggest that, compared with other current immunotherapies against DIPG, H3.3-K27M peptide vaccination may provide superior patient outcomes, for both life qualities and survival outcomes. Table 1. Clinical efficacy and adverse events Efficacy Complete response (CR) 1 (11.1%) Partial response (PR) 0 (0) Stable disease (SD) 8 (88.9%) Progressive disease (PD) 0 (0) Disease control rate (DCR) 100% 12-month overall survival 71.4% Median progression-free survival (mPFS) 11.7 months (95% CI, 7.0-NR) Median overall survival (mOS) 15.7 months (95% CI, 10.0-NR) Treatment-Related Adverse Events All grades Grade 3 Grade 4 Fever 9 (90.0%) 0 0 Injection site pain 6 (60.0%) 0 0 Bloating 1 (10.0%) 0 0 Abdominal pain 1 (10.0%) 0 0 Vomiting 1 (10.0%) 0 0 Increased blood LDH 1 (10.0%) 0 0 Proteinuria 1 (10.0%) 0 0 Hypocalcemia 1 (10.0%) 0 0 Citation Format: Yang Zhang, Nan Ji, Gang Chen, Haiyang Wu, Yi Wang, Xiao’ou Li, Wei Xu, Ling Peng, Tian Li, Yi Wang, Li-Feng Zhang, Shengjun Sun, Xiaobing Zhao, Si Li, Peter Alexander, Liwei Zhang, Qi-Jing Li. H3.3-K27M neoantigen vaccine elicits CD4+ and CD8+ T cells immunity and improved prognosis against diffuse intrinsic pontine glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT086.

Abstract LB196: NOUS-PEV, a personalized cancer immunotherapy targeting neoantigens, induces long lasting, tumor infiltrating memory T cells

Abstract Personalized vaccines hold great promise to exert meaningful clinical efficacy, with durable tumor control maintained by a vaccine–induced memory response. NOUS–PEV is a personalized viral prime–boost cancer vaccine that expresses 60 patient–specific neoantigens identified by next generation sequencing (NGS) and selected with a proprietary algorithm VENUS (Leoni &amp; D’Alise et al, Vaccines, 9, 2021). Administration is intramuscular, with a priming Great Ape Adenovirus (GAd) vaccination, followed by Modified Vaccinia Ankara (MVA) “boosts”, administered in combination with the PD–1 blocking antibody pembrolizumab in patients with metastatic malignant melanoma and non–small cell lung cancer. Data from the Part 1 dose–confirmation cohort of 3 patients demonstrated the combination of NOUS–PEV and pembrolizumab to be safe and well–tolerated, with early indications of efficacy and immunogenicity (Bechter, et al SITC 2022 Poster number: 706). Now in Part 2 extension–expansion cohorts, we present extended safety, immunogenicity and clinical data at 11 months median follow–up for 6 vaccinated melanoma patients. Tolerability remains good with no grade 3 or 4 vaccine related adverse events and activity encouraging, with 4 PRs, 1 SD and only 1 PD as best response. Immune responses were evaluated by ex–vivo interferon–gamma ELISpot on PBMC collected at baseline, post pembrolizumab, and post vaccination. Vaccine immunogenicity was demonstrated in all evaluable patients receiving the prime/boost regimen (n=4), with a mean of T cell response of ~ 650 IFN–γ spot forming cells (SFC) per million of PBMC (range 380–1,250 SFC/106) and with observed induction of both CD4 and CD8 T cell responses which lasted for at least 6 months. By analyzing the intratumoral TCR repertoire, we found increase of T cells by ~3 fold on average post treatment with NOUS–PEV in all evaluable patients (n=3), with expansion and diversification of intratumoral T cell clones. Vaccine–induced TCR clonotypes were found in on–treatment tumor biopsies of 2 vaccinated patients, providing the proof–of–concept for neoantigen induced T cells homing and infiltrating into the tumor. Overall, these data show that NOUS–PEV continues to be safe, and elicits a robust long lasting immune response and clinical activity. Citation Format: Oliver Bechter, Anna Morena D'Alise, Guido Leoni, Gabriella Cotugno, Loredana Siani, Rosa Vitale, Valentino Ruzza, Irene Garzia, Laura Antonucci, Elisa Micarelli, Sven Gogov, Alessia Capone, Juan Martin-Liberal, Emiliano Calvo, Victor Moreno, Stefan Symeonides, Elisa Scarselli. NOUS-PEV, a personalized cancer immunotherapy targeting neoantigens, induces long lasting, tumor infiltrating memory T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB196.

Abstract 6667: Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors

Abstract Introduction: Clinical benefit from Immune Checkpoint Blockade (ICB) is a function of local T-cell specificity for tumor-associated antigens. However, overcoming local T-cell dysfunction necessitates systemic immunity engagement. Therefore, studying the dynamics of both local and peripheral T-cell repertoires in response to ICB is required to identify features of T-cell repertoires associated with pathological response. Methods: We conducted TCRβ-sequencing on tumor-residing T-cells (n=59), Peripheral Blood Mononuclear Cells (PBMCs) (n=306) and cell-free DNA (cfDNA) (n=73) from pre- and multiple on-ICB timepoints collected from patients enrolled in the pan-cancer INvestigator-initiated Phase II Study of Pembrolizumab Immunological Response Evaluation (INSPIRE; NCT02644369) trial. To assess specificity-agnostic shifts in TCR repertoires, we first compared TCR diversity and clonal expansion in longitudinal tumor and PBMC samples. Then, to temporally track the specificity-associated features of local and systemic TCR repertoires, we leveraged a Graph Neural Network (GNN) model that took in unique TCRβ chains as nodes. The connectivity between the nodes was defined by multi-relational edges that represented VJ-gene usage and GLIPHII-identified (Grouping Lymphocyte Interactions by Paratope Hotspots) specificities derived from a compendium of TCR sequences with empirically confirmed specificities. Results: While absolute diversity and clonal expansion values in baseline tumor (n=33) were not associated with response to ICB, changes in these values were informative between pre- and on-ICB tumors. All patients (n=4) with low baseline tumor TCR diversity and lack of clonotypic re-structuring in tumor TCR repertoire on-ICB had either progressive or short-term stable disease. Furthermore, pairwise comparison of pre- and on-ICB tumors for each patient (n=17) revealed that all the patients, irrespective of their pathological response, experienced emergence of new TCR clonotypes (i.e., clonal replacement) in response to ICB, suggesting only a minority of these TCRs might consist of tumor-associated clonotypes. Patients with clinical benefit also had higher degree of GLIPHII-identified clustering at baseline tumor, highlighting the role of both specificity-agnostic and specificity-centric TCR analysis in determining the response to ICB. Analysis of TCR sequences in blood plasma found cfDNA contains a small number of TCR sequences (median 32, range 12-89) enriched for TCRs found in matched tumor tissues, suggesting that cfDNA TCR repertoire may provide an indirect measurement of tumor-residing T-cells. Conclusions: TCR diversity and functional clonal annotation are emerging biomarkers of ICB response and cfDNA TCR repertoire can potentially be exploited for clinical diagnostics and monitoring. Citation Format: Shirin Soleimani, Ben X. Wang, Stephanie Pedersen, Jenna Eagles, Jacob Brick, Marcus O. Butler, Scott V. Bratman, Lillian L. Siu, Pamela S. Ohashi, Trevor J. Pugh. Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors [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 6667.

Abstract 5934: Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer

Abstract Here we tracked T cell dynamics in 15 metastatic colorectal cancer (mCRC) patients who had multiple resections (median: 3, range: 2-7) over a period of &amp;gt;7 years (median: 10 years, range: 7-16 years), using a novel T cell receptor sequencing (TCRseq) method. These samples had been previously characterized for DNA and methylation alterations and gene expression, enabling an integrated analysis to determine potential cellular and molecular drivers and consequences of immune dynamics. This multi-region, multi-timepoint dataset presents a unique opportunity to study the co-evolution of mCRC and the T cell response over time, across metastatic sites and in response to therapy. T cell antigen specificity is defined by the TCR - a highly diverse sequence that enables tracking of specific T cell expansions across time and space. TCRseq quantifies the abundance of T cell clones and maps the dynamics of the TCR repertoire, however little is known about how these are altered in different metastatic sites, and post-chemotherapy. We developed and validated a new FFPE-compatible TCRseq method and sequenced 216 longitudinal samples representing the mCRC cohort described above. We detected a median of 348 unique TCRs per sample (range 69-9700), and revealed high levels of intra-tumor spatial heterogeneity. No significant difference was detected in the number of T cell clones or the TCR clonality between primary tumors (n=40), lung metastases (n=30) and liver metastases (n=50). Furthermore, these were not significantly different between tumor regions (n=139) and surrounding stroma (n=38). We found that compared to chemo-naïve tumors (n=36), those that had been exposed to recent chemotherapy (n=41) had a significant increase in both the number of unique T cell clones and Simpson’s evenness, likely reflecting a broad T cell response to DNA-damaging agents. After more than a year had passed without chemotherapy (n=64) these returned to pre-chemotherapy levels. In most cases the 10 most abundant TCR sequences in the primary tumor represented 15-40% of the total repertoire. We tracked these expanded clones through metastases, identifying ubiquitous clones which persisted across metastatic sites and through therapy. We found other expanded clones which were no longer present in metastases lesions, although some of these were found to expand again in later metastases. Finally, we examined correlations with tumor genomics, finding evidence in some patients that the TCR repertoire tracks closely with tumor clones even through metastasis and chemotherapy. In summary, this project represents the first comprehensive analysis of T cell dynamics through colorectal cancer metastasis, highlighting the changing T cell landscape post-chemotherapy and correlating the TCR repertoire with tumor genomics. Our results could have important clinical implications for mCRC immunotherapy and the design of personalized T cell-based therapy. Citation Format: Ann-Marie Baker, Alison Berner, Tahel Ronel, Nick Trahearn, Barbara Bravi, John Bridgewater, Benny Chain, Trevor A. Graham. Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer. [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 5934.

Abstract 6420: Harnessing immune responses in prostate MMRd tumors treated with immune checkpoint blockade

Abstract There is increasing evidence correlating tumor mutational burden with response to immunotherapy in many different types of cancer. Some tumors show high microsatellite instability (MSI-H) as a consequence of the loss of function of mismatch repair (MMR) genes, which would resolve DNA damage in normal conditions. MSH2 plays a critical role in MMR, and several studies have identified mutations in MSH2 as key drivers of MSI in tumors. In preclinical mouse models, MMR deficiency and high microsatellite instability have been previously shown to translate into higher sensitivity to anti-PD-1 treatment. Despite the advances led by the recent tumor-agnostic approval of checkpoint inhibitors for highly mutated tumors, response rates among MMR-deficient (MMRd) tumors in humans are variable, and the mechanisms behind such heterogeneity are still poorly understood. We successfully knocked out the MSH2 gene in the murine prostate adenocarcinoma TRAMP-C2 cell line by CRISPR gene editing. By sequential passaging, we generated a MSH2-KO subclonal population that presents MSI and MMR deficiency, validated by increased tumor mutational burden (TMB) observed by exome sequencing. In studies where we challenged immunodeficient and immunocompetent mice with MMR-proficient (MMRp) and MMRd tumors, the latter showed increase immunogenicity, which led us to interrogate and better characterize such immune responses in the context of immune checkpoint blockade by anti-PD-1.In our studies, MMRd tumor-infiltrating T cells presented significantly enhanced effector and cytotoxic profiles, which likely led to improved tumor control with or without anti-PD-1. We observed an intriguingly lower frequency of SPAS-1 (a well-known TRAMP-C2 immunodominant epitope) antigen-specific T cells in the tumor-reactive fraction of MMRd infiltrates compared to MMRp, which prompted us to interrogate tumor-infiltrate gene expression, TCR repertoire and the potential expansion of multiple antigen-reactive subsets against MMRd tumors in successful immune responses by single cell RNA sequencing and functional ex vivo studies. We also interrogated TCR repertoire data from patients harboring MMRd tumors to add translatability to our findings in mice.Our results constitute a relevant addition to the understanding of immune responses in MMRd tumors and the potential features that could be exploited to improve response rates in immunotherapeutic strategies targeting such malignancies. Citation Format: Marcel Arias Badia, Zenghua Fan, Yee May Lwin, PeiXi Chen, Aahir Srinath, Lawrence Fong. Harnessing immune responses in prostate MMRd tumors treated with immune checkpoint blockade [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 6420.

Abstract 5180: T cell receptor repertoire analysis revealed tissue tropism of tumor-reactive T-cell clones in cell cycle reporter mice

Abstract Tumor-reactive T cells are composed of clones with various TCRs, and each clone has different in vivo kinetics. By analyzing TCR repertoire of tumor and tumor-draining lymph node (dLN), we have demonstrated that Tumor-reactive CD8+ T cells can be classified into “dLN Major”, “Tumor Major”, and “Double Major” clones, which exhibited high frequency in the dLN, tumor, or both tissues. To investigate whether this classification was related to the tissue tropism in the proliferation of each clone, we here employed tumor-bearing Fucci transgenic mice expressing a fluorescent cell-cycle indicator to identify the proliferation of T-cell clones in each tissue. We purified proliferating- and resting-CD8+ T cells from the tumors and dLN and analyzed their TCR repertoire in an LLC subcutaneous tumor model. All Tumor Major clones were proliferated in the tumor, while nearly 0% for dLN Major, indicated their different proliferative capacity in the tumor. The percentage of proliferating clones in the dLN was 20% for Tumor Major and 15% for dLN Major, indicating that these clones had equivalent proliferative capacity in the dLN. These proliferating dLN major clones overlapped more with the tumor than the non-proliferating dLN major clones, suggesting that proliferating dLN Major clones had higher tumor migration capacity. Furthermore, these proliferating dLN major clones were more proliferative in the tumor. These results suggested that dLN Major responded to antigen presentation in the dLN but not in the tumor, whereas Tumor Major responded to those in the dLN and tumor. In addition, there are two types of dLN major, “clones that are proliferating in dLN” and “clones that are not proliferating in dLN” indicating that the former may contribute to the anti-tumor response. Immune checkpoint inhibitor (ICI) treatment not only reactivates clones in the tumor but also activates tumor-reactive clones in the dLN. In conformity with these previous studies, the percentage of proliferating clones among dLN Major increased to about 50% and 80% in the dLN in mice with anti-PD-L1 and anti-CD4 treatment, respectively. This result suggests ICI treatment enhances anti-tumor responses mainly by promoting the activation and proliferation of dLN Major clones. This study shows new findings that tumor-reactive T cells differ in the tissue tropism of their proliferation of each clone. In the future, a quantitative understanding of the contribution of each class of clones to the anti-tumor response will hopefully lead to the development of new combined immunotherapies that optimize the anti-tumor T-cell response. Citation Format: Mikiya Tsunoda, Hiroyasu Aoki, Munetomo Takahashi, Haruka Shimizu, Haru Ogiwara, Shigeyuki Shichino, Kouji Matsushima, Satoshi Ueha. T cell receptor repertoire analysis revealed tissue tropism of tumor-reactive T-cell clones in cell cycle reporter mice. [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 5180.

Abstract 1126: Disease monitoring with comprehensive genomics provides evidence of mechanism of action and immune evasion in patients receiving an individualized neoantigen cancer vaccine

Abstract Therapeutic vaccines hold promise to broaden the potency of immune checkpoint blockade (ICB) therapy in tumors lacking immune reactivity. A heterologous chimpanzee adenovirus (ChAd68) and self-amplifying mRNA (samRNA)-based individualized neoantigen vaccine regimen in combination with nivolumab 480 mg IV and ipilimumab 30mg SC (NCT03639714) has previously demonstrated safety, durable immunogenicity, and clinical benefit in patients with previously treated metastatic disease. Genomic correlates of response were studied over time in 29 patients (13 MSS-CRC, 13 GEA, 3 NSCLC) to understand novel mechanisms of action. Exome and transcriptome sequencing from archival biopsies was used for neoantigen selection. Monthly circulating tumor DNA (ctDNA) samples were collected for monitoring using a comprehensive tumor-naïve and tumor-informed hybrid-capture based ctDNA assay. Paired pre- and post-vaccine tumor transcriptomes were analyzed for 10 patients with 6 having accompanying DNA T cell receptor Β CDR3 repertoire sequencing (TCRseq) in biopsies and longitudinal PBMCs. Prior to vaccination patient tumors were not enriched for immune infiltration or tumor mutation burden (TMB), median 4.3 mut/Mb (range: 2-17 mut/Mb). Minimal neoantigen and mutation drift was observed with a median of 92.5% of neoantigens (range: 45-100%) and a median of 84% (range: 24-99%) of individual mutations detected in biopsies and ctDNA. Notably, paired pre- and post-vaccine biopsy gene expression analyses show upregulation in gene signatures associated with immune infiltration aligning with evidence of T cell expansion measured by significantly expanding CDR3 clonotypes (p &amp;lt0.01). Longitudinal TCRseq in PBMCs demonstrate vaccine induced TCR repertoire dynamics and expanding and contracting clones observed in tumor biopsies could be monitored throughout treatment. In 4 patients the most drastic TCR repertoire changes were observed at time points measured after a 2nd dose of ChAd68. Lastly, we observe evidence of acquired immune evasion through ctDNA monitoring in two patients each following a year of study treatment. One GEA patient acquired HLA-LOH after remaining stable on treatment and one MSS-CRC with a molecular response (MR) for &amp;gt7 months acquired novel biallelic loss-of-function mutations in TAP1 following 1 year of study treatment. We demonstrate that our neoantigen-directed immunotherapy regimen drives durable immune pressure on the tumor in patients with advanced disease where CPI alone has provided minimal benefit. Further, the evidence of acquired resistance supports the induction of immune pressure on tumors following individualized neoantigen vaccination. Comprehensive ctDNA longitudinal monitoring enables real-time assessment of clinical response and acquired resistance. Citation Format: Desiree Schenk, Rita Zhou, Olivia Petrillo, Alexis Mantilla, Italo Faria do Valle, Steven Maron, Brian S. Henick, Chih-Yi Liao, Daniel V.T. Catenacci, Sameek Roychowdhury, Benjamin Solomon, Alexander I. Spira, Ankur Dhanik, Andrew R. Fergusson, Karin Jooss, Matthew Davis. Disease monitoring with comprehensive genomics provides evidence of mechanism of action and immune evasion in patients receiving an individualized neoantigen cancer vaccine [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 1126.

Abstract 2282: Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments

Abstract Background: Immune checkpoint blockade therapeutics have revolutionized cancer therapy. However, most patients are either unresponsive or develop acquired resistance. Understanding patient-specific temporal T cell repertoires in the context of immune interventions will contribute to a better understanding of potential improvement strategies for better T cell anti-tumor immunity. Current methods to understand the T cell repertoire changes over time are limited due to the limited amount of material and prohibitive cost. In this study, we designed and performed longitudinal TCR sequencing in mice treated with multiple therapies. Methods: C57BL/6 mice were used in each treatment group, with blood drawn overtime before, during and after treatment. Mice were treated with a combination of immunotherapeutic agents and OVA peptide immunization, 100µl blood was drawn at multiple pre-, on- and post-treatment time points followed subsequently by TCR sequencing. Cyclophosphamide (CTX) is known to cause lymphodepletion followed by homeostatic proliferation. Thus, we also treated B16-F10 tumor bearing mice with CTX, and performed TCR sequencing on blood draws pre-, on-, and post-treatment to track TCR clone diversity and clonality over time. Results: We find that our method is sensitive enough to detect effects of immunotherapies on TCR diversity in small sample quantities. Using our method, we discovered that certain immunotherapeutic agents, most evidently CD40, have a significant but transient effect on the diversity of the T cell repertoire. We observed an initial increase in repertoire clonality, seven days post CD40 treatment followed by contraction. We show how we can identify antigen specific T cells and follow reacting T cell clones. In addition, we find that CTX treatment is associated with increased clonality in tumor bearing mice particularly in the week following treatment reflecting changes in the TCR repertoire. Conclusion: We have developed a method by which we can follow the TCR repertoire in mice treated with immunotherapy or chemotherapy. This enabled us to isolate and study the effects of different immune modulatory drugs of the endogenous T cell repertoire overtime. Citation Format: Yuval Elhanati, Mariam M. George, Hyejin Choi, Rachana Maniyar, Linda Hamadane, Neeman Mohibullah, Benjamin D. Greenbaum, Taha Merghoub. Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments [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 2282.

Abstract NG14: Dissecting immune microenvironment of T-cell acute lymphoblastic leukemia

Abstract NG14: Dissecting immune microenvironment of T-cell acute lymphoblastic leukemia

Abstract 526: RMC-9805, a first-in-class, mutant-selective, covalent and oral KRASG12D(ON) inhibitor that induces apoptosis and drives tumor regression in preclinical models of KRASG12D cancers

Abstract KRASG12D is the most frequent KRAS mutation in human cancers, with the highest prevalence in pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC) and non-small cell lung cancer (NSCLC). RMC-9805 is a first-in-class, oral, mutant-selective covalent inhibitor of the GTP-bound and active RAS(ON) form of KRASG12D. The formation of a stable, high affinity tri-complex between RMC-9805, KRASG12D and cyclophilin A results in the suppression of signaling downstream of KRASG12D(ON) by disrupting its interactions with downstream effectors such as RAF kinases. RMC-9805 treatment caused selective and persistent modification of KRASG12D leading to deep and durable suppression of RAS pathway activity, inhibition of cell proliferation, and apoptosis induction in KRASG12D human cancer cell lines in vitro and tumor models in vivo. In a mouse clinical trial with KRASG12D xenograft tumor models, RMC-9805 administered orally as a single agent was well tolerated and induced objective responses in 7 of 9 PDAC PDX and CDX models and 6 of 9 NSCLC PDX models, as assessed by mRECIST. In the few models that exhibited sub-optimal responses to RMC-9805 monotherapy, combination treatment with various RAS Companion Inhibitors improved depth and/or duration of anti-tumor response. In contrast to RASMUTANT NSCLC and PDAC, CRC tumors are less dependent on RAS driver mutations. For example, a more heterogeneous response to KRASG12C inhibitors has been reported in CRC than in NSCLC patients, suggesting combinations will be desired to achieve significant clinical benefit in CRC. Likewise, RMC-9805 monotherapy is less active in CRC models at doses that were highly active in KRASG12D NSCLC and PDAC models. However, combinations of RMC-9805 with vertical or parallel pathway RAS Companion Inhibitors such as SHP2, mTORC1 or RASMULTI(ON) inhibitors, achieved objective response rates up to 60% and delayed the onset of resistance in tumor models in vivo. RMC-9805 also synergized with anti-PD1 therapy in KRASG12D tumors in immune-competent animal models by shaping a favorable tumor immune microenvironment through cytokine modulation. In addition, RMC-9805 engaged the adaptive immune system by increasing presentation and recognition of tumor antigens, promoting a diversification of the TCR repertoire, and inducing immunological memory. Overall, RMC-9805 monotherapy elicited tumor regressions in most preclinical PDAC and NSCLC cancer models harboring KRASG12D. Furthermore, RMC-9805 combination therapies drove regressions in CRC models relatively less responsive to monotherapy. Supported by these findings, RMC-9805 is currently in IND-enabling development to permit clinical evaluation of single agent and combination strategies in patients with KRASG12D tumors. Citation Format: Lingyan Jiang, Marie Menard, Caroline Weller, Zhican Wang, Les Burnett, Ida Aronchik, Shelby Steele, Mike Flagella, Ruiping Zhao, James W W. Evans, Shook Chin, Kang-Jye Chou, Yunming Mu, Michael Longhi, Laura McDowell, John E. Knox, Adrian Gill, Jacqueline A. Smith, Mallika Singh, Elsa Quintana, Jingjing Jiang. RMC-9805, a first-in-class, mutant-selective, covalent and oral KRASG12D(ON) inhibitor that induces apoptosis and drives tumor regression in preclinical models of KRASG12D cancers [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 526.

Abstract 6664: Comprehensive immunoprofiling of peripheral blood reveals five conserved immunotypes with implications for immunotherapy in cancer patients

Abstract Recent advances in immunotherapy demonstrate the need to further understand the characteristics of an individual cancer patient’s immune system and how it influences responses to cancer treatment. Here, we developed an immunoprofiling platform to evaluate the features in the blood of cancer patients to test the hypothesis that peripheral immune cell heterogeneity could be used to stratify these patients into different categories or immunotypes to monitor disease progression and treatment response. To that end, we established a unique diagnostic immunoprofiling assay and analytical framework based on the analysis of leukocytes in the peripheral blood using multiparameter flow cytometry. Supervised manual gating of flow cytometry data from a cohort of 50 healthy donors identified 415 cell types and immune activation states that were used to train and later independently validate machine learning models to automatically identify immune cell subsets from raw cytometry data. By applying this tool to peripheral blood samples from a mixed cohort of 299 healthy donors and 323 cancer patients, we developed a machine-learning classification model that can differentiate between these two groups with 93% accuracy. This model was further refined using spectral clustering with bootstrapping, revealing 5 clusters, or immunotypes, characterized by specific physiological immune profiles: (1) Myeloid-derived suppressor/NK cell, (2) Terminally-differentiated CD8+ T cells, (3) Mixed CD4+ T helper cells, (4) CD4+ Th1 &amp; CD8+ T cell memory, and (5) Naive T and B lymphocytes. Interestingly, very few healthy donors could be found in clusters 1 and 2 but were assigned most frequently to cluster 5. Matched RNA-seq was used to further validate these profiles using the cellular deconvolution algorithm, Kassandra, and differential gene expression analysis revealed immunotype-specific signatures that are consistent with immune response potential. Patients in the terminally-differentiated CD8+ T cell cluster had a narrower range of HLA-types than the other clusters, and TCR repertoire analysis indicated significantly increased clonality and reduced clonotype diversity. Within this cluster there was a high degree of overlap between TCR sequences in the peripheral blood and the tumor, indicating a relationship between peripheral blood immunotype and tumor infiltration. Altogether, the establishment of these immunotypes using peripheral blood immunoprofiling represents a promising signature that can be used to identify and stratify cancer patients that will benefit from immune-based therapies. Citation Format: Daniiar Dyikanov, Iris Wang, Tatiana Vasileva, Polina Shpudeiko, Polina Turova, Arseniy A. Sokolov, Olga Golubeva, Evgenii Tikhonov, Anna Kamysheva, Ilya Krauz, Mary Abdou, Madison Chasse, Tori Conroy, Nicholas R. Merriam, Boris Shpak, Anastasia Radko, Anastasiia Kilina, Lira Nigmatullina, Linda Balabanian, Christopher J. Davitt, Alexander A. Ryabykh, Olga Kudryashova, Cagdas Tazearslan, Ravshan Ataullakhanov, Alexander Bagaev, Aleksandr Zaitsev, Nathan Fowler, Michael F. Goldberg. Comprehensive immunoprofiling of peripheral blood reveals five conserved immunotypes with implications for immunotherapy in cancer patients [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 6664.

Abstract 2257: Activation and clonotypic expansion of the native T cell repertoire identifies durable response to CD19 CAR T cell therapy

Abstract Background: Axicabtagene ciloleucel (Axi-cel), a CD19 directed CAR T cell therapy, results in durable response in a subset of patients with relapsed/refractory large B cell lymphoma (LBCL) in the absence of persistent circulating CAR T cells. Aim: We postulated that long-term efficacy of CAR T therapy depends on the downstream triggering of native T cell immunity. We performed single-cell transcriptomics of longitudinal peripheral blood (PB) samples and RNAseq of tumor samples from patients of the ZUMA 1 Axi-cel study. Methods: Single cell immunoprofiling (5’ expression + V(D)J, 10x Genomics) was performed on PB mononuclear cell samples from ZUMA-1 patients (N=32), collected at leukapheresis, 4 weeks, 6 and 12 months post Axi-cel infusion. RNAseq was performed on FFPE lymphoma samples (N=17). Patients were divided into 3 groups: non-responders, relapsed within 1 year from CAR T infusion, and long-term responders. A total of 405,775 cells passed quality check, capturing 73 cellular populations. Results: Long-term responders presented a distinct T cell landscape with increased CD8 T cells and CD8/CD4 ratios prior to CAR T therapy, compared to the other groups, with similar trends observed across time points. They also presented an increased abundance of 3 distinct CD8 T cell populations: (a) cells expressing cytotoxic and NK cell markers, (b) CD8 T effector memory cells characterized by CXCR4, TGFB1, and BCL3, and (c) proinflammatory CD8 T cells. In contrast, patients with early relapse showed increased levels of regulatory T cells pre-/post-CAR T infusion and lower abundance of CD4 cytotoxic T cells.Comparisons of the TCR repertoire pre-/post-CAR T demonstrated a greater clonal expansion of cytotoxic CD4 and CD8 T cell populations in the long-term responders, with high similarity of expanded clones post CAR T. Shared PB T cell clones and tumor antigen sequences derived from the RNAseq samples suggest an antigen-specific response driven by common epitopes. In contrast to the lack of expansion of T reg clones in responders, relapsed patients demonstrated high T reg-clonal expansion 6 months post treatment.Monocyte and NK cells were less prevalent in responders before treatment, driven by differences in phagocytic monocyte and inhibitory NK cell abundance. Modeling the interaction between monocyte and effector cell populations based on ligand receptor expression was suggestive of negative immunoregulatory impact on the T cell populations. Conclusion: The application of single-cell immunoprofiling on longitudinal samples from ZUMA-1 patients demonstrated distinct cellular and clonal profiles among long-term responders. These findings confirm our hypothesis of an important role for the native immune cell repertoire in response to CAR T therapeutics and can be utilized to further our understanding but also to potentially inform patient stratification, management, and treatment. Citation Format: Dimitra Karagkouni, Giulia Cheloni, Yered Pita-Juarez, Daniela Torres, Eleni Kanata, Zachary Avigan, Jessica Liegel, Dina Stroopinsky, Brodie Miles, Gayatri Tiwari, Jenny Kim, Mike Mattie, Jacalyn Rosenblatt, David Avigan, Ioannis Vlachos. Activation and clonotypic expansion of the native T cell repertoire identifies durable response to CD19 CAR T cell therapy [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 2257.

Deep characterization of human γδ T cell subsets defines shared and lineage-specific traits.

Under non-pathological conditions, human γδ T cells represent a small fraction of CD3+ T cells in peripheral blood (1-10%). They constitute a unique subset of T lymphocytes that recognize stress ligands or non-peptide antigens through MHC-independent presentation. Major human γδ T cell subsets, Vδ1 and Vδ2, expand in response to microbial infection or malignancy, but possess distinct tissue localization, antigen recognition, and effector responses. We hypothesized that differences at the gene, phenotypic, and functional level would provide evidence that γδ T cell subpopulations belong to distinct lineages. Comparisons between each subset and the identification of the molecular determinants that underpin their differences has been hampered by experimental challenges in obtaining sufficient numbers of purified cells. By utilizing a stringent FACS-based isolation method, we compared highly purified human Vδ1 and Vδ2 cells in terms of phenotype, gene expression profile, and functional responses. We found distinct genetic and phenotypic signatures that define functional differences in γδ T cell populations. Differences in TCR components, repertoire, and responses to calcium-dependent pathways suggest that Vδ1 and Vδ2 T cells are different lineages. These findings will facilitate further investigation into the ligand specificity and unique role of Vδ1 and Vδ2 cells in early immune responses.

Tumor-targeted superantigens produce curative tumor immunity with induction of memory and demonstrated antigen spreading

BackgroundDespite remarkable progress, the immunotherapies currently used in the clinic, such as immune checkpoint blockade (ICB) therapy, still have limited efficacy against many types of solid tumors. One major barrier to effective treatment is the lack of a durable long-term response. Tumor-targeted superantigen (TTS) therapy may overcome this barrier to enhance therapeutic efficacy. TTS proteins, such as the clinical-stage molecule naptumomab estafenatox (NAP), increase tumor recognition and killing by both coating tumor cells with bacterial-derived superantigens (SAgs) and selectively expanding T-cell lineages that can recognize them. The present study investigated the efficacy and mechanism of action of repeated TTS (C215Fab-SEA) treatments leading to a long-term antitumor immune response as monotherapy or in combination with PD-1/PD-L1 inhibitors in murine tumor models.MethodsWe used syngeneic murine tumor models expressing the human EpCAM target (C215 antigen) to assess the efficacy and mechanism of action of repeated treatment with TTS C215Fab-SEA alone or with anti-PD-1/PD-L1 monoclonal antibodies. Tumor draining lymph nodes (TDLNs) and tumor tissues were processed and analyzed by immunophenotyping and immunohistochemistry. Isolated RNA from tumors was used to analyze gene expression and the TCR repertoire. Tumor rechallenge and T-cell transfer studies were conducted to test the long-term antitumor memory response.ResultsTTS therapy inhibited tumor growth and achieved complete tumor rejection, leading to a T-cell-dependent long-term memory response against the tumor. The antitumor effect was derived from inflammatory responses converting the immunosuppressive TME into a proinflammatory state with an increase in T-cell infiltration, activation and high T-cell diversity. The combination of TTS with ICB therapy was significantly more effective than the monotherapies and resulted in higher tumor-free rates.ConclusionsThese new results indicate that TTSs not only can turn a “cold” tumor into a “hot” tumor but also can enable epitope spreading and memory response, which makes TTSs ideal candidates for combination with ICB agents and other anticancer agents.

Human thymic putative CD8aa precursors exhibit a biased TCR repertoire in single cell AIRR-seq

Human thymic putative CD8aa precursors exhibit a biased TCR repertoire in single cell AIRR-seq

Single-cell profiling identifies a novel human polyclonal unconventional T cell lineage.

In the human thymus, a CD10+ PD-1+ TCRαβ+ differentiation pathway diverges from the conventional single positive T cell lineages at the early double-positive stage. Here, we identify the progeny of this unconventional lineage in antigen-inexperienced blood. These unconventional T cells (UTCs) in thymus and blood share a transcriptomic profile, characterized by hallmark transcription factors (i.e., ZNF683 and IKZF2), and a polyclonal TCR repertoire with autoreactive features, exhibiting a bias toward early TCRα chain rearrangements. Single-cell RNA sequencing confirms a common developmental trajectory between the thymic and blood UTCs and clearly delineates this unconventional lineage in blood. Besides MME+ recent thymic emigrants, effector-like clusters are identified in this heterogeneous lineage. Expression of Helios and KIR and a decreased CD8β expression are characteristics of this lineage. This UTC lineage could be identified in adult blood and intestinal tissues. In summary, our data provide a comprehensive characterization of the polyclonal unconventional lineage in antigen-inexperienced blood and identify the adult progeny.

Associations of T-Cell Receptor Repertoire Diversity with L-Asparaginase Allergy in Childhood Acute Lymphoblastic Leukemia

Asparaginase is a critical component of therapy for childhood acute lymphoblastic leukemia (ALL), but it is commonly associated with allergy, which results in morbidity and poorer outcomes. The underlying basis of this allergy is undoubtedly immune-mediated, but the exact components of T-cell immunity have yet to be characterized. We performed longitudinal TCR sequencing of 180 bone marrow samples from 67 children with B-ALL treated as part of the Ma-Spore-ALL-2010 trial, and we evaluated the associations of TCR profile with asparaginase hypersensitivity, with functional validation of asparaginase activity in a separate cohort of 113 children. We found that a more diverse and dynamically changing TCR repertoire was associated with increased risk of clinical hypersensitivity and decreased L-asp activity. Allergic patients had a higher proportion of infrequent clonotypes, as well as a significantly lower degree of shared clonotypes amongst the cohort. Allergic patients also had significantly higher longitudinal variability of clonotypes across timepoints, where a higher dissimilarity between diagnosis and week 5 represented an 8.1-fold increased risk of an allergic event. After an allergy had occurred, there was shaping and convergence of the TCR repertoire towards a common antigen. Understanding the immunological basis of T-cell responses in allergy lays the groundwork for developing predictive biomarkers or strategies to mediate this common toxicity in childhood ALL.

SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity.

The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.

Human T cell generation is restored in CD3δ severe combined immunodeficiency through adenine base editing

CD3δ SCID is a devastating inborn error of immunity caused by mutations in CD3D, encoding the invariant CD3δ chain of the CD3/TCR complex necessary for normal thymopoiesis. We demonstrate an adenine base editing (ABE) strategy to restore CD3δ in autologous hematopoietic stem and progenitor cells (HSPCs). Delivery of mRNA encoding a laboratory-evolved ABE and guide RNA into a CD3δ SCID patient's HSPCs resulted in a 71.2%± 7.85% (n= 3) correction of the pathogenic mutation. Edited HSPCs differentiated in artificial thymic organoids produced mature Tcells exhibiting diverse TCR repertoires and TCR-dependent functions. Edited human HSPCs transplanted into immunodeficient mice showed 88% reversion of the CD3D defect in human CD34+ cells isolated from mouse bone marrow after 16weeks, indicating correction of long-term repopulating HSCs. These findings demonstrate the preclinical efficacy of ABE in HSPCs for the treatment of CD3δ SCID, providing a foundation for the development of a one-time treatment for CD3δ SCID patients.