Cell Clonotypes Research Articles

Functional characterization of CD4+ T cell receptors crossreactive for SARS-CoV-2 and endemic coronaviruses.

BACKGROUNDRecent studies have reported T cell immunity to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in unexposed donors, possibly due to crossrecognition by T cells specific for common cold coronaviruses (CCCs). True T cell crossreactivity, defined as the recognition by a single TCR of more than one distinct peptide-MHC ligand, has never been shown in the context of SARS-CoV-2.METHODSWe used the viral functional expansion of specific T cells (ViraFEST) platform to identify T cell responses crossreactive for the spike (S) glycoproteins of SARS-CoV-2 and CCCs at the T cell receptor (TCR) clonotype level in convalescent COVID-19 patients (CCPs) and SARS-CoV-2-unexposed donors. Confirmation of SARS-CoV-2/CCC crossreactivity and assessments of functional avidity were performed using a TCR cloning and transfection system.RESULTSMemory CD4+ T cell clonotypes that crossrecognized the S proteins of SARS-CoV-2 and at least one other CCC were detected in 65% of CCPs and unexposed donors. Several of these TCRs were shared among multiple donors. Crossreactive T cells demonstrated significantly impaired SARS-CoV-2-specific proliferation in vitro relative to monospecific CD4+ T cells, which was consistent with lower functional avidity of their TCRs for SARS-CoV-2 relative to CCC.CONCLUSIONSOur data confirm, for what we believe is the first time, the existence of unique memory CD4+ T cell clonotypes crossrecognizing SARS-CoV-2 and CCCs. The lower avidity of crossreactive TCRs for SARS-CoV-2 may be the result of antigenic imprinting, such that preexisting CCC-specific memory T cells have reduced expansive capacity upon SARS-CoV-2 infection. Further studies are needed to determine how these crossreactive T cell responses affect clinical outcomes in COVID-19 patients.FUNDINGNIH funding (U54CA260492, P30CA006973, P41EB028239, R01AI153349, R01AI145435-A1, R21AI149760, and U19A1088791) was provided by the National Institute of Allergy and Infectious Diseases, the National Cancer Institute, and the National Institute of Biomedical Imaging and Bioengineering. The Bloomberg~Kimmel Institute for Cancer Immunotherapy, The Johns Hopkins University Provost, and The Bill and Melinda Gates Foundation provided funding for this study.

Linking immune receptor sequence to transcriptional states with clonotype neighbor graph analysis (CoNGA)

Abstract Recent advances now allow for deep simultaneous profiling of T cell clonotypes, defined by T cell receptor (TCR) sequence, and phenotype, as reflected in gene expression (GEX) profile, surface protein expression, and epitope binding at the single-cell-level. However, there currently few tools available for unsupervised discovery of relationships between TCR sequence and cell phenotype. We hypothesized that by identifying correlations between “TCR neighborhoods”, defined by shared TCR sequence and GEX features, we could move beyond simply measuring GEX variation within clonal descendants and identify novel associations between T cell specificities and states. Previously, we introduced TCRdist, a measure for assessing inter-TCR similarity capable of identifying closely related clonotypes based on shared sequence features. Using TCRdist to quantify TCR similarity, we developed a graph-theoretic approach—clonotype neighbor-graph analysis or “CoNGA”—that identifies correlations between GEX profile and TCR sequence in an unbiased and automated manner through statistical analysis of GEX and TCR similarity graphs. Applying CoNGA, we uncovered novel associations between TCR and GEX space including a previously undescribed “natural lymphocyte” population of human blood CD8+ T cells; an association between TRBV gene usage and EPHB6 expression; and TCR sequence determinants of differentiation in thymocytes. These examples demonstrate that CoNGA is able to effectively deconvolve complex relationships between TCR sequence and cellular state. Conceptually, CoNGA could be extended to other clonally-related populations (e.g. B cells, tumors), and can easily incorporate other measurable features (e.g. ATAC-Seq).

T-cell receptor repertoire of mice with organ-specific autoimmunity resulting from a partial defect in T cell negative selection and dendritic cell enhancement

Abstract Previously, we reported a new genetic model of spontaneous autoimmune disease in which mice with a hypomorphic mutation of Aire (AireGW/+) combined with deletion of Lyn in dendritic cells develop autoimmune uveitis with a 50% penetrance. Here we demonstrate that a key autoantigen in this model is interphotoreceptor retinoid-binding protein (IRBP) as AireGW/+ Lyn−/− IRBP−/− mice failed to develop uveitis. The expansion of CD4+ T cells recognizing amino acids 271–290 (“P2”) of IRBP correlated strongly with autoimmune disease in mice with intact IRBP. To study the role of these T cells, we did single-cell RNA-seq with TCR sequencing for P2-specific CD4+ T cells isolated from eye-draining lymph nodes (LN) of AireGW/+ Lyn−/− mice with and without uveitis. Both mice showed an expansion of these T cells in eye-draining LNs, but it was greater in mice with disease. A remarkable clonal diversity of TCRs was seen, with some sharing of TCR Vα or Vβ sequences. Expansions of particular T cell clonotypes were more evident in LN of mice with disease, and even greater in the retinas of mice with disease. We reconstituted several P2–specific TCR clonotypes in a T cell hybridoma line and verified their specificity. One of the TCR clonotypes was expressed in developing thymocytes by retroviral transduction of bone marrow stem cells from Rag2−/− mice and transplanted into WT or AireGW/+ recipient mice. Remarkably, the small residual expression of IRBP in the thymus of AireGW/+ mice was sufficient to induce substantial negative selection of thymocytes with this TCR clonotype. Thus, deficiency of negative selection of P2 tetramer–specific TCR promotes the development of uveitis in AireGW/+ Lyn−/− mice, even if negative selection is only partly compromised.

Decreased Treg Cell and TCR Expansion Are Involved in Long-Lasting Graves’ Disease

Graves’ disease (GD) is a T cell-mediated organ-specific autoimmune disorder. GD patients who have taken anti-thyroid drugs (ATDs) for more than 5 years with positive anti-thyroid stimulating hormone receptor autoantibodies value were defined as persistent GD (pGD). To develop novel immunotherapies for pGD, we investigated the role of T cells in the long-lasting phase of GD. Clinical characteristics were compared between the pGD and newly diagnosed GD (nGD) (N = 20 respectively). Flow cytometric analysis was utilized to determine the proportions of Treg and Th17 cells (pGD, N = 12; nGD, N = 14). T cell receptor sequencing (TCR-seq) and RNA sequencing (RNA-seq) were also performed (pGD, N = 13; nGD, N = 20). Flow cytometric analysis identified lower proportions of Th17 and Treg cells in pGD than in nGD (P = 0.0306 and P = 0.0223). TCR-seq analysis revealed a lower diversity (P = 0.0025) in pGD. Specifically, marked clonal expansion, represented by an increased percentage of top V-J recombination, was observed in pGD patients. Interestingly, pGD patients showed more public T cell clonotypes than nGD patients (2,741 versus 966). Meanwhile, RNA-seq analysis revealed upregulation of the inflammation and chemotaxis pathways in pGD. Specifically, the expression of pro-inflammatory and chemotactic genes (IL1B, IL13, IL8, and CCL4) was increased in pGD, whereas Th17 and Treg cells associated genes (RORC, CARD9, STAT5A, and SATB1) decreased in pGD. Additionally, TCR diversity was negatively correlated with the expression of pro-inflammatory or chemotactic genes (FASLG, IL18R1, CCL24, and CCL14). These results indicated that Treg dysregulation and the expansion of pathogenic T cell clones might be involved in the long-lasting phase of GD via upregulating chemotaxis or inflammation response. To improve the treatment of pGD patients, ATDs combined therapies, especially those aimed at improving Treg cell frequencies or targeting specific expanded pathogenic TCR clones, are worth exploring in the future.

PD-1 Blockade Therapy Promotes Novel Infiltration of Tumor-Specific T-Cell Clonotypes

PD-1 blockade exerts clinical efficacy against various types of cancer by reinvigorating T cells that directly attack tumor cells (tumor-specific T cells) in the tumor microenvironment (TME), and tumor-infiltrating lymphocytes (TILs) also comprise nonspecific bystander T cells. Here, we show that TILs include skewed T cell clonotypes, which are characterized by exhaustion (Tex) or nonexhaustion signatures (Tnon-ex), using single-cell sequencing. Among skewed clonotypes, those in the Tex, but not those in the Tnon-ex, cluster responded to autologous tumor cell lines. After PD-1 blockade, new tumor-specific clonotypes in the Tex cluster appeared in the TME. Tumor-draining lymph nodes (TDLNs) without metastasis harbor a considerable number of such clonotypes, whereas these clonotypes are rarely detected in peripheral blood. We propose that tumor-infiltrating skewed T cell clonotypes with an exhausted phenotype directly attack tumor cells and that PD-1 blockade can promote novel infiltration of tumor-specific T-cell clonotypes, mainly from TDLNs.

Melanoma-reactive T cells take up residence.

Shedding light on the mechanisms that underlie a durable response to immunotherapy, a recent study evaluating long-term survivors of melanoma treated with immunotherapy finds that tumor-associated T cell clonotypes are sustained over years and persist as expanded, cytokine IFN-γ–expressing resident memory T cells in the skin, with effector memory counterparts in the blood.

Abstract PS17-21: Characterization of the immune microenvironment in ductal carcinoma in situ of the breast

Abstract Background Ductal carcinoma in situ (DCIS) is considered a low-risk disease of the breast. Current increases in its incidence have resulted in many women either being under- or over-treated due to our limited findings on independent prognostic and predictive biomarkers. The Van Nuys Prognostic Index, based on tumor size, margin status, grade and age, is one tool used in treatment decisions. Patients with a low score show no significant benefit from radiotherapy, in contrast to those with an intermediate score, while patients with high scores should be considered for mastectomy. In contrast, for invasive ductal carcinoma (IDC) of the breast there is a strong consensus for the prognostic and predictive value of tumor infiltrating lymphocytes (TIL). As very little is known about TIL in DCIS, the goal of this study is to fully characterize the immune infiltrate and compare it to IDC, examine differences in the balance between effector and regulatory subpopulations and potentially discover new biomarkers for risk stratification. Material and Methods Fourteen patients were prospectively enrolled at the St. Luc hospital in Brussels, including 4 pure DCIS, 5 mixt DCIS and IDC, and 5 normal breast tissues. Formalin-fixed paraffin-embedded sections were stained with three fluorescent multiplex immunohistochemistry (mIHC) panels that combined antibodies to CD45, CD4, CD8, CD20, FOXP3, CD68, GZMB, PD-1, Ki67 and cytokeratin. InForm® Tissue Finder™ software and PhenoptrReports (Akoya Biosciences®) were employed for TIL quantification and spatial distribution. Freshly resected DCIS tissues were used to isolate tumor-infiltrating CD4 and CD8 T cells for single cell RNAseq analysis to determine the T cell clonotypes present (A. Devaux’s poster) Results Our analyses reveal the DCIS stroma has a significant immune infiltrate dominated by CD4+ helper T cells and B cells (140 and 115 cells/mm2, respectively) followed by CD8+ cytotoxic T cells (72 cells/mm2), regulatory T cells (Treg) (27 cells/mm2) and to a lesser extent macrophages (23 cells/mm2). The immune pattern in DCIS is similar to IDC except there are fewer macrophages in the tumor areas and Treg increase in the stroma. Tumor areas are generally less infiltrated than the stroma but some DCIS cells are in direct contact with T cells and macrophages. Spatial distribution analysis within a radius of 30 μm confirms that Treg are in close proximity to the DCIS cells and in the proximity of CD4+ helper and CD8+ cytotoxic T cells. Moreover, proliferating GZMB+ cells, mainly CD8+ cytotoxic T cells, were observed in direct contact with DCIS cells. Only one patient out of 4 had PD1+ TIL in the stroma. A comparison of pure and mixt DCIS reveals lower stromal infiltration by T and B cells in the former, which is also associated with an increase in macrophages. Finally, the abundance of stromal TIL was frequently organized in tertiary lymphoid structures (TLS), composed by a B cell follicle surrounded by a T cell zone containing both CD4+ helper and CD8+ cytotoxic T cells. TLS were characterized by the presence of proliferating B cells and PD1high T follicular helper cells. FOXP3+ and GZMB+ cells were also observed in the T cell zone. Conclusions Examination of the immune infiltrate in DCIS shows an abundance of helper T cells, B cells and active cytotoxic T cells in association with stromal TLS. These observations reveal an active tumor immune microenvironment in DCIS and suggest that the immune response plays an active role in DCIS pathogenesis. Citation Format: Soizic Garaud, Alix Devaux, Anais Boisson, Céline Naveaux, Pierre Coulie, Ahmad Awada, Karen Willard-Gallo. Characterization of the immune microenvironment in ductal carcinoma in situ of the breast [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-21.

TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes

Ahmed and colleagues recently described a novel hybrid lymphocyte expressing both a B and Tcell receptor, termed double expresser (DE) cells. DE cells in blood of type 1 diabetes (T1D) subjects were present at increased numbers and enriched for a public B cell clonotype. Here, we attempted to reproduce these findings. While we could identify DE cells by flow cytometry, we found no association between DE cell frequency and T1D status. We were unable to identify the reported public B cell clone, or any similar clone, in bulk B cells or sorted DE cells from T1D subjects or controls. We also did not observe increased usage of the public clone VH or DH genes in B cells or in sorted DE cells. Taken together, our findings suggest that DE cells and their alleged public clonotype are not enriched in T1D. This Matters Arising paper is in response to Ahmed etal. (2019), published in Cell. See also the response by Ahmed etal. (2021), published in this issue.

STING agonist-based treatment promotes vascular normalization and tertiary lymphoid structure formation in the therapeutic melanoma microenvironment

BackgroundThe degree of immune infiltration in tumors, especially CD8+ T cells, greatly impacts patient disease course and response to interventional immunotherapy. Enhancement of tumor infiltrating lymphocyte (TIL) is a critical...

Early changes in the circulating T cells are associated with clinical outcomes after PD-L1 blockade by durvalumab in advanced NSCLC patients

Immune checkpoint inhibitors (ICI) are designed to activate exhausted tumor-reactive T cells thereby leading to tumor regression. Durvalumab, an ICI that binds to the programmed death ligand-1 (PD-L1) molecule, is approved as a consolidation therapy for treatment of patients with stage III, unresectable, non-small cell lung cancer (NSCLC). Immunophenotypic analysis of circulating immune cells revealed increases in circulating proliferating CD4 + and CD8 + T cells earlier after durvalumab treatment. To examine durvalumab’s mechanism of action and identify potential predictive biomarkers, we assessed the circulating T cells phenotypes and TCR genes of 71 NSCLC patients receiving durvalumab enrolled in a Phase I trial (NCT01693562, September 14, 2012). Next-generation sequencing of TCR repertoire was performed on these NSCLC patients’ peripheral blood samples at baseline and day 15. Though patients’ TCR repertoire diversity showed mixed responses to the treatment, patients exhibiting increased diversity on day 15 attained significantly longer overall survival (OS) (median OS was not reached vs 17.2 months for those with decreased diversity, p = 0.015). We applied network analysis to assess convergent T cell clonotypes indicative of an antigen-driven immune response. Patients with larger TCR clusters had improved OS (median OS was not reached vs 13.1 months for patients with smaller TCR clusters, p = 0.013). Early TCR repertoire diversification after durvalumab therapy for NSCLC may be predictive of increased survival and provides a mechanistic basis for durvalumab pharmacodynamic activity.

Beneficial autoimmunity links primary biliary cholangitis to the avoidance of cholangiocarcinoma

ABSTRACT It has been an open conundrum why primary sclerosing cholangitis (PSC) is a major risk factor for developing cholangiocarcinoma (CAA), while primary biliary cholangitis (PBC) is not. In mouse models of PSC and PBC, it turned out that the latter condition, an autoimmune disease affecting the bile ducts, reduces transgene-induced cholangiocarcinogenesis, as well as the progression of subcutaneously implanted CCA. This CCA-delaying effect is lost upon depletion of T lymphocytes and involves tumor infiltration by T cell clonotypes that are also found in PBC lesions. Hence, organ-specific autoimmunity may improve immunosurveillance.

Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics.

Many experimental and bioinformatics approaches have been developed to characterize the human T cell receptor (TCR) repertoire. However, the unknown functional relevance of TCR profiling significantly hinders unbiased interpretation of the biology of T cells. To address this inadequacy, we developed tessa, a tool to integrate TCRs with gene expression of T cells, in order to estimate the effect that TCRs confer upon the phenotypes of T cells. Tessa leveraged techniques combining single cell RNA-sequencing with TCR-sequencing. We validated tessa and showed its superiority over existing approaches that investigate only the TCR sequences. With tessa, we demonstrated that TCR similarity constrains the phenotypes of T cells to be similar, and dictates a gradient in antigen targeting efficiency of T cell clonotypes with convergent TCRs. We showed this constraint could predict a functional dichotomization of T cells post-immunotherapy treatment, and is weakened in tumor contexts.

A Structured Evaluation of Cryopreservation in Generating Single Cell Transcriptomes From Cerebrospinal Fluid

Abstract Importance A robust cerebrospinal fluid (CSF) cell cryopreservation protocol using high resolution single-cell (sc) transcriptomic data would enable the deployment of this important modality in multi-center translational research studies and clinical trials in which many sites do not have the expertise or resources to produce data from fresh samples. It would also serve to reduce technical variability in larger projects. Objective To test a reliable cryopreservation protocol adapted for CSF cells, facilitating the characterization of these rare, fragile cells in moderate to large scale studies. Design Diagnostic lumbar punctures were performed on twenty-one patients at two independent sites. Excess CSF was collected and cells were isolated. Each cell sample was split into two fractions for single cell analysis using one of two possible chemistries: 3’ sc-RNA-Sequencing or 5’sc-RNA-Sequencing. One cell fraction was processed fresh while the second sample was cryopreserved and profiled at a later time after thawing. Setting The research protocol was deployed at two academic medical centers taking care of multiple sclerosis and other neurological conditions. Participants 21 subjects (age 24 – 72) were recruited from individuals undergoing a diagnostic lumbar puncture for suspected neuroinflammatory disease or another neurologic illness; they donated excess CSF. Findings Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. The proportion of all cell types was similar between the fresh and the cryopreserved cells processed, and RNA expression was not significantly different. Results were comparable at both performance sites, and with different single cell sequencing chemistries. Cryopreservation also did not affect recovery of T and B cell clonotype diversity. Conclusion and relevance Our cryopreservation protocol for CSF-cells provides an important alternative to fresh processing of fragile CSF cells: cryopreservation enables the involvement of sites with limited capacity for experimental manipulation and reduces technical variation by enabling batch processing and pooling of samples. Key points Question How efficient is CSF cryopreservation for single-cell transcriptome analysis and can it be implemented in large multi-center translational and clinical trial settings? Findings We compared single-cell transcriptomes of paired fresh and cryopreserved CSF from 21 patients at two independent sites. We validate the efficacy of a simple and cost effective CSF cryopreservation method that preserves the composition and the transcriptomes of CSF cells stored for weeks-months. The protocol is deployed in a large multicenter Phase 4 MS clinical trial. Meaning A validated CSF cryopreservation method that would significantly advance basic science and biomarker research in neurological disorders by implementing single-cell transcriptome analyses in multi-center research and clinical trials.

Paired Rheumatoid Arthritis Synovial Biopsies From Small and Large Joints Show Similar Global Transcriptomic Patterns With Enrichment of Private Specificity TCRB and TCR Signaling Pathways.

ObjectivesWe explored histological and transcriptomic profiles of paired synovial biopsies from rheumatoid arthritis (RA) patients, in order to assess homogeneity in synovial tissue at the individual level.MethodsSynovial biopsies were performed simultaneously in one small and one large joint per patient using needle-arthroscopy for the knee and ultrasound-guided biopsy for the hand or wrist. Synovium from individuals with osteoarthritis was used as controls. Paraffin-embedded samples were stained for CD3, CD20, and CD68. Total RNA was hybridized on high-density microarrays. TCRB variable sequences were obtained from synovial and blood RNA samples.ResultsTwenty paired biopsies from 10 RA patients with active disease were analyzed. Semi-quantification of histological markers showed a positive correlation for synovial hyperplasia, inflammatory infiltrates and CD3-positive T cells between pairs. Pairwise comparison of transcriptomic profiles showed similar expression of RA-related molecular pathways (TCR signaling, T cell costimulation and response to TNFα). T cells clonotypes were enriched in all but one joints compared to blood, regardless of the magnitude of T cell infiltration. Enriched clonotypes were shared between pairs (23–100%), but this was less the case in pairs of joints displaying weaker T cell signatures and more pronounced germinal center-like transcriptomic profiles.ConclusionCellular and molecular alterations in RA synovitis are similar between small and large joints from the same patient. Interindividual differences in magnitude of T cell infiltrates and distribution of enriched T cell clonotypes support the concept of distinct synovial pathotypes in RA that are associated with systemic versus local antigen-driven activation of T cells.

IMMU-41. HIGH-THROUGHPUT RETRIEVAL OF THERAPEUTIC T CELL RECEPTORS FROM GLIOMA

Abstract Gliomas are tumors with low mutational burden with the majority of them being resistant to checkpoint inhibition due to few immunogenic antigens. Multicenter vaccine trials targeting personalized neoantigens in gliomas demonstrated feasibility and illustrated the challenges of retrieving neoepitope-specific T cells based on the prediction of immunogenic neoepitopes. Here we took an entirely different T cell-centric approach and established a single cell sequencing-based high-throughput T cell receptor (TCR) retrieval platform, exploiting the therapeutic potential of spontaneous intratumoral T cell clonotypes for the development of adoptive cell therapy. We conducted direct ex vivo TCR single cell sequencing from freshly sorted human glioma-infiltrating T cell samples. High fidelity PCR was established to clone TCRs from single cell libraries directly into episomal expression vectors further optimized for T cell therapy. In parallel to standard therapy, patient-derived xenografts were developed and characterized. Tumor-reactivity of retrieved TCRs was demonstrated against patient-derived cell lines. Collectively, we provide a novel sequencing-based platform for high-throughput identification and validation of endogenous glioma-targeting TCRs and demonstrate their therapeutic applicability.

UM171-Expanded Cord Blood Transplants Support Robust T-Cell Reconstitution with Low Rates of Severe Infections

Introduction Rapid T cell reconstitution following hematopoietic stem cell transplantation is essential for protection against infections and has been associated with lower incidence of chronic graft-vs-host disease (cGVHD), relapse and transplant-related mortality (TRM). While cord blood (CB) transplants are associated with lower rates of cGVHD and relapse, their low stem cell content results in slower immune reconstitution and higher risk of graft failure, severe infections and TRM. Recently, results of a Phase I/II trial revealed that single UM171-expanded CB transplant allowed the use of smaller CB units without compromising engraftment. We now report on T cell reconstitution and immune function in patients transplanted with UM171-expanded CB grafts. Methods We performed a retrospective analysis of 20 patients treated with UM171-expanded CB and compared it to a contemporary cohort of 12 patients treated in the same institution who received unmanipulated CB transplant with similar conditioning regimens. Of note, no patient received ATG as part of the conditioning in either cohort. We used flow cytometry and TCR sequencing to evaluate T cell reconstitution, and virus-specific ELISpot assays to evaluate T cell function in the first year post-transplantation. We also categorized infectious events as per definitions of infection severity in the BMT CTN Technical MOP Version 3.0 and report the mean cumulative count of infectious events for each cohort. Results While median T cell dose in graft was at least 2-3x lower for the cohort of patients treated with UM171-expanded CB due to the selection of smaller cords and to cell loss occurring during CD34 selection process, numbers and phenotype of T cells at 3, 6 and 12 months post-transplant were similar in patients treated with UM171-expanded or unmanipulated CB transplant. TCR sequencing analyses revealed that UM171 patients had greater T cell diversity and higher numbers of T cell clonotypes at 12 months post-transplant compared to patients who received unmanipulated CB. Younger UM171 patients (i.e. <40 years old) also showed a more pronounced increase in naïve T cells and recent thymic emigrants (RTE) between 3- and 12-months post-transplant compared to age-matched unmanipulated CB patients, suggesting that UM171-expansion improves thymopoiesis at least in the young patients. This also correlated with the demonstration that UM171 expands common lymphoid progenitors in vitro. ELISpot assays revealed that UM171 patients showed early virus-specific T cell reactivity, at 2- and 3-months post-transplant. Most importantly, UM171 patients had a 2-fold lower frequency of severe (i.e. grade 2-3) infections at 1 year post-transplant, even though time to engraftment of 500 neutrophils was similar between the two cohorts (17 and 20 days for the UM171-expanded and unmanipulated CB cohorts respectively, p=0.94). Conclusion Our data show that the relative T-cell paucity of the UM171 graft is rapidly compensated after transplant with no significant difference observed between the two cohorts in terms of numbers and phenotypes of T cells at 3, 6 or 12 months post-transplant. Although it is difficult to dissect the relative contribution of homeostatic expansion and de novo thymopoiesis, recipients of UM171 grafts had a greater TCR diversity at one year, which was more evident among patients younger than 40 years of age. The prompt immune reconstitution observed in UM171 patients translated into a low rate of severe (grade 2-3) infections and no infection-related mortality. These results support rapid and functional T cell reconstitution following UM171 expanded CB transplantation, which likely contributes to the absence of moderate/severe cGVHD, infection-related mortality and late TRM observed in this cohort. Figure legend: Mean cumulative counts of infectious events in patients transplanted with UM171-expanded (blue) or unmanipulated (red) CB. Mean cumulative counts are shown for all infectious events (A), bacterial (B) and viral (C) infections. Events were categorized by type and severity as per BMT CTN guidelines (Appendix 4A). Infectious events of grade 1-3 are shown in pale colors, while more severe events (grade 2-3) are shown in dark colors. Censored patients (including those who relapsed) are indicated with white circles. Figure 1 Disclosures Dumont-Lagacé: ExCellThera: Current Employment. Busque:Novartis: Honoraria; BMS: Honoraria; Pfizer: Honoraria. Sauvageau:ExCellThera: Current equity holder in private company, Other: CEO, Patents & Royalties. Cohen:ExCellThera: Consultancy, Other: principal investigator of an ongoing UM171 clinical trial.

Azacitidine (AZA) with Nivolumab (Nivo), and AZA with Nivo + Ipilimumab (Ipi) in Relapsed/Refractory (R/R) Acute Myeloid Leukemia: Clinical and Immune Biomarkers of Response

Azacitidine (AZA) with Nivolumab (Nivo), and AZA with Nivo + Ipilimumab (Ipi) in Relapsed/Refractory (R/R) Acute Myeloid Leukemia: Clinical and Immune Biomarkers of Response

Neoantigens Are Typically Associated with Intact HLA Class I Presentation in Early-Stage Follicular Lymphoma

Neoantigens Are Typically Associated with Intact HLA Class I Presentation in Early-Stage Follicular Lymphoma

Single-Cell Characterization of Acute Myeloid Leukemia (AML) and Its Microenvironment Identifies Signatures of Resistance to PD-1 Blockade Based Therapy

Single-Cell Characterization of Acute Myeloid Leukemia (AML) and Its Microenvironment Identifies Signatures of Resistance to PD-1 Blockade Based Therapy

RNA and TCR Sequencing Shed Light on Mechanisms of Treg Suppression in a Murine Model of Acute GvHD

Introduction Regulatory T cell (Treg) based therapies are a promising approach for graft-versus-host disease (GvHD) prevention and treatment. However, mechanisms of Treg suppression of alloreactive conventional T cells (Tcon) in GvHD are incompletely understood. In this study, we performed paired RNA and T cell receptor (TCR) sequencing analysis on Tcon and Treg before and after transplantation to further elucidate Treg suppressive function during in vivo suppression of acute GvHD in an MHC major-mismatch mouse model. Methods CD45.2 Thy1.2 BALB/c mice were lethally irradiated (8.8 Gy) and transplanted with 5x106 T cell- depleted bone marrow cells (TCD-BM) from CD45.1 Thy1.2 C57Bl/6 mice alone or together with CD45.2 Thy1.2 C57Bl/6 FoxP3/GFP+ Treg (1x106) on day 0. On day 2, CD45.1 Thy1.1 C57Bl/6 Tcon (1x106; CD4:CD8 ratio = 2:1) were injected to induce GvHD. Irradiated (11 Gy) syngeneic C57Bl/6 recipients receiving C57Bl/6 TCD-BM and CD45.1 Thy1.1 Tcon alone were used as controls. On day 8, donor Thy1.1+ CD45.1+ CD4 and CD8 Tcon and Thy1.2+CD45.2+ FoxP3/GFP+ Treg were isolated by FACS from spleens and lymph nodes. T cell subsets before injection and recovered at day 8 were analyzed by paired RNA and TCR sequencing. Results The transcriptomic analysis revealed a dominant effect of the allogeneic transplant procedure on the clustering of the different T cell populations. Principal component analysis (PCA) of the top 1000 most differentially expressed genes revealed that 68% of the variance was explained by PC1, which clearly segregated CD4and CD8Tcon recovered at day 8 from allogeneic recipients from cells before injection or recovered from syngeneic recipients (Fig. 1). PC1 was mainly driven by naïve T cell genes (Ccr7, Sell, Il6ra, Il6st, Foxo1) that were progressively downregulated along PC1. Analysis of the TCR repertoire based on sequencing of the TCR alpha chain revealed a progressive clonal restriction along PC1 in CD4 and CD8 T cells (Fig. 1). Accordingly, clonal overlap between cells collected at day 8 and cells analyzed before injection were reduced in allogeneic recipients (Morisita Index [MI], CD4: 0.06±0.01; CD8: 0.02±0.01) compared to syngeneic controls (MI, CD4: 0.23±0.26; CD8: 0.57±0.05). Treg administration did not affect CD4 or CD8 T cell segregation along PC1, suggesting that they minimally interfered with cell activation and differentiation during GvHD. Accordingly, Treg did not inhibit clonal restriction (Fig.1) nor the reduction in clonal overlap (MI, CD4: 0.04±0.01; CD8: 0.01±0.01), indicating that Treg did not inhibit the initial activation of alloreactive T cells clones. Treg impact on CD4 but not CD8 Tcon transcriptome was revealed by PC2 (Fig.1). Treg induced the downregulation of TH1-signature genes (Tbx21, Il12rb1, Il12rb2, Stat4) and proinflammatory genes (Il18rap) while promoting up-regulation of anti-inflammatory genes (Il18bp), TH2 signature genes (Ccr4, Il4) and Il2 in CD4Tcon. Moreover, gene set enrichment analysis (GSEA) revealed that Treg treatment significantly impacted gene sets involved in metabolic processes in CD4and CD8Tcon, leading to a global up-regulation of genes encoding for enzymes involved in oxidative phosphorylation (OXPHOS) and downregulation of genes encoding for enzymes contributing to glycolysis (Slc2a1, Hk1, Pfkl, Pfkp, Pkm). Treg recovered at day 8 preserved a distinct transcriptomic signature observed before injection and further enhanced by the up-regulation of genes involved in Treg activation and suppressive function (Gata3, Tnfrsf18, Tnfrsf4, Icos, Ccr1, Ccr4, Il9r). GSEA in Treg revealed significant up-regulation of genes in the OXPHOS signature. TCR repertoire analysis showed clonal restriction of Treg during GvHD. Direct comparison of clone frequencies in Treg and CD4Tcon showed smaller clonal overlap on day 8 (MI=0.005±0.006) compared to day 0 (MI= 0.11±0.004) suggesting that Treg and CD4Tcon responses during GvHD are engaging different cell clonotypes triggered by different epitopes or antigens. Conclusion Our results indicate that Treg treatment did not interfere with Tcon activation and differentiation of alloreactive Tcon clones in a model of acute GvHD. Treg predominantly affected CD4Tcon and to a lesser extent CD8Tcon transcriptome, modulating the transcription of genes encoding pro- and anti-inflammatory molecules as well as enzymes involved in metabolic processes. Disclosures Turkoz: Adicet Bio: Current Employment, Current equity holder in private company. Negrin:Magenta Therapeutics: Consultancy, Current equity holder in publicly-traded company; BioEclipse Therapeutics: Current equity holder in private company; Amgen: Consultancy; KUUR Therapeutics: Consultancy; Biosource: Current equity holder in private company; UpToDate: Honoraria.