Cell Clonotypes Research Articles

Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8+ T cells in persons with previous COVID-19.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.

Abstract A047: Tumor specific γδ T cells expand and respond to PD-1 blockade

Abstract With the breakthrough of checkpoint blockade, immunotherapies targeting PD-1/PD-L1 have had remarkable success in the clinic and are now widely used to treat a variety of malignancies. While the majority of research on T cell exhaustion and PD-1 blockade has been focused on conventional αβ T cells, the contribution of innate-like T cells such as γδ T cells to PD-1 blockade is not clear. γδ T cells are generally not restricted to conventional MHC-peptide molecules and can recognize a diverse range of ligands including phosphoantigens presented on butyrophilins and MHC class I-like family members MR1, and CD1 isoforms. Using flow cytometry, we evaluated the γδ T cell responses in tumor biopsies and peripheral blood from six MCC patients treated with pembrolizumab. Furthermore, bulk and single cell γδ TCR sequencing was used to measure diversity and clonal expansion in the blood upon PD-1 blockade. TCRs were cloned and expressed in Jurkat cells to screen for reactivity against tumor cells lines. Finally, we used CRISPR-Cas9 to knockout known γδ T cell ligands to identify potential tumor antigen recognized by γδ T cells. We identified a MCC patient who experienced a complete response to pembrolizumab treatment and had a ten-fold expansion of γδ T cells in their tumor biopsies. Tumor-infiltrating γδ T cells expressed high levels of inhibitory receptors PD-1 and TIGIT. Furthermore, γδ T cells characterized in peripheral blood were predominantly Vδ1 cells and had increased Ki-67 expression upon pembrolizumab treatment. From TCR sequencing of peripheral blood, we observed the emergence of a dominant γδ T cell clonotype that was also found in the tumor. Upon TCR gene transfer into Jurkat 76 cells, we identified a γδ TCR that was able to recognize multiple Merkel cancer cell lines. CRISPR knockout of B2M in tumor cells still retained γδ TCR reactivity, suggesting that γδ TCR recognition is independent of B2M expression. Together, these results show innate-like T cells such as γδ T cells also have the capacity to respond to checkpoint blockade. As mutations in antigen presentation can be a resistance mechanism to PD-1 blockade, our study provides the rationale to utilize γδ T cells for treating cancer variants that have escaped the immune system and warrants further investigation of the interplay between γδ T cells and checkpoint blockade. Citation Format: Scott C. Lien, Dalam Ly, S.Y. Cindy Yang, Ben X. Wang, Michael St. Paul, Ramy Gadalla, Babak Noamani, Sarah Boross-Harmer, Trevor J. Pugh, Anna Spreafico, Naoto Hirano, Albiruni R.A. Razak, Pamela S. Ohashi. Tumor specific γδ T cells expand and respond to PD-1 blockade [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A047.

Recruitment of naive CD4+ T cells by the recombinant zoster vaccine correlates with persistent immunity.

Herpes zoster (HZ) is a substantial problem for people with decreased cell-mediated immunity, including older adults. The first vaccine approved for HZ prevention, the zoster vaccine live (ZVL), which provided limited and short-lived protection, has been supplanted by the superior recombinant zoster vaccine (RZV), which provides robust and durable protection. To understand the mechanisms underlying the differential immunologic characteristics of the 2 vaccines, we used T cell receptor β chain sequencing and peptide-MHC class II tetramer staining to analyze recombinant glycoprotein E-specific (gE-specific) CD4+ T cell clonotypes in RZV and ZVL recipients. Compared with ZVL, RZV expanded more gE-specific CD4+ clonotypes, with greater breadth and higher frequency of public clonotypes. RZV recruited a higher proportion of clonotypes from naive than from memory cells, while ZVL recruited equally from memory and naive compartments. Compared with memory-derived, naive-derived clonotypes were more likely to last 5 or more years after immunization. Moreover, the frequency of tetramer+ persistent clones correlated with the frequency of tetramer+ naive CD4+ prevaccination T cells. We conclude that the ability of RZV to recruit naive CD4+ T cells into the response may contribute to the durability of its effect. The abundance, breadth, and frequency of public clonotypes may further add to its protective effect.

Post-Transplant T Cell Clonotype Diversity Is Associated with Survival in Patients with TP53-Mutated Acute Myeloid Leukemia

Background TP53 mutations are associated with unfavorable outcomes in various cancer types and present an obstacle to achieving sustained remission in acute myeloid leukemia (AML). Even with allogeneic hematopoietic stem cell transplantation (HSCT), the risk of relapse approximates 80%, with dismal long-term survival. This could imply methods of immune escape in TP53 mutated leukemias that allow them to evade the graft-versus-leukemia (GVL) effect, which is a critical mechanism of disease control with HSCT. This study investigates the dynamics of immune reconstitution at single-cell resolution in TP53-mutated AML at pre- and multiple post-HSCT timepoints in patients who either remain in long-term remission or relapse following HSCT. Methods We collected 26 longitudinal bone marrow aspirates and 1 peripheral blood sample from 12 patients with TP53-mutated AML who underwent HSCT at the Dana-Farber Cancer Institute between 2015-21. All patients received HLA-matched T-cell replete HSCT in morphologic remission, with standard tacrolimus/methotrexate-based prophylaxis and peripheral blood stem cells. We categorized the patients into two cohorts based on their treatment response: long-term remission (>3.5 years, cohort 1, n=4) or relapse (cohort 2, n=8). We performed paired 5' single-cell RNA and T cell receptor (TCR) sequencing on sorted viable mononuclear from each sample and CD3+ T cells from selected samples using 10x Genomics procedures. In total, we analyzed 44 samples (27 mononuclear, 17 CD3+), resulting in 250,640 high-quality single-cell transcriptomes, including 137,649 T cells and NK cells. Data analysis was performed using Cell Ranger Multi (10x Genomics) and R 4.3 with the tidyverse 2.0, Seurat 5.1, and scRepertoire 1.1 packages. Results We focused our initial analysis on the 2-6-month post-HSCT period that is critical for immune reconstitution. This included eight samples from seven patients in the two cohorts (1: remission, 2: relapse, pink box in Figure 1). Of these 7 patients, 4 were in the relapse cohort, with these relapses occurring >4 months post-HSCT. No significant difference in T-cell chimerism was seen between these 7 patients in this 2-6 month period. Based on canonical gene expression signatures, we annotated cell types and selected T cells for further evaluation (Figure 2). First, we found that the CD4/CD8 ratio differed between the cohorts, indicating a relative CD8+ T cell expansion in the relapse cohort (cohort 1: 1.69, cohort 2: 0.55, P<0.0001). Second, we found lower TCR diversity in the relapse cohort (inverse Simpson index, cohort 1: 234.6, cohort 2: 83.0, P<0.0001). This difference remained significant when subsampling the same number of T cells per patient and when restricting all samples to the 3 to 4-month timepoint. Considering the disparity in CD8 T cell numbers between the cohorts, we also analyzed repertoire diversity, specifically in CD8+ T cells, and found that the observed significance persisted. To further investigate TCR diversity, we overlaid T cell clonotypes (cells that share the same TCR sequence) in a UMAP visualization, which highlighted increased hyperexpanded CD8+ T cells in the relapse cohort (Figure 2). Finally, we found that greater clonotype expansion was correlated with the expression of key T cell genes, including CD8A, CD8B, PRF1, NKG7, and GZMA. These results suggest that cytotoxic CD8+ T cells link lower TCR diversity to the likelihood of disease relapse. Conclusions By performing deep analysis of single-cell gene expression linked to TCR clonotypes, we discover new insights into the biology of hematopoietic reconstitution after HSCT of patients with TP53-mutated AML. Despite having analyzed a limited number of samples, we find that patients who remain in long-term remission have significantly higher CD8+ TCR diversity between 2-6 months post-HSCT, while those who relapsed between 5-18 months post-HSCT showed lower TCR diversity and hyperexpanded CD8+ clones at the same timepoints. This work suggests that early post-HSCT TCR diversity could be a biomarker associated with GVL and warrants further study. In ongoing and future analyses, we will mine the current dataset for further insights into the factors influencing survival in TP53-mutated AML patients. We also plan to extend the measurement of TCR diversity as a predictor of survival for validation in a larger cohort.

High-Throughput Identification of Graft-Vs-Leukemia TCRs in AML Patient Samples after Allogeneic Stem Cell Transplantation

For patients with intermediate and high-risk AML/MDS, allogeneic stem cell transplantation (aSCT) is a potentially curative therapy. Efficacy is driven by the graft-versus-leukemia (GvL) response, in which donor-derived T cells recognize peptide:MHC antigens presented by leukemia cells, and subsequently kill them. The antigens that drive GvL responses are attractive therapeutic targets for engineered cell therapies and/or biologics. However, only a small number of GvL antigens have been identified, limiting the therapeutic potential of targeted immunotherapies. Deep interrogation of the T cell repertoires of patients who have responded favorably to aSCT presents an opportunity to identify bona fide GvL antigens, but high-throughput methods need to be developed to do this effectively. A popular method to identify antigen-specific T cells is fluorescent peptide:MHC tetramer staining, whereby T cells whose T cell receptors (TCR) bind a particular peptide:MHC antigen become fluorescent and identifiable by flow cytometry. However, a major challenge to identifying GvL T cells using tetramers is that the prediction of immunogenic antigens - that is, those that induce a T cell response in vivo - is poor; studies of solid tumors suggest that only ~1% of predicted MHC-binding neoantigens are immunogenic in patients. In AML/MDS aSCT patients, there are thousands of peptides that are predicted to bind MHCI and represent potential GvL antigens, but due to practical limitations of patient blood and bone marrow sample quantities, only a small subset can be screened by flow cytometry. Other higher throughput methods using heavy-metal tagged peptide:MHC tetramers followed by mass cytometry, or DNA-barcoded tetramers followed by bulk sequencing have been employed to increase antigen screening scale, but these methods are limited in sensitivity and destroy the T cell without providing TCR sequences. To overcome these limitations and rapidly identify GvL T cells in patient samples, we developed a single cell sequencing based method that enables the screening of thousands of peptide:MHC antigens simultaneously, using a single patient sample. We generated peptide: MHCI monomers using UV-mediated peptide exchange and generated large panels of combinatorial DNA-barcoded peptide:MHCI tetramers at microscale. We integrated our methodology into the 10X Genomics Single Cell Immune Profiling workflow to enable simultaneous recovery of TCR antigen-specificity, paired TCR alpha beta sequences, and single cell RNA-Seq data. These methods were used to screen post-transplant AML patient blood and bone marrow, and we identified expanded GvL T cell clonotypes that target novel minor histocompatibility antigens, overexpressed “aberrant self” proteins, and other leukemia associated antigens. We generated primary CD8 T cells that retrovirally express these TCRs and demonstrate that they are potent and have the expected antigen specificities. The methods described are highly sensitive, specific, efficient, and scalable, and enable high confidence identification of antigen specific clonotypes in patient samples. They markedly expand the throughput compared to existing methods, and simultaneously yield paired alpha beta TCR sequences, facilitating a full characterization of the antigen-TCR drivers of GvL. Furthermore, these methods have broad utility beyond SCT, as they are applicable to studying T cell responses to other immune settings, including anti-cancer, autoimmune, and anti-microbial responses.

The Effect of Preemptive Rituximab Treatment in Patients with EBV Viremia after Solid Organ Transplantation on the Development of Post-Transplant Lymphoproliferative Disorder

The association between Epstein-Barr Virus (EBV) reactivation after solid organ transplantation (SOT) and Post-Transplant Lymphoproliferative Disorder (PTLD) is well described. There are currently no guidelines regarding the use of rituximab preemptively in patients with EBV viremia after SOT to reduce the risk of PTLD. We sought to determine whether rituximab in SOT patients with EBV viremia has benefit in preventing PTLD. This retrospective analysis of electronic medical record data identified SOT recipients who experienced EBV viremia post-transplant between January 2010 and February 2023 at Columbia University Irving Medical Center (CUIMC). Data queries were clinically reviewed. Logistic regression analysis was performed to investigate the relationship between predictor variables including rituximab administration, log-transformed EBV peak titer, duration of EBV viremia, and time from SOT to EBV reactivation, with the binary primary outcome of PTLD diagnosis status. The analysis encompassed both univariate and multivariate logistic regression. There were 2,168 patients who met the inclusion criteria of having EBV reactivation after SOT, out of 6,395 total SOT performed at CUIMC during this timeframe. Patient characteristics are described in table 1. The median peak EBV titer was 154 (range: not quantifiable - 5,335,816), the median duration of EBV viremia was 78 days (range: 1 - 6,980), and the median time from SOT to EBV reactivation was 688 days (range: 0-11103). Of the 2,168 patients, 185/2168 (8.5%) received rituximab for indications other than PTLD including EBV viremia, treatment of rejection, antibody desensitization therapy/immunosuppression peri-transplant, and other non-transplant related indications (e.g. lupus nephritis). Of the patients who received rituximab, 182/185 (98.4%) did not develop PTLD. The 3/185 (1.6%) patients who did develop PTLD were all ≤ 20 years-old at time of diagnosis, and had EBER(+), monomorphic PTLD, diffuse large B-cell lymphoma type, with a non-germinal center phenotype, involving the gastrointestinal tract. Two were CD20 positive, all 3 had partial weak CD30 positivity, and all 3 had clonal immunoglobulin heavy chain rearrangements. Among the patients who did not receive preemptive rituximab post-SOT, 195/1983 (9.8%) developed PTLD, whereas 1788/1983 (90.2%) did not. Prior rituximab therapy for any indication in patients with EBV viremia post-SOT was associated with lower risk of subsequent PTLD by univariate analysis (0.14% vs 8.39%, OR 0.15, p = 0.0013, 95% CI 0.048-0.48). Receipt of rituximab (OR 0.12, p=0.0002), log-transformed peak EBV titer (OR 1.10, p<0.0001), and duration of EBV viremia in months (OR 1.01, p<0.0001) were all independently associated with risk for PTLD by multivariate analysis (figure 1). The relationship between time from SOT to EBV viremia was not significantly associated with development of PTLD. This retrospective analysis suggests that administering preemptive rituximab in SOT patients with EBV viremia may lower the risk of developing PTLD. The fact that peak EBV titer and duration of EBV viremia remain associated with PTLD in multivariate analyses suggests that the benefit of rituximab may be independent of the degree or duration of EBV viremia. A prospective analysis of factors such as area under the curve of EBV exposure, HLA status, T cell clonotype diversity, organ type, and immunosuppression type, is needed to better understand individual risks for improved selection of those who would benefit from preemptive rituximab.

Overall avidity declines in TCR repertoires during latent CMV but not EBV infection.

The avidity of the T-cell receptor (TCR) for antigenic peptides presented by the MHC (pMHC) on cells is an essential parameter for efficient T cell-mediated immunity. Yet, whether the TCR-ligand avidity can drive the clonal evolution of virus antigen-specific CD8 T cells, and how this process is determined in latent Cytomegalovirus (CMV)- against Epstein-Barr virus (EBV)-mediated infection remains largely unknown. To address these issues, we quantified monomeric TCR-pMHC dissociation rates on CMV- and EBV-specific individual TCRαβ clonotypes and polyclonal CD8 T cell populations in healthy donors over a follow-up time of 15-18 years. The parameters involved during the long-term persistence of virus-specific T cell clonotypes were further evaluated by gene expression profiling, phenotype and functional analyses. Within CMV/pp65-specific T cell repertoires, a progressive contraction of clonotypes with high TCR-pMHC avidity and low CD8 binding dependency was observed, leading to an overall avidity decline during long-term antigen exposure. We identified a unique transcriptional signature preferentially expressed by high-avidity CMV/pp65-specific T cell clonotypes, including the inhibitory receptor LILRB1. Interestingly, T cell clonotypes of high-avidity showed higher LILRB1 expression than the low-avidity ones and LILRB1 blockade moderately increased T cell proliferation. Similar findings were made for CD8 T cell repertoires specific for the CMV/IE-1 epitope. There was a gradual in vivo loss of high-avidity T cells with time for both CMV specificities, corresponding to virus-specific CD8 T cells expressing enhanced LILRB1 levels. In sharp contrast, the EBV/BMFL1-specific T cell clonal composition and distribution, once established, displayed an exceptional stability, unrelated to TCR-pMHC binding avidity or LILRB1 expression. These findings reveal an overall long-term avidity decline of CMV- but not EBV-specific T cell clonal repertoires, highlighting the differing role played by TCR-ligand avidity over the course of these two latent herpesvirus infections. Our data further suggest that the inhibitor receptor LILRB1 potentially restricts the clonal expansion of high-avidity CMV-specific T cell clonotypes during latent infection. We propose that the mechanisms regulating the long-term outcome of CMV- and EBV-specific memory CD8 T cell clonotypes in humans are distinct.

Composition and Dynamic Evolution of the Bone Marrow Microenvironment in AL Amyloidosis during Daratumumab Based Therapy

Background: Immunoglobulin light chain (AL) amyloidosis is caused by clonal B or plasma cells proliferating in the bone marrow that produce immunoglobulin (MIg) proteins that misfold and aggregate in tissue(s), leading to multi-organ failure. The monoclonal antibody targeting CD38, daratumumab is an approved and very efficient treatment in multiple myeloma and AL Amyloidosis by inducing plasma cell death through immune mediated mechanisms including complement and antibody-dependent cytotoxicity, direct apoptosis and T cell subsets modifications. While the role of the bone marrow microenvironment (BME) as a major oncogenic actor in multiple myeloma (MM) is well established, the BME composition and role in AL Amyloidosis is largely undefined. Here, we used single-cell RNA-seq combined with CITE-seq and TCR sequencing to characterize the immune ecosystem and microenvironment in AL amyloidosis in comparison to healthy donors, as well as in comparison to other plasma cell disorders including monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM) and multiple myeloma (MM). Methods: BM aspirates from 6 AL amyloidosis patients were collected at diagnosis or before treatment with daratumumab based therapy and 12 months post-treatment, alongside samples from 13 healthy donors, 5 MGUS, 9 SMM and 8 MM patients at diagnosis. We performed unbiased mRNA profiling (5' sequencing) and feature barcoding for cell surface proteins (CITE-seq) of bone marrow mononuclear cells using 10x Genomics. We processed data via the Cell Ranger pipeline, which grouped T cells into clonotypes based on shared TCR α/β sequences. Further data processing was done with Seurat, scRepertoire and Immunarch. Overall, 83703 cells were sequenced from 45 samples, including 3065 plasma cells and 80639 BME cells. Results: Compared to other plasma cell disorders (PCD) at diagnosis, AL BME had more cellular diversity and its plasma cells were more similar to normal plasma cells. They also had more TCR diversity than other PCD samples. When compared to healthy samples, AL BME had a trend towards more CD8+ T cells (p value = 0.078) at diagnosis, which became more pronounced 12 months post-treatment (p value = 0.012), and a trend towards fewer monocytes (p value = 0.036). When compared to PCD samples, AL BME tended to have more hematopoietic stem cells (p value = 0.018 vs MGUS, 0.052 vs SMM and 0.02 vs MM) and fewer NK cells (p values respectively 0.03, 0.059, 0.05) and CD4+ T cells (p values respectively 0.05, 0.018, 0.02) (Figure 1). The number of memory T cells and exhausted T cells were similar. Importantly, AL samples were significantly enriched in early/young CD4 memory T cells (p value < 2.6e-16) and NK/T like CD8+ T cells (p value = 7.99e-11) suggesting an ongoing and active T cell mediated immune response. We next analyzed serial samples from 4 AL patients at diagnosis and ~12 months after Daratumumab-based therapy, with half the patients achieving complete hematologic and organ responses (CR) and half with incomplete responses. We found broad changes in the BME, but in particular, there were more CD4+ and CD8+ T cells at 12 months expressing cytokine signaling genes (p value 1.19e-35) and adaptive immune system pathway genes (p value = 2.59e-33). Importantly, the distributions of CD8+ cells and T cell clonotypes were different between patients achieving CR and those who did not, underlying the role of the immune microenvironment and especially CD8+ T cells in the pathogenesis of the disease and response to Daratumumab based treatment. Conclusion: We identified unique characteristics of the BME in AL amyloidosis and dynamic changes within the T cell compartment following Daratumumab based therapy. Further validations are needed to evaluate the potential of BME profiling to diagnose the disease, predict treatment response and potentially develop new therapeutic strategies in AL Amyloidosis.

SARS-CoV-2 specific immune responses in overweight and obese COVID-19 patients.

Obesity is a known risk factor for severe respiratory tract infections. In this prospective study, we assessed the impact of being obese or overweight on longitudinal SARS-CoV-2 humoral and cellular responses up to 18 months after infection. 274 patients provided blood samples at regular time intervals up to 18 months including obese (BMI ≥30, n=32), overweight (BMI 25-29.9, n=103) and normal body weight (BMI 18.5-24.9, n=134) SARS-CoV-2 patients. We determined SARS-CoV-2 spike-specific IgG, IgA, IgM levels by ELISA and neutralising antibody titres by neutralisation assay. RBD- and spike-specific memory B cells were investigated by ELISpot, spike- and non-spike-specific IFN-γ, IL-2 and IFN-γ/IL-2 secreting T cells by FluoroSpot and T cell receptor (TCR) sequencing was performed. Higher BMI correlated with increased COVID-19 severity. Humoral and cellular responses were stronger in overweight and obese patients than normal weight patients and associated with higher spike-specific IgG binding titres relative to neutralising antibody titres. Linear regression models demonstrated that BMI, age and COVID-19 severity correlated independently with higher SARS-CoV-2 immune responses. We found an increased proportion of unique SARS-CoV-2 specific T cell clonotypes after infection in overweight and obese patients. COVID-19 vaccination boosted humoral and cellular responses irrespective of BMI, although stronger immune boosting was observed in normal weight patients. Overall, our results highlight more severe disease and an over-reactivity of the immune system in overweight and obese patients after SARS-CoV-2 infection, underscoring the importance of recognizing overweight/obese individuals as a risk group for prioritisation for COVID-19 vaccination.

The Impact of Treatment-Free Intervals on T-Cell Exhaustion and Clonotypic Diversity in Myeloma Patients Treated with BCMA Bispecific Antibodies

Background: BCMAxCD3 bispecific antibodies (BsAb) have changed the treatment landscape in relapsed refractory multiple myeloma (RRMM). However, despite high response rates, the majority of patients continue to relapse. Infectious complications, mainly viral, represent another challenge with BsAb, seen in up to 90% of patients with half of them requiring hospitalization. Both issues, loss of response as well as infectious complications, can be linked to impaired T-cell function potentially emerging during BsAb therapy. Most BsAbs have been developed as weekly treatments and one hypothesis is that dose dense treatment could overstimulate T cells finally leading to exhaustion and dysfunctionality. Thus, we compared T cell profiles and their functionality from patients with weekly dosing to patients who switched to a monthly schedule due to toxicity or patient request. Methods: We longitudinally biobanked peripheral blood samples of 19 patients of whom 7 switched from a weekly (q1w) to a monthly (q4w) BsAb treatment schedule. Peripheral blood mononuclear cells (PBMCs) were analysed using 16-color flow cytometry, including T-cell subset phenotyping and the exhaustion marker PD1, TIM3, SLAMF6 and KLRG1. Furthermore, CITEseq, scTCRseq, and Seahorse metabolic studies were performed on selected patients. Results: The enrolled patients were heavily pretreated with a median number of 6 prior therapy lines. All patients responded to BCMA BsAb with VGPR or better and were on treatment for >3 month. Only one patient from the q4w cohort relapsed during the study period. High-risk cytogenetics, lines of previous therapy, and penta-refractory disease status were equally distributed between patients on weekly and monthly schedule. Infectious complications occurred in 10/19 (q1w) (52.6%) and 1/7 patients (q4w) (14.2%). First, we addressed the question if a monthly treatment schedule confers less T-cell exhaustion by comparing PD-1 checkpoint expression and T-cell subsets between q1w and q4w administration. Indeed, flow cytometry showed a significant decrease in the CD4+PD1+ (36.9 vs. 21.1% p<0.05, unpaired t-test) and in the CD8+PD1+ (29.44 vs. 16.54% p<0.05) T cells. We also observed a decrease in the frequency of the effector memory subsets (CD45RA-, CD62L-, TEM) of CD4+ (66.19 vs. 49.63% p<0.05) and CD8+ (53.7 vs. 40.32% p=0.09), further supporting a concept in which a treatment free interval leads to recovery of the T-cell system. We also had access to paired samples of five patients who switched from q1w (1 st sample) to q4w dosing (2 nd sample). Here, flow cytometry showed a decrease of exhausted CD4+PD1+ T cells (33.68 vs. 21.76% p=0.046, paired t-test) and CD8+PD1+ T cells (29.2% vs. 15.1% p=0.117), confirming our cross-sectional analysis. Likewise, expression of SLAMF6, a regulator of T cell exhaustion, also decreased from weekly to monthly schedule (SLAMF6/CD4+:20.7 vs. 15.2% p=0.06; and CD8+:17.8 vs. 11.3% p=0.1), but differences were not statistically significant probably due to sample size. Our analysis on T-cell metabolism did not reveal significant differences between weekly and monthly dosing schedules. After strict quality control, three of the paired samples were further analysed using CITE-seq and scTCRseq. In line with our flow results, patients showed a significant decrease in CD8+ pre-exhausted T-cell subset (CD8+TCF-1+CD27+) (3.55 vs. 1.54% p=0.02) and CD8+ terminal differentiated effector memory T-cells (CD8+ TEMRA) (4.66 vs. 3.57% p=0.04) from weekly to monthly schedules, again suggesting recovery of the T-cells after a longer treatment-free interval. We also observed a trend towards decrease in the CD4+ effector memory subset (CD4+TEM, 6.96 vs. 4.89% p=0.07). Interestingly, the number of hyper-expanded T cell clonotypes increased from weekly to monthly dosing in paired samples. This was somewhat unexpected but expansion could be interpreted as reactivation of a few previously exhausted T cells. Conclusions: The optimal dosing schedule of bispecific antibodies has yet to be determined. Our results support a more extended dose schedule to allow T-cell-recovery between BsAb administrations. Whether such a strategy will result in higher antitumor efficacy or reduced susceptibility to infections, has to be evaluated in future studies.

High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope.

A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.

Clinical trial links oncolytic immunoactivation to survival in glioblastoma

Immunotherapy failures can result from the highly suppressive tumour microenvironment that characterizes aggressive forms of cancer such as recurrent glioblastoma (rGBM)1,2. Here we report the results of a first-in-human phase I trial in 41 patients with rGBM who were injected with CAN-3110—an oncolytic herpes virus (oHSV)3. In contrast to other clinical oHSVs, CAN-3110 retains the viral neurovirulence ICP34.5 gene transcribed by a nestin promoter; nestin is overexpressed in GBM and other invasive tumours, but not in the adult brain or healthy differentiated tissue4. These modifications confer CAN-3110 with preferential tumour replication. No dose-limiting toxicities were encountered. Positive HSV1 serology was significantly associated with both improved survival and clearance of CAN-3110 from injected tumours. Survival after treatment, particularly in individuals seropositive for HSV1, was significantly associated with (1) changes in tumour/PBMC T cell counts and clonal diversity, (2) peripheral expansion/contraction of specific T cell clonotypes; and (3) tumour transcriptomic signatures of immune activation. These results provide human validation that intralesional oHSV treatment enhances anticancer immune responses even in immunosuppressive tumour microenvironments, particularly in individuals with cognate serology to the injected virus. This provides a biological rationale for use of this oncolytic modality in cancers that are otherwise unresponsive to immunotherapy (ClinicalTrials.gov: NCT03152318).

IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients

Sensitization to human leukocyte antigens (HLA) is a persistent problem in heart transplant (HT) candidates. We sought to characterize the anti-HLA antibody and circulating B cell repertoire in a cohort of highly sensitized HT candidates. We assessed immunoglobulin G (IgG) and immunoglobulin M (IgM) anti-HLA antibodies using Luminex single antigen bead assays in a cohort of 11 highly sensitized (HS; calculated panel reactive antibody≥90%) and 3 mildly sensitized (MS) candidates. We also performed B cell receptor repertoire sequencing (BCRseq) in HS candidates and 33 non-candidate controls. HLA antibody strength was measured by mean fluorescence intensity (MFI). We found that IgM anti-HLA antibodies were present in all HS candidates, but with a lower breadth and strength as compared to IgG. When anti-HLA IgG specificities intersected with IgM, binding strength was higher. In contrast, there were IgM but no intersecting IgG specificities for the MS group. In four candidates in the HS group, IgG anti-HLA antibodies decreased in both breadth and strength after HT, but the decrease in strength was smaller if the IgG possessed a specificity that intersected with pre-transplant IgM. BCRseq revealed larger B cell clonotypes in HS candidates but similar diversity as compared to controls. IgM marks IgG anti-HLA antibodies with higher strength before HT and persistence after HT. The presence of IgM intersecting IgG for an anti-HLA specificity may be a useful approach to determine which donor HLA should be avoided for a sensitized candidate.

PD-1 Blockade Induces Reactivation of Nonproductive T-Cell Responses Characterized by NF-κB Signaling in Patients with Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) trials have evaluated CTLA-4 and/or PD-(L)1 blockade in patients with advanced disease in which bulky tumor burden and limited time to develop antitumor T cells may have contributed to poor clinical efficacy. Here, we evaluated peripheral blood and tumor T cells from patients with PDAC receiving neoadjuvant chemoradiation plus anti-PD-1 (pembrolizumab) versus chemoradiation alone. We analyzed whether PD-1 blockade successfully reactivated T cells in the blood and/or tumor to determine whether lack of clinical benefit could be explained by lack of reactivated T cells versus other factors. We used single-cell transcriptional profiling and TCR clonotype tracking to identify TCR clonotypes from blood that match clonotypes in the tumor. PD-1 blockade increases the flux of TCR clonotypes entering cell cycle and induces an IFNγ signature like that seen in patients with other GI malignancies who respond to PD-1 blockade. However, these reactivated T cells have a robust signature of NF-κB signaling not seen in cases of PD-1 antibody response. Among paired samples between blood and tumor, several of the newly cycling clonotypes matched activated T-cell clonotypes observed in the tumor. Cytotoxic T cells in the blood of patients with PDAC remain sensitive to reinvigoration by PD-1 blockade, and some have tumor-recognizing potential. Although these T cells proliferate and have a signature of IFN exposure, they also upregulate NF-κB signaling, which potentially counteracts the beneficial effects of anti-PD-1 reinvigoration and marks these T cells as non-productive contributors to antitumor immunity. See related commentary by Lander and DeNardo, p. 474.

Abstract PR02: Tumor sequestered, neoantigen specific T cells are dynamically increased in circulation following neoadjuvant immunotherapy

Abstract Improved recurrence free survival is observed following neoadjuvant immune checkpoint blockade (ICB), but the mechanisms underlying this clinical benefit are incompletely understood. To gain insights into changes in the tumor microenvironment (TME) that occur following ICB, we performed paired single-cell transcriptomic and T cell receptor (TCR) RNA sequencing on sorted tumor infiltrating T-lymphocytes before and after neoadjuvant treatment of patients with newly diagnosed oral carcinoma with bintrafusp alfa, a bifunctional PD-L1 mAb and TGF-b neutralizing construct. Analysis of pre- and post-treatment TIL with identical TCRs allowed characterization of changes within individual clonotypes after treatment. The addition of deep TCRb complimentary determining region 3 (CDR3) sequencing of peripheral T cells allowed assessment of dynamic changes in individual T cell clonotypes between the tumor and peripheral blood. Within the TME, multiple clearly defined clusters of CD8+ and CD4+ T cells with distinct transcriptional profiles were observed, including T cells expressing activation, exhaustion, and tissue-resident markers (exhausted) as well as T cells expressing progenitor and memory markers (memory). Multiple TCRs from clonotypes observed to be present in the exhausted and memory compartments were cloned for study of their antigen specificity. Putative neoepitopes were synthesized following in silico prediction of putative mutation derived neoantigens. Several TCRs from the exhausted compartment were specific for mutation-derived neoantigens. Conversely, TCRs from the memory compartment were specific for common viral antigens. With treatment, exhausted tumor-specific T cells transitioned between different exhausted clusters and some transitioned into a proliferating cluster and expanded in number. Expression of genes associated with TCR signaling and glycolysis increased in exhausted clonotypes that expanded with treatment. Expression of GLS, a key gene associated with glutaminolysis, associated with clonotypes that did not expand with treatment. Study of the peripheral blood revealed that CDR3 sequences matching exhausted, tumor specific TCRs from the TME were not detected or detected at very low frequencies prior to treatment. However, detected of CDR3 sequences matching exhausted, tumor specific TCRs from the TME significantly increased after treatment. CDR3 sequences matching memory, viral specific TCRs from the TME were detected at high levels in the peripheral blood prior to treatment, did not significantly change with treatment. Thus, neoadjuvant immunotherapy appears to expand exhausted, tumor specific T cells in the TME and results in increased frequency of these T cells in circulation. These data imply that tumor specific T cells may be largely sequestered into tissues, such as the tumor and possibly draining lymph nodes, in patients with newly diagnosed oral carcinoma and that surgical removal of disease without the use of neoadjuvant immunotherapy may remove a significant proportion of the patient’s anti-tumor T cell immunity. Citation Format: Cem Sievers, Marco Craveiro, Jason Redman, Clint T. Allen. Tumor sequestered, neoantigen specific T cells are dynamically increased in circulation following neoadjuvant immunotherapy [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Innovating through Basic, Clinical, and Translational Research; 2023 Jul 7-8; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2023;29(18_Suppl):Abstract nr PR02.

Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses

Nanoparticles for multivalent display and delivery of vaccine antigens have emerged as a promising avenue for enhancing B cell responses to protein subunit vaccines. Here, we evaluated B cell responses in rhesus macaques immunized with prefusion-stabilized respiratory syncytial virus (RSV) F glycoprotein trimer compared with nanoparticles displaying 10 or 20 copies of the same antigen. We show that multivalent display skews antibody specificities and drives epitope-focusing of responding B cells. Antibody cloning and repertoire sequencing revealed that focusing was driven by the expansion of clonally distinct B cells through recruitment of diverse precursors. We identified two antibody lineages that developed either ultrapotent neutralization or pneumovirus cross-neutralization from precursor B cells with low initial affinity for the RSV-F immunogen. This suggests that increased avidity by multivalent display facilitates the activation and recruitment of these cells. Diversification of the B cell response by multivalent nanoparticle immunogens has broad implications for vaccine design.

P-390 The differentiation and expansion of T cell clonotypes in the bone marrow following ASCT: insights from the Phase 2 CARDAMON study

P-390 The differentiation and expansion of T cell clonotypes in the bone marrow following ASCT: insights from the Phase 2 CARDAMON study

Abstract PR015: Tumor-specific immunity generated by a personalized neoantigen vaccination incorporating locally delivered ipilimumab in renal cell carcinoma

Abstract Personalized cancer vaccines can generate circulating immune responses against predicted neoantigen targets, but whether such responses lead to actual immune recognition of a patient’s tumor and consequent clinical activity is largely unknown. To investigate this, we conducted a phase I clinical trial of a personalized neoantigen vaccine as adjuvant therapy in high-risk, completely surgically resected, stage III/IV clear cell renal cell carcinoma (RCC; NCT02950766). This first-in-disease study included several modifications from prior neoantigen vaccine studies, including: (i) the use of an improved antigen prediction tool (HLAthena), a neural network model that was trained on a large HLA class I immunopeptidome dataset; (ii) the subcutaneous and intradermal administration of the vaccine to engage a broader repertoire of antigen-presenting cells in the skin; and (iii) the inclusion of ipilimumab administered subcutaneously next to the vaccination site (for pre-specified cohorts) intended to improve T cell priming and activation at the local draining lymph node. Across all nine patients, a median of 15 vaccinating peptides (range: 8 – 19) were successfully manufactured and administered per study subject, targeting a median of 13 unique mutations (range: 7 – 17). Six of nine patients were vaccinated against a neoantigen formed through a mutation in at least one known RCC driver gene (VHL, PBRM1, BAP1, KDM5C, or PIK3CA). Single-cell transcriptomic and T cell receptor (TCR) sequencing analysis of vaccine site immune populations in the skin revealed a substantial increase in the number of T cells (p = 0.003) and T cell clonotypes (p < 0.001) following vaccination. No patient had a pre-existing ex vivo peripheral T cell response against any of the neoantigen peptides in the vaccine. Following vaccination, all nine patients developed detectable ex vivo peripheral T cell response (by IFN-gamma ELISPOT) against neoantigen peptides in the vaccine. Nearly all detectable ex vivo responses were derived from CD4+ T cells as assessed by flow cytometry analysis, and a substantial proportion of responses (27.4% - 99.8% of total responses for an individual pool of vaccine peptides) were polyfunctional (with T cells producing at least 2 of the following cytokines: IFN-gamma, IL-2, or TNF-alpha). Among peripheral immune responses, there were no observable differences in the quantity or phenotype of T cells responding to vaccine alone versus the vaccine co-administered with ipilimumab. In seven of nine patients, neoantigen vaccine-specific T cells exhibited in vitro anti-tumor reactivity against autologous RCC cells. Clinically, there were no dose limiting toxicities, and no disease recurrences were observed in this high-risk population (median follow-up of 23.9 months at time of data cutoff). Overall, these data suggest that personalized neoantigen vaccines (with or without co-administered subcutaneous CTLA-4 blockade) can induce anti-tumor immune responses in patients with RCC. Citation Format: David A. Braun, Derin B. Keskin, Sachet A. Shukla, Bradley A. McGregor, Nicholas R. Schindler, Eryn Blass, Susan Klaeger, Lucas Pomerance, Siranush Sarkizova, Shuqiang Li, Jackson Southard, Giorgia Moranzoni, Christina B. Pedersen, Yiwen Liu, Steven L. Chang, Michelle S. Hirsch, Nicole R. LeBoeuf, Matthew Mossanen, Vipheaviny Chea, Isabel Carulli, Oriol Olive, Ambica Mehndiratta, Haley Greenslade, Giacomo Oliveira, J. Bryan Iorgulescu, Sabina Signoretti, Jon C. Aster, Liudmila Elagina, Ignaty Leshchiner, Gad Getz, Maegan Harden, Stacey Gabriel, Lars R. Olsen, Donna S. Neuberg, Edward F. Fritsch, Nir Hacohen, Kenneth J. Livak, Steven Carr, Patrick A. Ott, Catherine J. Wu, Toni K. Choueiri. Tumor-specific immunity generated by a personalized neoantigen vaccination incorporating locally delivered ipilimumab in renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR015.

Abstract B013: T cell clonotype expansion is common in advanced renal cell carcinoma but is not associated with altered response to PD-1 blockade

Abstract The diversity of T cell receptors (TCRs) becomes increasingly restricted with advancing stage in renal cell carcinoma (RCC), with individual T cell clones becoming dramatically expanded. Further, prior studies have suggested that TCR clonality (i.e. less diversity) could be associated with improved clinical response to anti-PD-1 treatment. To further interrogate the TCR landscape of advanced RCC and its relation to both T cell phenotype and clinical outcomes, single-cell TCR sequencing (scTCR-seq) was performed in parallel with single-cell RNA sequencing (scRNA-seq) for eligible patients with clear cell or non-clear cell metastatic RCC both pre- (baseline) or post- (progression) treatment with front-line nivolumab monotherapy as part of the HCRN GU16-260 trial (NCT03117309). Clonotype assignments and diversity metrics for 19 tumor samples were determined using VDJdive (R/Bioconductor). Overall, the top 10 clonotypes accounted for 12.3% of all T cells (range by sample: 4.2-34.6%). Of note, 5 of 16 (31%) samples with at least 100 T cells displayed substantial clonotype expansion, with the top 10 clonotypes accounting for at least 20% of tumor-infiltrating T cells. Average TCR diversity (normalized Shannon entropy) was 0.55 (range: 0.38-0.91) for all 19 samples. There were no significant differences in T cell diversity both between baseline (n=10) and post-treatment (n=9) samples (p= 0.66) or between clear cell (n=14) and non-clear cell (n=5) histologies (p= 0.75). To assess the relationship between T cell specificity and phenotypic state, we investigated the distribution of the most expanded clonotypes along a trajectory of T cells. Previous trajectory analysis of T cell populations revealed a bifurcating structure with naïve T cells at the root and lineages terminating in either terminally exhausted CD8+ T cells or SLAMF7+ CD8+ T cells (Braun, ASCO GU, 2023). Of the top 20 most expanded clonotypes across all T cells, 95% were distributed almost exclusively in the terminally exhausted lineage. The TCR diversity decreased along each lineage, from naïve T cell cluster at the root (TCR diversity = 0.61) to either the terminally exhausted CD8+ T cell cluster (0.42) or the SLAMF7+ CD8+ T cell cluster (0.56). There were no significant differences in TCR diversity between patients with progressive disease (n=6) versus complete/partial response (n= 6), (p= 0.96). Similarly, there was no association between TCR diversity and either progression-free (p= 0.41) or overall (p=0.39) survival. Altogether, these data reaffirm the presence of clonal expansion in advanced RCC, with the degree varying by sample. The localization of most expanded clonotypes to a single T cell lineage suggests a low degree of phenotypic plasticity. Enrichment of these clonotypes along an exhausted lineage is consistent with prior findings of lower TCR diversity in terminally exhausted CD8+ T cells. Future directions will focus on inferring the tumor specificity of infiltrating T cells along the diverging lineages. Citation Format: Miya B. Hugaboom, Neil Ruthen, Opeyemi Jegede, Nicholas R. Schindler, Lena Wirth, Sasha Kyrysyuk, David F. McDermott, Elizabeth R. Plimack, Jeffrey A. Sosman, Naomi B. Haas, Michael E. Hurwitz, Hans J. Hammers, Sabina Signoretti, Michael B. Atkins, Catherine J. Wu, David A. Braun, Kelly Street. T cell clonotype expansion is common in advanced renal cell carcinoma but is not associated with altered response to PD-1 blockade [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B013.

Single-cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality.

Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding of how rejection occurs despite immunosuppression (IS). We performed combined single-cell RNA transcriptomic and TCR-α/β sequencing on rBx from patients with ACR under differing IS drugs: tacrolimus, iscalimab, and belatacept. We found distinct CD8+ T cell phenotypes (e.g., effector, memory, exhausted) depending upon IS type, particularly within expanded CD8+ T cell clonotypes (CD8EXP). Gene expression of CD8EXP identified therapeutic targets that were influenced by IS type. TCR analysis revealed a highly restricted number of CD8EXP, independent of HLA mismatch or IS type. Subcloning of TCR-α/β cDNAs from CD8EXP into Jurkat 76 cells (TCR-/-) conferred alloreactivity by mixed lymphocyte reaction. Analysis of sequential rBx samples revealed persistence of CD8EXP that decreased, but were not eliminated, after successful antirejection therapy. In contrast, CD8EXP were maintained in treatment-refractory rejection. Finally, most rBx-derived CD8EXP were also observed in matching urine samples, providing precedent for using urine-derived CD8EXP as a surrogate for those found in the rejecting allograft. Overall, our data define the clonal CD8+ T cell response to ACR, paving the next steps for improving detection, assessment, and treatment of rejection.