178 results on '"TCR sequencing"'
Search Results
52. Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'.
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Davydov, Alexey N, Bolotin, Dmitry A, Poslavsky, Stanislav V, and Chudakov, Dmitry M
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B cells , *RNA sequencing , *T cell receptors , *MOLECULAR cloning , *TRUST - Abstract
Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell/B-cell receptors sequencing (TCR-Seq/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis. [ABSTRACT FROM AUTHOR]
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- 2023
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53. Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia.
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Chang, Che-Mai, Feng, Po‐Hao, Wu, Tsung-Hsun, Alachkar, Houda, Lee, Kang-Yun, and Chang, Wei-Chiao
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COVID-19 , *T cells , *T cell receptors , *VIRUS diseases , *PNEUMONIA - Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. So far, little has been known about differences in the T cell repertoires between COVID-19 patients with and without pneumonia during SARS-CoV-2 infection. Herein, we aimed to investigate T cell receptor (TCR) repertoire profiles and patient-specific SARS-CoV-2-associated TCR clusters between COVID-19 patients with mild disease (no sign of pneumonia) and pneumonia. The TCR sequencing was conducted to characterize the peripheral TCR repertoire profile and diversity. The TCR clustering and CDR3 annotation were exploited to further discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. Our study indicated a slight decrease in the TCR repertoire diversity and a skewed CDR3 length usage in patients with pneumonia compared to those with mild disease. The SARS-CoV-2-associated TCR clusters enriched in patients with mild disease exhibited significantly higher TCR generation probabilities and most of which were highly shared among patients, compared with those from pneumonia patients. Importantly, using similarity network-based clustering followed by the sequence conservation analysis, we found different patterns of CDR3 sequence motifs between mild disease- and pneumonia-specific SARS-CoV-2-associated public TCR clusters. Our results showed that characteristics of overall TCR repertoire and SARS-CoV-2-associated TCR clusters/clonotypes were divergent between COVID-19 patients with mild disease and patients with pneumonia. These findings provide important insights into the correlation between the TCR repertoire and disease severity in COVID-19 patients. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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54. T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer
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Lucia Mazzotti, Anna Gaimari, Sara Bravaccini, Roberta Maltoni, Claudio Cerchione, Manel Juan, Europa Azucena-Gonzalez Navarro, Anna Pasetto, Daniela Nascimento Silva, Valentina Ancarani, Vittorio Sambri, Luana Calabrò, Giovanni Martinelli, and Massimiliano Mazza
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TCR repertoire ,TCR sequencing ,infectious diseases ,cancer immunotherapy ,HLA ,TILs ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.
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- 2022
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55. Dynamics of T-cell receptor repertoire in patients with ankylosing spondylitis after biologic therapy.
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Liu, Wei-Chih, Chang, Che-Mai, Zhang, Yanfeng, Liao, Hsien-Tzung, and Chang, Wei-Chiao
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ANKYLOSING spondylitis , *BIOTHERAPY , *T cells , *AUTOIMMUNE diseases , *IMMUNE response - Abstract
• TCR diversity increased in biologic-treated AS patients with better improvement. • Higher difference of contracted minus expanded TCRs related to better improvement. • IL-23 level positively correlated with TCR diversity in AS patients. • AS-associated TCRs contracted in biologic-treated patients with better improvement. Ankylosing spondylitis (AS) is a chronic inflammatory autoimmune disease in which T-cell immune responses play important roles. AS has been characterized by altered T-cell receptor (TCR) repertoire profiles, which are thought to be caused by expansion of disease-related TCR clonotypes. However, how biological agents affect the TCR repertoire status and whether their therapeutic outcomes are associated with certain features or dynamic patterns of the TCR repertoire are still elusive. We collected clinical samples from AS patients pre- and post-treatment with biologics. TCR repertoire sequencing was conducted to investigate associations of TCRα and TCRβ repertoire characteristics with disease activity and inflammatory indicators/cytokines. Our results showed that good responders were associated with an increase in the TCR repertoire diversity with higher proportions of contracted TCR clonotypes. Additionally, we further identified a positive correlation between TCR repertoire diversity and interleukin (IL)–23 levels in AS patients. A network analysis revealed that contracted AS-associated TCR clonotypes with the same complementary-determining region 3 (CDR3) motifs, which represented high probabilities of sharing TCR specificities to AS-related antigens, were dominant in good responders of AS after treatment with biologic therapies. Our findings suggested an important connection between TCR repertoire changes and therapeutic outcomes in biologic-treated AS patients. The status and dynamics of TCR repertoire profiles are useful for assessing the prognosis of biologic treatments in AS patients. [ABSTRACT FROM AUTHOR]
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- 2024
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56. The Proximal Airway Is a Reservoir for Adaptive Immunologic Memory in Idiopathic Subglottic Stenosis.
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Gelbard, Alexander, Wanjalla, Celestine, Wootten, Christopher T., Drake, Wonder P., Lowery, Anne S., Wheeler, David A., Cardenas, Maria F., Sikora, Andrew G., Pathak, Ravi R., McDonnell, Wyatt, Mallal, Simon, and Pilkinton, Mark
- Abstract
Objectives/Hypothesis: Characterization of the localized adaptive immune response in the airway scar of patients with idiopathic subglottic stenosis (iSGS). Study Design: Basic Science. Methods: Utilizing 36 patients with subglottic stenosis (25 idiopathic subglottic stenosis [iSGS], 10 iatrogenic post‐intubation stenosis [iLTS], and one granulomatosis with polyangiitis [GPA]) we applied immunohistochemical and immunologic techniques coupled with RNA sequencing. Results: iSGS, iLTS, and GPA demonstrate a significant immune infiltrate in the subglottic scar consisting of adaptive cell subsets (T cells along with dendritic cells). Interrogation of T cell subtypes showed significantly more CD69+ CD103+ CD8+ tissue resident memory T cells (TRM) in the iSGS airway scar than iLTS specimens (iSGS vs. iLTS; 50% vs. 28%, P =.0065). Additionally, subglottic CD8+ clones possessed T‐cell receptor (TCR) sequences with known antigen specificity for viral and intracellular pathogens. Conclusions: The human subglottis is significantly enriched for CD8+ tissue resident memory T cells in iSGS, which possess TCR sequences proven to recognize viral and intracellular pathogens. These results inform our understanding of iSGS, provide a direction for future discovery, and demonstrate immunologic function in the human proximal airway. Laryngoscope, 131:610–617, 2021 [ABSTRACT FROM AUTHOR]
- Published
- 2021
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57. Large T cell clones expressing immune checkpoints increase during multiple myeloma evolution and predict treatment resistance
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Tumor recognition by T cells is essential for antitumor immunity. A comprehensive characterization of T cell diversity may be key to understanding the success of immunomodulatory drugs and failure of PD-1 blockade in tumors such as multiple myeloma (MM). Here, we use single-cell RNA and T cell receptor sequencing to characterize bone marrow T cells from healthy adults (n = 4) and patients with precursor (n = 8) and full-blown MM (n = 10). Large T cell clones from patients with MM expressed multiple immune checkpoints, suggesting a potentially dysfunctional phenotype. Dual targeting of PD-1 + LAG3 or PD-1 + TIGIT partially restored their function in mice with MM. We identify phenotypic hallmarks of large intratumoral T cell clones, and demonstrate that the CD27− and CD27+ T cell ratio, measured by flow cytometry, may serve as a surrogate of clonal T cell expansions and an independent prognostic factor in 543 patients with MM treated with lenalidomide-based treatment combinations.
- Published
- 2023
58. Merkel cell polyomavirus-specific and CD39 + CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma.
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Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, and Newell EW
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- Humans, Programmed Cell Death 1 Receptor metabolism, CD8-Positive T-Lymphocytes, Biomarkers metabolism, Carcinoma, Merkel Cell drug therapy, Carcinoma, Merkel Cell metabolism, Carcinoma, Merkel Cell pathology, Merkel cell polyomavirus metabolism, Skin Neoplasms drug therapy, Skin Neoplasms metabolism, Sialyl Lewis X Antigen analogs & derivatives, Oligosaccharides
- Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39
+ CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+ CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells., Competing Interests: Declaration of interests E.W.N. is a co-founder, advisor, and shareholder for ImmunoScape Pte. Ltd., a scientific advisory board member and shareholder for Neogene Therapeutics, and a scientific advisory board member for Nanostring Biotechnologies and Trojan Biotechnologies. D.M.K. and P.N. are co-inventors on an institutionally owned patent concerning MCPyV-specific TCRs., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2024
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59. Diagnosing Viral Infections Through T-Cell Receptor Sequencing of Activated CD8+ T Cells.
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Vujkovic A, Ha M, de Block T, van Petersen L, Brosius I, Theunissen C, van Ierssel SH, Bartholomeus E, Adriaensen W, Vanham G, Elias G, Van Damme P, Van Tendeloo V, Beutels P, van Frankenhuijsen M, Vlieghe E, Ogunjimi B, Laukens K, Meysman P, and Vercauteren K
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- Humans, Receptors, Antigen, T-Cell genetics, SARS-CoV-2, T-Lymphocyte Subsets, Epitopes, Epitopes, T-Lymphocyte, COVID-19 Testing, CD8-Positive T-Lymphocytes, COVID-19 diagnosis
- Abstract
T-cell-based diagnostic tools identify pathogen exposure but lack differentiation between recent and historical exposures in acute infectious diseases. Here, T-cell receptor (TCR) RNA sequencing was performed on HLA-DR+/CD38+CD8+ T-cell subsets of hospitalized coronavirus disease 2019 (COVID-19) patients (n = 30) and healthy controls (n = 30; 10 of whom had previously been exposed to severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]). CDR3α and CDR3β TCR regions were clustered separately before epitope specificity annotation using a database of SARS-CoV-2-associated CDR3α and CDR3β sequences corresponding to >1000 SARS-CoV-2 epitopes. The depth of the SARS-CoV-2-associated CDR3α/β sequences differentiated COVID-19 patients from the healthy controls with a receiver operating characteristic area under the curve of 0.84 ± 0.10. Hence, annotating TCR sequences of activated CD8+ T cells can be used to diagnose an acute viral infection and discriminate it from historical exposure. In essence, this work presents a new paradigm for applying the T-cell repertoire to accomplish TCR-based diagnostics., Competing Interests: Potential conflicts of interest . B. O., K. L., and P. M. are cofounders, board directors, and shareholders of ImmuneWatch. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
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- 2024
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60. Profiling Virus-Specific Tcf1+ T Cell Repertoires During Acute and Chronic Viral Infection
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Alexander Yermanos, Ioana Sandu, Alessandro Pedrioli, Mariana Borsa, Franziska Wagen, Nathalie Oetiker, Suzanne P. M. Welten, Katharina Pallmer, Sai T. Reddy, and Annette Oxenius
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viral infection ,deep sequencing ,TCF1 ,TCR sequencing ,adaptive immune receptor repertoire sequencing ,Immunologic diseases. Allergy ,RC581-607 - Abstract
CD8 T cells play a crucial role in providing protection from viral infections. It has recently been established that a subset of CD8 T cells expressing Tcf1 are responsible for sustaining exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. Many of these studies, however, have been performed using T cell receptor (TCR) transgenic mice, in which CD8 T cells express a monoclonal TCR specific for the LCMV glycoprotein. To investigate whether the Tcf1+ and Tcf1- repertoires are naturally composed of similar or different clones in wild-type mice exposed to acute or chronic LCMV infection, we performed TCR repertoire sequencing of virus-specific CD8 T cells, including Tcf1+ and Tcf1- populations. Our analysis revealed that the Tcf1+ TCR repertoire is maintained at an equal or higher degree of clonal diversity despite harboring fewer cells. Additionally, within the same animal, there was extensive clonal overlap between the Tcf1+ and Tcf1- repertoires in both chronic and acute LCMV infection. We could further detect these virus-specific clones in longitudinal blood samples earlier in the infection. With respect to common repertoire parameters (clonal overlap, germline gene usage, and clonal expansion), we found minor differences between the virus-specific TCR repertoire of acute and chronic LCMV infection 40 days post infection. Overall, our results indicate that the Tcf1+ population emerging during chronic LCMV infection is not clonally distinct from the Tcf1- population, supporting the notion that the Tcf1+ pool is indeed a fuel for the more exhausted Tcf1– population within the heterogenous repertoire of LCMV-specific CD8 T cells.
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- 2020
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61. Profiling Virus-Specific Tcf1+ T Cell Repertoires During Acute and Chronic Viral Infection.
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Yermanos, Alexander, Sandu, Ioana, Pedrioli, Alessandro, Borsa, Mariana, Wagen, Franziska, Oetiker, Nathalie, Welten, Suzanne P. M., Pallmer, Katharina, Reddy, Sai T., and Oxenius, Annette
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T cells ,VIRUS diseases ,LYMPHOCYTIC choriomeningitis virus ,T cell receptors ,TRANSGENIC mice - Abstract
CD8 T cells play a crucial role in providing protection from viral infections. It has recently been established that a subset of CD8 T cells expressing Tcf1 are responsible for sustaining exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. Many of these studies, however, have been performed using T cell receptor (TCR) transgenic mice, in which CD8 T cells express a monoclonal TCR specific for the LCMV glycoprotein. To investigate whether the Tcf1+ and Tcf1- repertoires are naturally composed of similar or different clones in wild-type mice exposed to acute or chronic LCMV infection, we performed TCR repertoire sequencing of virus-specific CD8 T cells, including Tcf1+ and Tcf1- populations. Our analysis revealed that the Tcf1+ TCR repertoire is maintained at an equal or higher degree of clonal diversity despite harboring fewer cells. Additionally, within the same animal, there was extensive clonal overlap between the Tcf1+ and Tcf1- repertoires in both chronic and acute LCMV infection. We could further detect these virus-specific clones in longitudinal blood samples earlier in the infection. With respect to common repertoire parameters (clonal overlap, germline gene usage, and clonal expansion), we found minor differences between the virus-specific TCR repertoire of acute and chronic LCMV infection 40 days post infection. Overall, our results indicate that the Tcf1+ population emerging during chronic LCMV infection is not clonally distinct from the Tcf1- population, supporting the notion that the Tcf1+ pool is indeed a fuel for the more exhausted Tcf1– population within the heterogenous repertoire of LCMV-specific CD8 T cells. [ABSTRACT FROM AUTHOR]
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- 2020
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62. Dominant CD4 + T cell receptors remain stable throughout antiretroviral therapy-mediated immune restoration in people with HIV.
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Sponaugle A, Weideman AMK, Ranek J, Atassi G, Kuruc J, Adimora AA, Archin NM, Gay C, Kuritzkes DR, Margolis DM, Vincent BG, Stanley N, Hudgens MG, Eron JJ, and Goonetilleke N
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- Humans, CD8-Positive T-Lymphocytes, CD4-Positive T-Lymphocytes, Anti-Retroviral Agents therapeutic use, Receptors, Antigen, T-Cell, Immune Reconstitution, HIV Infections drug therapy
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In people with HIV (PWH), the post-antiretroviral therapy (ART) window is critical for immune restoration and HIV reservoir stabilization. We employ deep immune profiling and T cell receptor (TCR) sequencing and examine proliferation to assess how ART impacts T cell homeostasis. In PWH on long-term ART, lymphocyte frequencies and phenotypes are mostly stable. By contrast, broad phenotypic changes in natural killer (NK) cells, γδ T cells, B cells, and CD4
+ and CD8+ T cells are observed in the post-ART window. Whereas CD8+ T cells mostly restore, memory CD4+ T subsets and cytolytic NK cells show incomplete restoration 1.4 years post ART. Surprisingly, the hierarchies and frequencies of dominant CD4 TCR clonotypes (0.1%-11% of all CD4+ T cells) remain stable post ART, suggesting that clonal homeostasis can be independent of homeostatic processes regulating CD4+ T cell absolute number, phenotypes, and function. The slow restoration of host immunity post ART also has implications for the design of ART interruption studies., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2023
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63. Comprehensive immune profiling of SARS-CoV-2 infected kidney transplant patients.
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Fenninger F, Sherwood KR, Wu V, Wong P, DeMarco ML, Wang M, Benedicto V, Dwarka KA, Günther OP, Tate L, Yoshida E, Keown PA, Kadatz M, and Lan JH
- Abstract
Introduction: The immune responses of kidney transplant recipients against SARS-CoV-2 remains under studied., Methods: In this prospective pilot study, we performed comprehensive immune profiling using cellular, proteomic, and serologic assays on a cohort of 9 kidney transplant recipients and 12 non-transplant individuals diagnosed with COVID-19., Results: Our data show that in addition to having reduced SARS-CoV-2 specific antibody levels, kidney transplant recipients exhibited significant cellular differences including a decrease in naïve-but increase in effector T cells, a high number of CD28+ CD4 effector memory T cells, and increased CD8 T memory stem cells compared with non-transplant patients. Furthermore, transplant patients had lower concentrations of serum cytokine MIP-1β as well as a less diverse T cell receptor repertoire., Conclusion: Overall, our results show that compared to non-transplant patients, kidney transplant recipients with SARS-CoV-2 infection exhibit an immunophenotype that is reminiscent of the immune signature observed in patients with severe COVID-19., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (© 2023 Fenninger, Sherwood, Wu, Wong, DeMarco, Wang, Benedicto, Dwarka, Günther, Tate, Yoshida, Keown, Kadatz and Lan.)
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- 2023
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64. TRB sequences targeting ORF1a/b are associated with disease severity in hospitalized COVID-19 patients
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Jorn L. J. C. Assmann, Willem A. Dik, P Martijn Kolijn, Vincent H.J. van der Velden, Anton W. Langerak, Ton A.A.M. Ermens, Daan W Loth, Benjamin Schrijver, Adriaan J van Gammeren, and Immunology
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0301 basic medicine ,Time Factors ,Receptors, Antigen, T-Cell, alpha-beta ,Immunology ,Brief Conclusive Report ,Genome, Viral ,Immunogenetics ,Biology ,medicine.disease_cause ,Severity of Illness Index ,Genome ,SARS‐CoV‐2 ,DNA sequencing ,Viral Proteins ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,COVID‐19 ,TCR sequencing ,medicine ,Humans ,Immunology and Allergy ,Amino Acid Sequence ,T-Cell Receptor Beta Chain ,Aged ,Polyproteins ,Genetics ,SARS-CoV-2 ,Repertoire ,COVID-19 ,Cell Biology ,Immune dysregulation ,Acquired immune system ,Complementarity Determining Regions ,immunogenetics ,Hospitalization ,030104 developmental biology ,030220 oncology & carcinogenesis - Abstract
The potential protective or pathogenic role of the adaptive immune response to SARS‐CoV‐2 infection has been vigorously debated. While COVID‐19 patients consistently generate a T lymphocyte response to SARS‐CoV‐2 antigens, evidence of significant immune dysregulation in these patients continues to accumulate. In this study, next generation sequencing of the T cell receptor beta chain (TRB) repertoire was conducted in hospitalized COVID‐19 patients to determine if immunogenetic differences of the TRB repertoire contribute to disease course severity. Clustering of highly similar TRB CDR3 amino acid sequences across COVID‐19 patients yielded 781 shared TRB sequences. The TRB sequences were then filtered for known associations with common diseases such as EBV and CMV. The remaining sequences were cross‐referenced to a publicly accessible dataset that mapped COVID‐19 specific TCRs to the SARS‐CoV‐2 genome. We identified 158 SARS‐CoV‐2 specific TRB sequences belonging to 134 clusters in our COVID‐19 patients. Next, we investigated 113 SARS‐CoV‐2 specific clusters binding only one peptide target in relation to disease course. Distinct skewing of SARS‐CoV‐2 specific TRB sequences toward the nonstructural proteins (NSPs) encoded within ORF1a/b of the SARS‐CoV‐2 genome was observed in clusters associated with critical disease course when compared to COVID‐19 clusters associated with a severe disease course. These data imply that T‐lymphocyte reactivity towards peptides from NSPs of SARS‐CoV‐2 may not constitute an effective adaptive immune response and thus may negatively affect disease severity., Graphical Abstract The T cell receptor beta chain (TRB) repertoire of hospitalized COVID‐19 patients revealed that TRB sequences targeting nonstructural proteins of SARS‐CoV‐2 may negatively affect disease severity.
- Published
- 2022
65. Apprentissage d'atlas cellulaires par la méthode de Factorized embeddings
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Trofimov, Assya, Lemieux, Sébastien, and Perreault, Claude
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machine learning ,apprentissage automatique ,atlas cellulaires ,TCR sequencing ,séquençage à haut débit ,séquençage de TCR ,cell atlas ,réseaux de neurones artificiels ,artificial neural network ,high throughput sequencing - Abstract
Le corps humain contient plus de 3.72X10^13 cellules qui se distinguent par leur morphologie, fonction et état. Leur catalogage en atlas cellulaires c'est entamé il y a plus de 150 ans, avec l'invention des colorants cellulaires en microscopie. Notre connaissance des types cellulaires et leur phénotypes moléculaires nous permet de connaître et prédire leurs fonctions et patrons d'interactions. Ces connaissances sont à la base de la capacité à poser des diagnostics, créer des médicaments et même faire pousser des organes en biologie synthétique. Surprenamment, notre connaissance est loin d'être complète et c'est pourquoi la caractérisation systématique des cellules et l'assemblage des connaissances en atlas cellulaires est nécessaire. Le développement du séquençage à haut débit a révolutionné la biologie des systèmes et ce type de données est parfait pour la construction d'atlas cellulaires entièrement basés sur les données. Un tel atlas cellulaire contiendra une représentation des cellules par des vecteurs de nombres, où chaque vecteur encode le profil moléculaire capturant des informations biologiques de chaque cellule. Chaque expérience de séquençage d'ARN (RNA-Seq) produit des dizaines de milliers de mesures extrêmement riches en information dont l'analyse demeure non-triviale. Des algorithmes de réduction de dimensionnalité, entre autres, permettent d'extraire des données des patrons importants et encoder les échantillons dans des espaces plus interprétables. De cette manière, les cellules similaires sont groupés sur la base d'une multitude de mesures qu'offre le RNA-Seq. Nous avons donc créé un modèle, le Factorized Embedding (FE), qui permet d'organiser les données de séquençage d'ARN de la sorte. Le modèle apprend simultanément deux espaces d'encodage: un pour les échantillons et l'autre pour les gènes. Nous avons observé qu'une fois entraîné, que ce modèle groupe les échantillons sur la base de leur similarité d'expression génique et permet l'interpolation dans l'espace d'encodage et donc une certaine interprétabilité de l'espace d'encodage. Du côté de l'encodage des gènes, nous avons remarqué que les gènes se regroupaient selon leurs patrons de co-expression ainsi que selon des similarité de fonctions, trouvées via des ontologies de gènes (Gene Ontology, GO). Nous avons ensuite exploré les propriétés d'une modification du modèle FE, baptisée le Transcriptome Latent (TLT, de l'anglais The Latent Transcriptome), où l'encodage des gènes est remplacé par une fonction d'encodage de k-mers provenant de données brutes de RNA-Seq. Cette modification du modèle capture dans son espace d'encodage des séquence à la fois de l'information sur la similarité et l'abondance des séquences ADN. L'espace d'encodage a ainsi permis de détecter des anormalités génomiques tels les translocations, ainsi que des mutations spécifiques au patient, rendant cet espace de représentation utile autant pour la visualisation que pour l'analyse de données. Finalement, la dernière itération explorée dans cette thèse, du modèle FE, baptisée cette fois-ci le TCRome, encode des séquences TCR (récepteurs de cellules T) plutôt que des k-mers, venant du séquençage de répertoires immuns (TCR-Seq). Une irrégularité dans la performance du modèle a mené à une analyse des séquences plus approfondie et à la détection de deux sous-types de TCR. Nous avons analysé les répertoires TCR de plus de 1000 individus et rapportons que le répertoire TCR est composé de deux types de TCR ontogéniquement et fonctionellement distincts. Nous avons découvert des patrons distincts dans les abondances de l'un ou l'autre type, changeant en fonction du sexe, l'âge et dans le cadre de maladies telles chez les sujets portant des mutations dans le gène AIRE et dans le cadre de la maladie du greffon contre l'hôte (GVHD). Ces résultats pointent vers la nécessité d'utiliser des données de séquençage multi-modales pour la construction d'atlas cellulaires, c'est à dire en plus des séquence TCR, des données sur l'expression génique ainsi que des caractérisation moléculaires seront probablement utiles, mais leur intégration sera non-triviale. Le modèle FE (et ses modifications) est un bon candidat pour ce type d'encodage, vu sa flexibilité d'architecture et sa résilience aux données manquantes., The human body contains over 3.72 x 10^13 cells, that distinguish themselves by their morphology, function and state. Their cataloguing into cell atlases has started over 150 years ago, with the invention of cellular stains for microscopy. Our knowledge of cell types and molecular phenotypes allows is to better know and predict their functions and interaction patterns. This knowledge is at the basis of the ability to diagnose disease, create drugs and even grow organs in synthetic biology. Surprisingly, our knowledge is far from complete and this is why a systematic characterization of cells and the assembly of cell atlases is important. The development of high throughput sequencing has revolutionized systems biology and this type of data is perfect for the construction of entirely data-driven cell atlases. Such an atlas will contain a representation of cells by vectors of numbers, where each vector encodes a molecular profile, capturing biological data about each cell. Each sequencing experiment yields tens of thousands of measurements, extremely rich in information, but their analysis remains non-trivial. Dimensionnality reduction algorithms allow to extract from the data important patterns and encode samples into interpretable spaces. This way, similar cells are grouped on the basis of a multitude of measurements that comes from high throughput sequencing. We have created a model, the Factorized Embedding (FE), that allows to organize RNA sequencing (RNA-Seq) data in such a way. The FE model learns simultaneously two encoding spaces: one for samples and one for genes. We have found that the model groups samples on the basis of similar gene expression and allows for smooth interpolation in the encoding space and thus some manner of interpretability. As for the gene encoding space, we observed that gene coordinates were grouped according to co-expression patterns as well as similarity in function, found via gene ontology (GO). We then explored a modification of the FE model, names The Latent Transcriptome (TLT), where the gene encoding function is replaced by a function encoding k-mers, calculated from raw RNA-Seq data. This modification of the model captured in the k-mer encoding space both sequence similarity and sequence abundance. The encoding space allowed for the detection of genomic abnormalities such as translocations, as well as patient-specific mutations, making the encoding space useful for both visualisation and data analysis. Finally, the last iteration of the FE model that we explored, called TCRome, encodes amino-acid TCR sequences rather than k-mers. An irregularity in the model's performance led us to discover two TCR subtypes, entirely based on their sequence. We have thus analyzed TCR repertoires of over 1000 individuals and report that the TCR repertoire is composed of two ontogenically and functionally distinct types. We have discovered distinct pattens in the abundances of each of the sub-types, changing with age, sex and in the context of some diseases such as in individuals carrying a mutated AIRE gene and in graft versus host disease (GVHD). Collectively, these results point towards the necessity to use multi-modal sequencing data for the construction of cell atlases, namely gene expression data, TCR sequencing data and possibly various molecular characterizations. The integration of all this data will however be non-trivial. The FE model (and its modifications) is a good candidate for this type of data organisation, namely because of its flexibility in architecture and resilience to missing data.
- Published
- 2022
66. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features
- Author
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Sylvain Simon, Zhong Wu, J. Cruard, Virginie Vignard, Agnes Fortun, Amir Khammari, Brigitte Dreno, Francois Lang, Samuel J. Rulli, and Nathalie Labarriere
- Subjects
TCR sequencing ,melanoma ,Melan-A ,MELOE-1 ,immunotherapy ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Among Immunotherapeutic approaches for cancer treatment, the adoptive transfer of antigen specific T cells is still a relevant approach, that could have higher efficacy when further combined with immune check-point blockade. A high number of adoptive transfer trials have been performed in metastatic melanoma, due to its high immunogenic potential, either with polyclonal TIL or antigen-specific polyclonal populations. In this setting, the extensive characterization of T cell functions and receptor diversity of infused polyclonal T cells is required, notably for monitoring purposes. We developed a clinical grade procedure for the selection and amplification of polyclonal CD8 T cells, specific for two shared and widely expressed melanoma antigens: Melan-A and MELOE-1. This procedure is currently used in a clinical trial for HLA-A2 metastatic melanoma patients. In this study, we characterized the T-cell diversity (T-cell repertoire) of such T cell populations using a new RNAseq strategy. We first assessed the added-value of TCR receptor sequencing, in terms of sensitivity and specificity, by direct comparison with cytometry analysis of the T cell populations labeled with anti-Vß-specific antibodies. Results from these analyzes also confirmed specific features already reported for Melan-A and MELOE-1 specific T cell repertoires in terms of V-alpha recurrence usage, on a very high number of T cell clonotypes. Furthermore, these analyses also revealed undescribed features, such as the recurrence of a specific motif in the CDR3α region for MELOE-1 specific T cell repertoire. Finally, the analysis of a large number of T cell clonotypes originating from various patients revealed the existence of public CDR3α and ß clonotypes for Melan-A and MELOE-1 specific T cells. In conclusion, this method of high throughput TCR sequencing is a reliable and powerful approach to deeply characterize polyclonal T cell repertoires, and to reveal specific features of a given TCR repertoire, that would be useful for immune follow-up of cancer patients treated by immunotherapeutic approaches.
- Published
- 2018
- Full Text
- View/download PDF
67. Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors
- Author
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Erika J. Crosby, Junping Wei, Xiao Yi Yang, Gangjun Lei, Tao Wang, Cong-Xiao Liu, Pankaj Agarwal, Alan J. Korman, Michael A. Morse, Kenneth Gouin, Simon R. V. Knott, H. Kim Lyerly, and Zachary C. Hartman
- Subjects
breast cancer ,checkpoint blockade ,immunomodulation ,immune responses to cancer ,tcr sequencing ,triple-negative breast cancer ,tumor antigens ,Immunologic diseases. Allergy ,RC581-607 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of
- Published
- 2018
- Full Text
- View/download PDF
68. Blocking CTLA-4 while priming with a whole cell vaccine reshapes the oligoclonal T cell infiltrate and eradicates tumors in an orthotopic glioma model
- Author
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Cameron S. Field, Martin K. Hunn, Peter M. Ferguson, Christiane Ruedl, Lindsay R. Ancelet, and Ian F. Hermans
- Subjects
vaccine ,checkpoint blockade ,anti-ctla-4 ,glioma ,tcr sequencing ,Immunologic diseases. Allergy ,RC581-607 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Vaccine-mediated cancer treatment is unlikely to induce long-term survival unless suppressive mechanisms are overcome. Given the success of antibody-mediated immune checkpoint blockade in relieving regulation of endogenous anti-tumor T cell responses in tumor-burdened hosts, we investigated whether checkpoint blockade could improve the efficacy of responses induced with a whole tumor-cell vaccine. We show that administration of a single dose of blocking antibody was sufficient to significantly enhance antitumor activity of the vaccine, inducing complete radiological regression of established intracranial tumors. The antibody or vaccine alone were ineffective in this setting. The antibody had to be administered before, or close to, vaccine administration, suggesting CTLA-4 blockade had an impact on early priming events. The combined treatment resulted in enhanced trapping of leukocytes in the lymphoid tissues, including T cells that had undergone significant proliferation. There were no obvious changes in the stimulatory function of antigen-presenting cells or the number and function of regulatory T cells, suggesting T cells were the targets of the checkpoint blockade. While tumors regressing under combined treatment were highly infiltrated with a variety of leukocytes, tumor eradication was dependent on CD4+ T cells. Analysis of the TCR repertoire showed that the addition of anti-CTLA-4 at priming reshaped the repertoire of tumor infiltrating T cells. In particular, the oligoclonal populations became greater in magnitude and more diverse in specificity. Using anti-CTLA-4 in a restricted way to promote the priming phase of an anti-cancer vaccine may offer a useful way of harnessing clinical benefit from this powerful agent.
- Published
- 2018
- Full Text
- View/download PDF
69. Corrigendum: Systematic pattern analyses of Vδ2+ TCRs reveal that shared "public" Vδ2+ γδ T cell clones are a consequence of rearrangement bias and a higher expansion status.
- Subjects
T cells - Published
- 2022
- Full Text
- View/download PDF
70. A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid.
- Author
-
Touil H, Roostaei T, Calini D, Diaconu C, Epstein S, Raposo C, Onomichi K, Thakur KT, Craveiro L, Callegari I, Bryois J, Riley CS, Menon V, Derfuss T, De Jager PL, and Malhotra D
- Subjects
- Humans, Gene Expression Profiling methods, B-Lymphocytes, Transcriptome genetics, Cryopreservation methods
- Abstract
Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an unprecedented level. Here, we report a robust cryopreservation protocol adapted for the characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate- to large-scale studies. Fresh CSF was collected from twenty-one participants at two independent sites. Each CSF sample was split into two fractions: one was processed fresh, while the second was cryopreserved for months and profiled after thawing. B and T cell receptor sequencing was also performed. Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. We find no significant difference in cell type proportions and cellular transcriptomes between fresh and cryopreserved cells. Results were comparable at both sites and with different single-cell sequencing chemistries. Cryopreservation did not affect recovery of T and B cell clonotype diversity. Our CSF cell cryopreservation protocol provides an important alternative to fresh processing of fragile CSF cells., Competing Interests: D.M., D.C., C.R., L.C., and J.B. are full-time employees of F. Hoffmann-La Roche. D.M. was employed by F. Hoffmann-La Roche when the study was completed and the manuscript submitted. D.M. moved to Biogen while the manuscript was under review., (© 2023 The Authors.)
- Published
- 2023
- Full Text
- View/download PDF
71. Single-cell transcriptome landscape and antigen receptor dynamic during SARS-CoV-2 vaccination.
- Author
-
Cao X, Chen X, Zhu Y, Gou X, Yan K, Yang B, Men D, Liu L, Zhang YA, and Cao G
- Abstract
Vaccination by inactivated vaccine is an effective strategy to prevent the COVID-19 pandemic. However, the detailed molecular immune response at single-cell level is poorly understood. In this study, we systematically delineated the landscape of the pre- and post-vaccination single-cell transcriptome, TCR (T cell antigen receptor) and BCR (B cell antigen receptor) expression profile of vaccinated candidates. The bulk TCR sequencing analysis of COVID-19 patients was also performed. Enrichment of a clonal CD8
+ T cell cluster expressing specific TCR was identified in both vaccination candidates and COVID-19 patients. These clonal CD8+ T cells showed high expression of cytotoxicity, phagosome and antigen presentation related genes. The cell-cell interaction analysis revealed that monocytes and dendritic cells could interact with these cells and initiate phagocytosis via ICAM1-ITGAM and ITGB2 signaling. Together, our study systematically deciphered the detailed immunological response during SARS-CoV-2 vaccination and infection. It may facilitate understanding the immune response and the T-cell therapy against COVID-19., (© 2022 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.)- Published
- 2023
- Full Text
- View/download PDF
72. Single-cell TCR sequencing of antigen-specific CD4 T cells
- Author
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Gomez-Tourino, Iria, Kamra, Yogesh, Baptista, Roman, Lorenc, Anna, and Peakman, Mark
- Subjects
Tnaive ,Tmem ,CD4 cells ,TCR sequencing ,autoimmune ,Tregs ,CDR3 ,T1D ,Tscm - Published
- 2022
- Full Text
- View/download PDF
73. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features.
- Author
-
Simon, Sylvain, Wu, Zhong, Cruard, J., Vignard, Virginie, Fortun, Agnes, Khammari, Amir, Dreno, Brigitte, Lang, Francois, Rulli, Samuel J., and Labarriere, Nathalie
- Subjects
SLC45A2 gene ,T cells - Abstract
Among Immunotherapeutic approaches for cancer treatment, the adoptive transfer of antigen specific T cells is still a relevant approach, that could have higher efficacy when further combined with immune check-point blockade. A high number of adoptive transfer trials have been performed in metastatic melanoma, due to its high immunogenic potential, either with polyclonal TIL or antigen-specific polyclonal populations. In this setting, the extensive characterization of T cell functions and receptor diversity of infused polyclonal T cells is required, notably for monitoring purposes. We developed a clinical grade procedure for the selection and amplification of polyclonal CD8 T cells, specific for two shared and widely expressed melanoma antigens: Melan-A and MELOE-1. This procedure is currently used in a clinical trial for HLA-A2 metastatic melanoma patients. In this study, we characterized the T-cell diversity (T-cell repertoire) of such T cell populations using a new RNAseq strategy. We first assessed the added-value of TCR receptor sequencing, in terms of sensitivity and specificity, by direct comparison with cytometry analysis of the T cell populations labeled with anti-Vß-specific antibodies. Results from these analyzes also confirmed specific features already reported for Melan-A and MELOE-1 specific T cell repertoires in terms of V-alpha recurrence usage, on a very high number of T cell clonotypes. Furthermore, these analyses also revealed undescribed features, such as the recurrence of a specific motif in the CDR3α region for MELOE-1 specific T cell repertoire. Finally, the analysis of a large number of T cell clonotypes originating from various patients revealed the existence of public CDR3α and ß clonotypes for Melan-A and MELOE-1 specific T cells. In conclusion, this method of high throughput TCR sequencing is a reliable and powerful approach to deeply characterize polyclonal T cell repertoires, and to reveal specific features of a given TCR repertoire, that would be useful for immune follow-up of cancer patients treated by immunotherapeutic approaches. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
74. Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia
- Author
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Houda Alachkar, Po Hao Feng, Kang Yun Lee, Che Mai Chang, Tsung Hsun Wu, and Wei Chiao Chang
- Subjects
Adult ,Male ,2019-20 coronavirus outbreak ,medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,T-Lymphocytes ,Immunology ,Receptors, Antigen, T-Cell ,chemical and pharmacologic phenomena ,Biology ,Severity of Illness Index ,Medical microbiology ,TCR sequencing ,medicine ,Immunology and Allergy ,Humans ,Mild disease ,Pandemics ,Aged ,T cell repertoire ,SARS-CoV-2 ,T-cell receptor ,COVID-19 ,hemic and immune systems ,Pneumonia ,Sequence Analysis, DNA ,Middle Aged ,medicine.disease ,Virology ,respiratory tract diseases ,TCR repertoire ,Disease Progression ,Original Article ,Female ,T cell receptor - Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. So far, little has been known about differences in the T cell repertoires between COVID-19 patients with and without pneumonia during SARS-CoV-2 infection. Herein, we aimed to investigate T cell receptor (TCR) repertoire profiles and patient-specific SARS-CoV-2-associated TCR clusters between COVID-19 patients with mild disease (no sign of pneumonia) and pneumonia. The TCR sequencing was conducted to characterize the peripheral TCR repertoire profile and diversity. The TCR clustering and CDR3 annotation were exploited to further discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. Our study indicated a slight decrease in the TCR repertoire diversity and a skewed CDR3 length usage in patients with pneumonia compared to those with mild disease. The SARS-CoV-2-associated TCR clusters enriched in patients with mild disease exhibited significantly higher TCR generation probabilities and most of which were highly shared among patients, compared with those from pneumonia patients. Importantly, using similarity network-based clustering followed by the sequence conservation analysis, we found different patterns of CDR3 sequence motifs between mild disease- and pneumonia-specific SARS-CoV-2-associated public TCR clusters. Our results showed that characteristics of overall TCR repertoire and SARS-CoV-2-associated TCR clusters/clonotypes were divergent between COVID-19 patients with mild disease and patients with pneumonia. These findings provide important insights into the correlation between the TCR repertoire and disease severity in COVID-19 patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10875-021-01045-z.
- Published
- 2021
75. Human decidual gamma/delta T cells possess unique effector and TCR repertoire profiles during pregnancy
- Author
-
D. Manchorova, M. Papadopoulou, M. Alexandrova, V. Dimitrova, L. Djerov, S. Zapryanova, P. Dimitrova, I. Vangelov, D. Vermijlen, T. Dimova, and Dimova, Tanya
- Subjects
Cytotoxic molecules ,T-Lymphocytes ,Immunology ,Receptors, Antigen, T-Cell, gamma-delta ,Human pregnancy ,Gamma delta T cells ,Flow Cytometry ,Mice ,Pregnancy ,TCR sequencing ,Decidua ,Humans ,Animals ,Cytokines ,Female - Abstract
Human γδ T cells are enriched at the maternal-fetal interface (MFI, decidua basalis) showing a highly differentiated phenotype. However, their functional potential is not well-known and it is not clear whether this decidua-enrichment is associated with specific γδ T cell receptors (TCR) as is observed in mice. Here we addressed these open questions by investigating decidual γδ T cells during early and late gestation, in comparison with paired blood samples, with flow cytometry (cytotoxic mediators, cytokines) and TCR high-throughput sequencing. While decidual γδ T cells expressed less perforin than their counterparts in the blood, they expressed significant more granulysin during early pregnancy. Strikingly, this high granulysin expression was limited to early pregnancy, as it was reduced at term pregnancy. In contrast to this granulysin expression pattern, decidual γδ T cells produced reduced levels of IFNγ and TNFα (compared to paired blood) in early pregnancy that then increased by term pregnancy. TCR repertoire analysis indicated that human decidual γδ T cells are not generated early in life as in the mouse. Despite this, a specific enrichment of the Vγ2 chain in the decidua in early pregnancy was observed that disappeared later onwards, reflecting dynamic changes in the decidual γδ TCR repertoire during human gestation. In conclusion, our data indicate that decidual γδ T cells express a specific and dynamic pattern of cytotoxic mediators, Th1 cytokines and TCR repertoire suggesting an important role for these unconventional T cells in assuring a healthy pregnancy in human.
- Published
- 2022
76. TCR-sequencing in cancer and autoimmunity: barcodes and beyond
- Author
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Kristen E. Pauken, Kaitlyn A. Lagattuta, Benjamin Y. Lu, Liliana E. Lucca, Adil I. Daud, David A. Hafler, Harriet M. Kluger, Soumya Raychaudhuri, and Arlene H. Sharpe
- Subjects
T-Lymphocytes ,PD-1 immunotherapy ,Inflammatory and immune system ,Immunology ,Receptors, Antigen, T-Cell ,T cell ,Autoimmunity ,T-Cell ,Article ,single cell sequencing ,Neoplasms ,Antigen ,TCR sequencing ,Receptors ,Genetics ,Immunology and Allergy ,Humans ,cancer ,Generic health relevance ,molecular barcode - Abstract
The T cell receptor (TCR) endows T cells with antigen specificity and is central to nearly all aspects of T cell function. Each naïve T cell has a unique TCR sequence that is stably maintained during cell division. In this way, the TCR serves as a molecular barcode that tracks processes such as migration, differentiation, and proliferation of T cells. Recent technological advances have enabled sequencing of the TCR from single cells alongside deep molecular phenotypes on an unprecedented scale. In this review, we discuss strengths and limitations of TCR sequences as molecular barcodes and their application to study immune responses following Programmed Death-1 (PD-1) blockade in cancer. Additionally, we consider applications of TCR data beyond use as a barcode.
- Published
- 2022
77. A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications.
- Author
-
Palianina D, Di Roberto RB, Castellanos-Rueda R, Schlatter F, Reddy ST, and Khanna N
- Abstract
Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track them in vivo . While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells. Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against Epstein-Barr virus-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This approach has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
78. A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires
- Author
-
Paul Ogongo, Anne-Laure Flamar, Jung Hwa Kirschman, Heather L. Mead, Jean-Philippe Blanck, Joel D. Ernst, Sandra Zurawski, Caroline E. Harms, Annalee S. Boyle, Erin Kelley, John A. Altin, Gerard Zurawski, Yves Levy, and Valentina Ceglia
- Subjects
medicine.drug_class ,T cell ,medicine.medical_treatment ,T-Lymphocytes ,Immunology ,Receptors, Antigen, T-Cell ,Computational biology ,Cell Separation ,Biology ,Monoclonal antibody ,Epitope ,Deep sequencing ,Vaccine Related ,Antigen ,TCR sequencing ,Receptors ,medicine ,Humans ,Immunology and Allergy ,T cell receptor (TCR) ,dendritic cells ,Original Research ,Prevention ,Repertoire ,T-cell receptor ,Immunotherapy ,vaccines ,RC581-607 ,T-Cell ,Good Health and Well Being ,medicine.anatomical_structure ,Medical Microbiology ,T cell responses ,Immunologic Techniques ,Immunization ,monoclonal antibodies ,T cell receptor ,Immunologic diseases. Allergy - Abstract
Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire provides a global view that is limited only in terms of theoretical sensitivity due to the depth of available sampling; however, the assignment of antigen specificities within TCR repertoires has become a bottleneck. This study combines antigen-driven expansion, deep TCR sequencing, and a novel analysis framework to show that homologous ‘Clusters of Expanded TCRs (CETs)’ can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse uncultured repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.
- Published
- 2021
79. Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform
- Author
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Ulrike Gerdemann, Ryan A. Fleming, James Kaminski, Connor McGuckin, Xianliang Rui, Jennifer F. Lane, Paula Keskula, Lorenzo Cagnin, Alex K. Shalek, Victor Tkachev, and Leslie S. Kean
- Subjects
alloreactive T cells ,Gene Expression Profiling ,Immunology ,GVHD ,Receptors, Antigen, T-Cell ,High-Throughput Nucleotide Sequencing ,chemical and pharmacologic phenomena ,RC581-607 ,Lymphocyte Activation ,Macaca mulatta ,single cell sequencing ,Rhesus Macaque (Macaca mulatta) ,Gene Expression Regulation ,Cell Tracking ,T-Lymphocyte Subsets ,TCR sequencing ,Immunology and Allergy ,Animals ,Immunologic diseases. Allergy ,Lymphocyte Culture Test, Mixed ,Transcriptome - Abstract
T cell receptor clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell’s transcriptional program with its T cell receptor (TCR) identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques, a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, ‘RM-scTCR-Seq’, which, for the first time, enables RM specific single cell TCR amplification, reconstitution and pairing of RM TCR’s with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.
- Published
- 2021
80. Exercise mobilizes diverse antigen specific T-cells and elevates neutralizing antibodies in humans with natural immunity to SARS CoV-2.
- Author
-
Baker FL, Zúñiga TM, Smith KA, Batatinha H, Kulangara TS, Seckeler MD, Burgess SC, Katsanis E, and Simpson RJ
- Abstract
Epidemiological data suggest that physical activity protects against severe COVID-19 and improves clinical outcomes, but how exercise augments the SARS-CoV-2 viral immune response has yet to be elucidated. Here we determine the antigen-specific CD4 and CD8 T-cell and humoral immunity to exercise in non-vaccinated individuals with natural immunity to SARS CoV-2, using whole-blood SARS-CoV-2 peptide stimulation assays, IFN-γ ELISPOT assays, 8-color flow cytometry, deep T-cell receptor (TCR) β sequencing, and anti-RBD-1 neutralizing antibody serology. We found that acute exercise reliably mobilized (∼2.5-fold increase) highly functional SARS-CoV-2-specific T-cells to the blood compartment in those with natural immunity to the virus. The mobilized cells reacted with spike protein (including alpha (α) and delta (δ)-variants), membrane, and nucleocapsid peptides in those previously infected but not in controls. Both groups reliably mobilized T-cells reacting with Epstein-Barr viral peptides. Exercise mobilized SARS-CoV-2 specific T-cells maintained broad TCR-β diversity with no impact on CDR3 length or V and J family gene usage. Exercise predominantly mobilized MHC I restricted (i.e. CD8
+ ) SARS-CoV-2 specific T-cells that recognized ORF1ab, surface, ORF7b, nucleocapsid, and membrane proteins. SARS-CoV-2 neutralizing antibodies were transiently elevated ∼1.5-fold during exercise after infection. In conclusion, we provide novel data on a potential mechanism by which exercise could increase SARS-CoV-2 immunosurveillance via the mobilization and redistribution of antigen-specific CD8 T-cells and neutralizing antibodies. Further research is needed to define the tissue specific disease protective effects of exercise as SARS-CoV-2 continues to evolve, as well as the impact of COVID-19 vaccination on this response., Competing Interests: All authors have no conflicts of interest to disclose., (© 2023 The Authors.)- Published
- 2023
- Full Text
- View/download PDF
81. Pipeline to characterize antigen-specific TCR repertoires in tumors: Examples from an HPV16 tumor model.
- Author
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Rudqvist NP
- Subjects
- Mice, Animals, Receptors, Antigen, T-Cell genetics, Receptors, Antigen, T-Cell metabolism, T-Lymphocytes metabolism, Tumor Microenvironment, Human papillomavirus 16 metabolism, Neoplasms metabolism
- Abstract
Immunotherapies that improve T cell-based anti-tumor immunity have revolutionized cancer. However, the underlying mechanisms of cancer immune responsiveness are still not fully understood. Using immune competent mice for preclinical development of novel mono and combination therapies is a common strategy, and to monitor the T cell response inside tumors and in the periphery offers valuable insight. T cells recognize target cells by based on the binding between the T cell receptor (on T cells) and peptides presented on MHC-I (on tumor cells). As such, the T cell receptor can be used as a "barcode" for a specific T cell clone. Via TCR sequencing, the sequence of this "barcode" can be identified, and eventually, the TCR repertoire in a sample can be assessed as a whole. This information can be useful in multiple ways, including but not excluded to: (i) tracing specific clones in tissues and in blood, and (ii) determine clonal expansion of a specific clone in the tumor microenvironment which suggest anti-tumor activity of the clone in question. This protocol can be used as a guide from experimental design through TCR-sequencing to analysis of the repertoire. Instead of being specifically focused on one type of TCR-sequencing, this protocol can be used as a resource and contains links and references to useful information that has to be considered. Lastly, certain common metrics when analyzing the TCR repertoire are given and discussed., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
82. Human decidual gamma/delta T cells possess unique effector and TCR repertoire profiles during pregnancy.
- Author
-
Manchorova, D., Papadopoulou, M., Alexandrova, M., Dimitrova, V., Djerov, L., Zapryanova, S., Dimitrova, P., Vangelov, I., Vermijlen, D., and Dimova, T.
- Subjects
- *
T cells , *T cell receptors , *PREGNANCY , *NUCLEOTIDE sequencing - Abstract
[Display omitted] • Decidual γδT cells during human early pregnancy showed: • high cytotoxic potential despite low perforin expression. • low production of Th1 cytokines IFNγ and TNFα. • private CDR3 repertoire and enriched for TRGV2/TRDV1 segments. Human γδ T cells are enriched at the maternal-fetal interface (MFI, decidua basalis) showing a highly differentiated phenotype. However, their functional potential is not well-known and it is not clear whether this decidua-enrichment is associated with specific γδ T cell receptors (TCR) as is observed in mice. Here we addressed these open questions by investigating decidual γδ T cells during early and late gestation, in comparison with paired blood samples, with flow cytometry (cytotoxic mediators, cytokines) and TCR high-throughput sequencing. While decidual γδ T cells expressed less perforin than their counterparts in the blood, they expressed significant more granulysin during early pregnancy. Strikingly, this high granulysin expression was limited to early pregnancy, as it was reduced at term pregnancy. In contrast to this granulysin expression pattern, decidual γδ T cells produced reduced levels of IFNγ and TNFα (compared to paired blood) in early pregnancy that then increased by term pregnancy. TCR repertoire analysis indicated that human decidual γδ T cells are not generated early in life as in the mouse. Despite this, a specific enrichment of the Vγ2 chain in the decidua in early pregnancy was observed that disappeared later onwards, reflecting dynamic changes in the decidual γδ TCR repertoire during human gestation. In conclusion, our data indicate that decidual γδ T cells express a specific and dynamic pattern of cytotoxic mediators, Th1 cytokines and TCR repertoire suggesting an important role for these unconventional T cells in assuring a healthy pregnancy in human. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
83. Corrigendum: Systematic pattern analyses of Vδ2 + TCRs reveal that shared "public" Vδ2 + γδ T cell clones are a consequence of rearrangement bias and a higher expansion status.
- Author
-
Deng L, Harms A, Ravens S, Prinz I, and Tan L
- Abstract
[This corrects the article DOI: 10.3389/fimmu.2022.960920.]., (Copyright © 2022 Deng, Harms, Ravens, Prinz and Tan.)
- Published
- 2022
- Full Text
- View/download PDF
84. The CSF in neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells.
- Author
-
Paley, Michael A., Baker, Brandi J., Dunham, S. Richard, Linskey, Nicole, Cantoni, Claudia, Lee, Kenneth, Hassman, Lynn M., Laurent, Jennifer, Roberson, Elisha D.O., Clifford, David B., and Yokoyama, Wayne M.
- Subjects
- *
T cells , *B cell receptors , *CD8 antigen , *T cell receptors , *CD4 antigen - Abstract
The tissue-specific drivers of neurosarcoidosis remain poorly defined. To identify cerebrospinal fluid (CSF) specific, antigen-driven T and B cell responses, we performed single-cell RNA sequencing of CSF and blood cells from neurosarcoid participants coupled to T and B cell receptor sequencing. In contrast to pulmonary sarcoidosis, which is driven by CD4 T cells, we found CD8 T cell clonal expansion enriched in the neurosarcoid CSF. These CSF-enriched CD8 T cells were composed of two subsets with differential expression of EBI2, CXCR3, and CXCR4. Lastly, our data suggest that IFNγ signaling may distinguish neurosarcoidosis from other neurological disorders. [Display omitted] • The CSF from neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells. • CSF-enriched CD8 T cell clones express CD27, EBI2, and Granzyme K in both the CSF and the blood. • An interferon signature marks CSF CD8 T cells in neurosarcoidosis. • Elevated CSF levels of IFNγ distinguish active neurosarcoidosis from other CNS disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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85. Profiling virus-specific Tcf1+ T cell repertoires during acute and chronic viral infection
- Author
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Nathalie Oetiker, Ioana Sandu, Katharina Pallmer, Alessandro Pedrioli, Annette Oxenius, Mariana Borsa, Suzanne P. M. Welten, Sai T. Reddy, Alexander Yermanos, and Franziska Wagen
- Subjects
Time Factors ,T cell ,viruses ,Immunology ,Population ,Receptors, Antigen, T-Cell ,chemical and pharmacologic phenomena ,CD8-Positive T-Lymphocytes ,Biology ,Lymphocytic choriomeningitis ,Virus ,deep sequencing ,TCR sequencing ,medicine ,Animals ,Arenaviridae Infections ,Lymphocytic choriomeningitis virus ,Cytotoxic T cell ,Hepatocyte Nuclear Factor 1-alpha ,TCF1 ,adaptive immune receptor repertoire sequencing ,education ,Original Research ,Mice, Knockout ,education.field_of_study ,viral infection ,Gene Expression Profiling ,Repertoire ,T-cell receptor ,medicine.disease ,Virology ,Disease Models, Animal ,Phenotype ,medicine.anatomical_structure ,Acute Disease ,Chronic Disease ,Monoclonal ,Female ,Transcriptome - Abstract
CD8 T cells play a crucial role in providing protection from viral infections. It has recently been established that a subset of CD8 T cells expressing Tcf1 are responsible for sustaining exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. Many of these studies, however, have been performed using T cell receptor (TCR) transgenic mice, in which CD8 T cells express a monoclonal TCR specific for the LCMV glycoprotein. To investigate whether the Tcf1+ and Tcf1- repertoires are naturally composed of similar or different clones in wild-type mice exposed to acute or chronic LCMV infection, we performed TCR repertoire sequencing of virus-specific CD8 T cells, including Tcf1+ and Tcf1- populations. Our analysis revealed that the Tcf1+ TCR repertoire is maintained at an equal or higher degree of clonal diversity despite harboring fewer cells. Additionally, within the same animal, there was extensive clonal overlap between the Tcf1+ and Tcf1- repertoires in both chronic and acute LCMV infection. We could further detect these virus-specific clones in longitudinal blood samples earlier in the infection. With respect to common repertoire parameters (clonal overlap, germline gene usage, and clonal expansion), we found minor differences between the virus-specific TCR repertoire of acute and chronic LCMV infection 40 days post infection. Overall, our results indicate that the Tcf1+ population emerging during chronic LCMV infection is not clonally distinct from the Tcf1- population, supporting the notion that the Tcf1+ pool is indeed a fuel for the more exhausted Tcf1– population within the heterogenous repertoire of LCMV-specific CD8 T cells., Frontiers in Immunology, 11, ISSN:1664-3224
- Published
- 2020
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86. Systematic pattern analyses of Vδ2 + TCRs reveal that shared "public" Vδ2 + γδ T cell clones are a consequence of rearrangement bias and a higher expansion status.
- Author
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Deng L, Harms A, Ravens S, Prinz I, and Tan L
- Subjects
- Adult, Infant, Infant, Newborn, Humans, T-Lymphocyte Subsets, Clone Cells, Thymus Gland, Receptors, Antigen, T-Cell, gamma-delta genetics, Intraepithelial Lymphocytes
- Abstract
Background: Vγ9Vδ2
+ T cells are a major innate T cell subset in human peripheral blood. Their Vδ2+ VDJ-rearrangements are short and simple in the fetal thymus and gradually increase in diversity and CDR3 length along with development. So-called "public" versions of Vδ2+ TCRs are shared among individuals of all ages. However, it is unclear whether such frequently occurring "public" Vγ9Vδ2+ T cell clones are derived from the fetal thymus and whether they are fitter to proliferate and persist than infrequent "private" clones., Methods: Shared "public" Vδ2+ TCRs were identified from Vδ2+ TCR-repertoires collected from 89 individuals, including newborns (cord blood), infants, and adults (peripheral blood). Distance matrices of Vδ2+ CDR3 were generated by TCRdist3 and then embedded into a UMAP for visualizing the heterogeneity of Vδ2+ TCRs., Results: Vδ2+ CDR3 distance matrix embedded by UMAP revealed that the heterogeneity of Vδ2+ TCRs is primarily determined by the J-usage and CDR3aa length, while age or publicity-specific motifs were not found. The most prevalent public Vδ2+ TCRs showed germline-like rearrangement with low N-insertions. Age-related features were also identified. Public Vδ2+ TRDJ1 TCRs from cord blood showed higher N-insertions and longer CDR3 lengths. Synonymous codons resulting from VDJ rearrangement also contribute to the generation of public Vδ2+ TCRs. Each public TCR was always produced by multiple different transcripts, even with different D gene usage, and the publicity of Vδ2+ TCRs was positively associated with expansion status., Conclusion: To conclude, the heterogeneity of Vδ2+ TCRs is mainly determined by TRDJ -usage and the length of CDR3aa sequences. Public Vδ2+ TCRs result from germline-like rearrangement and synonymous codons, associated with a higher expansion status., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Deng, Harms, Ravens, Prinz and Tan.)- Published
- 2022
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87. Commensal Cryptosporidium colonization elicits a cDC1-dependent Th1 response that promotes intestinal homeostasis and limits other infections.
- Author
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Russler-Germain, Emilie V., Jung, Jisun, Miller, Aidan T., Young, Shannon, Yi, Jaeu, Wehmeier, Alec, Fox, Lindsey E., Monte, Kristen J., Chai, Jiani N., Kulkarni, Devesha H., Funkhouser-Jones, Lisa J., Wilke, Georgia, Durai, Vivek, Zinselmeyer, Bernd H., Czepielewski, Rafael S., Greco, Suellen, Murphy, Kenneth M., Newberry, Rodney D., Sibley, L. David, and Hsieh, Chyi-Song
- Subjects
- *
CRYPTOSPORIDIUM , *REGULATORY T cells , *INTESTINES , *HOMEOSTASIS , *LARGE intestine , *CRYPTOSPORIDIOSIS - Abstract
Cryptosporidium can cause severe diarrhea and morbidity, but many infections are asymptomatic. Here, we studied the immune response to a commensal strain of Cryptosporidium tyzzeri (Ct -STL) serendipitously discovered when conventional type 1 dendritic cell (cDC1)-deficient mice developed cryptosporidiosis. Ct -STL was vertically transmitted without negative health effects in wild-type mice. Yet, Ct -STL provoked profound changes in the intestinal immune system, including induction of an IFN-γ-producing Th1 response. TCR sequencing coupled with in vitro and in vivo analysis of common Th1 TCRs revealed that Ct -STL elicited a dominant antigen-specific Th1 response. In contrast, deficiency in cDC1s skewed the Ct -STL CD4 T cell response toward Th17 and regulatory T cells. Although Ct -STL predominantly colonized the small intestine, colon Th1 responses were enhanced and associated with protection against Citrobacter rodentium infection and exacerbation of dextran sodium sulfate and anti-IL10R-triggered colitis. Thus, Ct -STL represents a commensal pathobiont that elicits Th1-mediated intestinal homeostasis that may reflect asymptomatic human Cryptosporidium infection. [Display omitted] • Cryptosporidium tyzzeri in our colony (Ct -STL) is a commensal pathobiont • Ct -STL elicits a dominant antigen-specific Th1 response • cDC1s are required for efficient Th1 induction and blockade of Th17/Treg generation • Ct -STL markedly affects the immune system of both the small and large intestine Cryptosporidium are protozoan parasites that cause gastrointestinal illness in humans and animals worldwide. We identified a commensal strain of Cryptosporidium tyzzeri endemic in our mouse colony. This strain of Cryptosporidium does not cause disease in wild-type mice but changes the composition and function of the intestinal immune system. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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88. Acute exercise increases immune responses to SARS CoV-2 in a previously infected man.
- Author
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Baker FL, Smith KA, Zúñiga TM, Batatinha H, Niemiro GM, Pedlar CR, Burgess SC, Katsanis E, and Simpson RJ
- Abstract
Evidence is emerging that exercise and physical activity provides protection against severe COVID-19 disease in patients infected with SARS-CoV-2, but it is not known how exercise affects immune responses to the virus. A healthy man completed a graded cycling ergometer test prior to and after SARS-CoV-2 infection, then again after receiving an adenovirus vector-based COVID-19 vaccine. Using whole blood SARS-CoV-2 peptide stimulation assays, IFN-γ ELISPOT assays, flow cytometry, ex vivo viral-specific T-cell expansion assays and deep T-cell receptor (TCR) β sequencing, we found that exercise robustly mobilized highly functional SARS-CoV-2 specific T-cells to the blood compartment that recognized spike protein, membrane protein, nucleocapsid antigen and the B.1.1.7 α-variant, and consisted mostly of CD3+/CD8+ T-cells and double-negative (CD4-/CD8-) CD3
+ T-cells. The magnitude of SARS-CoV-2 T-cell mobilization with exercise was intensity dependent and robust when compared to T-cells recognizing other viruses (e.g. CMV, EBV, influenza). Vaccination enhanced the number of exercise-mobilized SARS-CoV-2 T-cells recognizing spike protein and the α-variant only. Exercise-mobilized SARS-CoV-2 specific T-cells proliferated more vigorously to ex vivo peptide stimulation and maintained broad TCR-β diversity against SARS-CoV-2 antigens both before and after ex vivo expansion. Neutralizing antibodies to SARS-CoV-2 were transiently elevated during exercise after both infection and vaccination. Finally, infection was associated with an increased metabolic demand to defined exercise workloads, which was restored to pre-infection levels after vaccination. This case study provides impetus for larger studies to determine if these immune responses to exercise can facilitate viral clearance, ameliorate symptoms of long COVID syndrome, and/or restore functional exercise capacity following SARS-CoV-2 infection., Competing Interests: We have no conflicting interests to declare., (© 2021 Published by Elsevier Inc.)- Published
- 2021
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89. A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires.
- Author
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Ceglia V, Kelley EJ, Boyle AS, Zurawski S, Mead HL, Harms CE, Blanck JP, Flamar AL, Kirschman JH, Ogongo P, Ernst JD, Levy Y, Zurawski G, and Altin JA
- Subjects
- Humans, Cell Separation methods, Immunologic Techniques methods, Receptors, Antigen, T-Cell analysis, Receptors, Antigen, T-Cell immunology, T-Lymphocytes immunology
- Abstract
Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire provides a global view that is limited only in terms of theoretical sensitivity due to the depth of available sampling; however, the assignment of antigen specificities within TCR repertoires has become a bottleneck. This study combines antigen-driven expansion, deep TCR sequencing, and a novel analysis framework to show that homologous 'Clusters of Expanded TCRs (CETs)' can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse uncultured repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity., Competing Interests: VC, SZ, YL, and GZ are inventors on patent application WO2020193718. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ceglia, Kelley, Boyle, Zurawski, Mead, Harms, Blanck, Flamar, Kirschman, Ogongo, Ernst, Levy, Zurawski and Altin.)
- Published
- 2021
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90. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.
- Author
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Krishna, Chirag, DiNatale, Renzo G., Kuo, Fengshen, Srivastava, Raghvendra M., Vuong, Lynda, Chowell, Diego, Gupta, Sounak, Vanderbilt, Chad, Purohit, Tanaya A., Liu, Ming, Kansler, Emily, Nixon, Briana G., Chen, Ying-Bei, Makarov, Vladimir, Blum, Kyle A., Attalla, Kyrollis, Weng, Stanley, Salmans, Michael L., Golkaram, Mahdi, and Liu, Li
- Subjects
- *
T cell differentiation , *T cell receptors , *RENAL cell carcinoma - Abstract
Clear cell renal cell carcinomas (ccRCCs) are highly immune infiltrated, but the effect of immune heterogeneity on clinical outcome in ccRCC has not been fully characterized. Here we perform paired single-cell RNA (scRNA) and T cell receptor (TCR) sequencing of 167,283 cells from multiple tumor regions, lymph node, normal kidney, and peripheral blood of two immune checkpoint blockade (ICB)-naïve and four ICB-treated patients to map the ccRCC immune landscape. We detect extensive heterogeneity within and between patients, with enrichment of CD8A + tissue-resident T cells in a patient responsive to ICB and tumor-associated macrophages (TAMs) in a resistant patient. A TCR trajectory framework suggests distinct T cell differentiation pathways between patients responding and resistant to ICB. Finally, scRNA-derived signatures of tissue-resident T cells and TAMs are associated with response to ICB and targeted therapies across multiple independent cohorts. Our study establishes a multimodal interrogation of the cellular programs underlying therapeutic efficacy in ccRCC. [Display omitted] • Single-cell RNA-seq reveals the architecture of the ccRCC immune microenvironment • Multiregional immune phenotypes integrated with bulk RNA-seq and tumor pathology • TCR usage varies by phenotype and defines T cell differentiation trajectories • Signatures of tissue-resident T cells and TAMs predict clinical outcome Krishna et al. dissect the immune microenvironment and TCR clonotype dynamics in multiregional clear cell renal cell carcinoma (ccRCC) samples at single-cell resolution. They show that CD8+ tissue-resident T cells and distinct tumor-associated macrophage (TAM) populations are associated with response and resistance to immune checkpoint blockade (ICB) in ccRCC. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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- View/download PDF
91. Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors
- Author
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H. Kim Lyerly, Gangjun Lei, Zachary C. Hartman, Michael A. Morse, Xiao Yi Yang, Pankaj K. Agarwal, Alan J. Korman, Kenneth Gouin, Cong-Xiao Liu, Tao Wang, Simon R.V. Knott, Erika J. Crosby, and Junping Wei
- Subjects
lcsh:Immunologic diseases. Allergy ,0301 basic medicine ,T cell ,Immunology ,chemical and pharmacologic phenomena ,immunomodulation ,lcsh:RC254-282 ,03 medical and health sciences ,0302 clinical medicine ,Breast cancer ,breast cancer ,TCR sequencing ,medicine ,Immunology and Allergy ,Triple-negative breast cancer ,Original Research ,biology ,business.industry ,Tumor-infiltrating lymphocytes ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.disease ,Immune checkpoint ,3. Good health ,Blockade ,Clinical trial ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,tumor antigens ,030220 oncology & carcinogenesis ,immune responses to cancer ,biology.protein ,Cancer research ,triple-negative breast cancer ,checkpoint blockade ,Antibody ,lcsh:RC581-607 ,business - Abstract
Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of
- Published
- 2018
92. SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors.
- Author
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Shomuradova, Alina S., Vagida, Murad S., Sheetikov, Savely A., Zornikova, Ksenia V., Kiryukhin, Dmitry, Titov, Aleksei, Peshkova, Iuliia O., Khmelevskaya, Alexandra, Dianov, Dmitry V., Malasheva, Maria, Shmelev, Anton, Serdyuk, Yana, Bagaev, Dmitry V., Pivnyuk, Anastasia, Shcherbinin, Dmitrii S., Maleeva, Alexandra V., Shakirova, Naina T., Pilunov, Artem, Malko, Dmitry B., and Khamaganova, Ekaterina G.
- Subjects
- *
T cell receptors , *SARS-CoV-2 , *COVID-19 pandemic , *EPITOPES , *T cells - Abstract
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion or activation of preexisting immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike protein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity. • Healthy donors sampled in 2020 had an increased T cell response to SARS-CoV-2 • SARS-CoV-2 glycoprotein S-specific TCR repertoire features public CDR3 motifs • Two epitopes are recognized by the majority of the HLA-A2+ COVID-19 convalescents Shomuradova et al. assessed the immune response to SARS-CoV-2 in convalescent patients and healthy donors. Antigen-specific T cells were increased in convalescents and in donors sampled during the pandemic. The work identified two public epitopes from S-glycoprotein. T cell receptor repertoire profiling of S-glycoprotein-specific lymphocytes revealed public CDR3 motifs. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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93. Detecting Tumor Antigen-Specific T Cells via Interaction-Dependent Fucosyl-Biotinylation.
- Author
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Liu, Zilei, Li, Jie P., Chen, Mingkuan, Wu, Mengyao, Shi, Yujie, Li, Wei, Teijaro, John R., and Wu, Peng
- Subjects
- *
T cell receptors , *CYTOLOGY - Abstract
Re-activation and clonal expansion of tumor-specific antigen (TSA)-reactive T cells are critical to the success of checkpoint blockade and adoptive transfer of tumor-infiltrating lymphocyte (TIL)-based therapies. There are no reliable markers to specifically identify the repertoire of TSA-reactive T cells due to their heterogeneous composition. We introduce FucoID as a general platform to detect endogenous antigen-specific T cells for studying their biology. Through this interaction-dependent labeling approach, intratumoral TSA-reactive CD4+, CD8+ T cells, and TSA-suppressive CD4+ T cells can be detected and separated from bystander T cells based on their cell-surface enzymatic fucosyl-biotinylation. Compared to bystander TILs, TSA-reactive TILs possess a distinct T cell receptor (TCR) repertoire and unique gene features. Although exhibiting a dysfunctional phenotype, TSA-reactive CD8+ TILs possess substantial capabilities of proliferation and tumor-specific killing. Featuring genetic manipulation-free procedures and a quick turnover cycle, FucoID should have the potential of accelerating the pace of personalized cancer treatment. • Fucosyl-biotinylation enables the detection of endogenous tumor antigen-specific T cells • Dysfunctional tumor antigen-specific CD8+ T cells upregulate steroid biosynthesis genes • Tumor antigen-suppressive and reactive CD4+ T cells co-exist in tumor microenvironments • Intratumoral bystander T cells are separated into two groups based on PD-1 expression FucoID enables identification of endogenous tumor antigen-specific T cells based on an interaction-dependent fucosyl-biotinylation. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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- View/download PDF
94. Blocking CTLA-4 while priming with a whole cell vaccine reshapes the oligoclonal T cell infiltrate and eradicates tumors in an orthotopic glioma model
- Author
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Ian F. Hermans, Peter M. Ferguson, Martin K. Hunn, Christiane Ruedl, Cameron S. Field, Lindsay R. Ancelet, and School of Biological Sciences
- Subjects
lcsh:Immunologic diseases. Allergy ,0301 basic medicine ,tcr sequencing ,T cell ,Immunology ,Priming (immunology) ,lcsh:RC254-282 ,Checkpoint Blockade ,03 medical and health sciences ,vaccine ,glioma ,Glioma ,Blocking antibody ,medicine ,Immunology and Allergy ,Original Research ,biology ,business.industry ,anti-ctla-4 ,Biological sciences [Science] ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.disease ,Immune checkpoint ,Blockade ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,CTLA-4 ,biology.protein ,checkpoint blockade ,Antibody ,lcsh:RC581-607 ,business ,Vaccine - Abstract
Vaccine-mediated cancer treatment is unlikely to induce long-term survival unless suppressive mechanisms are overcome. Given the success of antibody-mediated immune checkpoint blockade in relieving regulation of endogenous anti-tumor T cell responses in tumor-burdened hosts, we investigated whether checkpoint blockade could improve the efficacy of responses induced with a whole tumor-cell vaccine. We show that administration of a single dose of blocking antibody was sufficient to significantly enhance antitumor activity of the vaccine, inducing complete radiological regression of established intracranial tumors. The antibody or vaccine alone were ineffective in this setting. The antibody had to be administered before, or close to, vaccine administration, suggesting CTLA-4 blockade had an impact on early priming events. The combined treatment resulted in enhanced trapping of leukocytes in the lymphoid tissues, including T cells that had undergone significant proliferation. There were no obvious changes in the stimulatory function of antigen-presenting cells or the number and function of regulatory T cells, suggesting T cells were the targets of the checkpoint blockade. While tumors regressing under combined treatment were highly infiltrated with a variety of leukocytes, tumor eradication was dependent on CD4+ T cells. Analysis of the TCR repertoire showed that the addition of anti-CTLA-4 at priming reshaped the repertoire of tumor infiltrating T cells. In particular, the oligoclonal populations became greater in magnitude and more diverse in specificity. Using anti-CTLA-4 in a restricted way to promote the priming phase of an anti-cancer vaccine may offer a useful way of harnessing clinical benefit from this powerful agent.
- Published
- 2017
95. UM171-Expanded Cord Blood Transplants Support Robust T Cell Reconstitution with Low Rates of Severe Infections.
- Author
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Dumont-Lagacé M, Li Q, Tanguay M, Chagraoui J, Kientega T, Cardin GB, Brasey A, Trofimov A, Carli C, Ahmad I, Bambace NM, Bernard L, Kiss TL, Roy J, Roy DC, Lemieux S, Perreault C, Rodier F, Dufresne SF, Busque L, Lachance S, Sauvageau G, Cohen S, and Delisle JS
- Subjects
- Fetal Blood, Humans, Retrospective Studies, T-Lymphocytes, Cord Blood Stem Cell Transplantation adverse effects, Graft vs Host Disease
- Abstract
Rapid T cell reconstitution following hematopoietic stem cell transplantation (HSCT) is essential for protection against infections and has been associated with lower incidence of chronic graft-versus-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 (www.clinicaltrials.gov, NCT02668315). We assessed T cell reconstitution in patients who underwent transplantation with UM171-expanded CB grafts and retrospectively compared it to that of patients receiving unmanipulated CB transplants. While median T cell dose infused was at least 2 to 3 times lower than that of unmanipulated CB, numbers and phenotype of T cells at 3, 6, and 12 months post-transplant were similar between the 2 cohorts. T cell receptor sequencing analyses revealed that UM171 patients had greater T cell diversity and higher numbers of clonotypes at 12 months post-transplant. This was associated with higher counts of naive T cells and recent thymic emigrants, suggesting active thymopoiesis and correlating with the demonstration that UM171 expands common lymphoid progenitors in vitro. UM171 patients also showed rapid virus-specific T cell reactivity and significantly reduced incidence of severe infections. These results suggest that UM171 patients benefit from rapid T cell reconstitution, which likely contributes to the absence of moderate/severe cGVHD, infection-related mortality, and late TRM observed in this cohort., (Copyright © 2020 American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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- View/download PDF
96. T cell receptor sequencing in autoimmunity.
- Author
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Mitchell AM and Michels AW
- Abstract
T cells are an integral component of the adaptive immune response via the recognition of peptides by the cell surface-expressed T cell receptor (TCR). Rearrangement of the TCR genes results in a highly polymorphic repertoire on the T cells within a given individual. Although the diverse repertoire is beneficial for immune responses to foreign pathogens, recognition of self-peptides by T cells can contribute to the development of autoimmune disorders. Increasing evidence supports a pathogenic role for T cells in autoimmune pathology, and it is of interest to determine the TCR repertoires involved in autoimmune disease development. In this review, we summarize methodologies and advancements in the TCR sequencing field and discuss recent studies focused on TCR sequencing in a variety of autoimmune conditions. The rapidly evolving methodology of TCR sequencing has the potential to allow for a better understanding of autoimmune disease pathogenesis, identify disease-specific biomarkers, and aid in developing therapies to prevent and treat a number of these disorders.
- Published
- 2020
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97. Analysis of TCR β CDR3 sequencing data for tracking anti-tumor immunity.
- Author
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Zhang J, Ji Z, and Smith KN
- Subjects
- Adaptive Immunity genetics, Antigens, Neoplasm genetics, Antigens, Neoplasm immunology, Computational Biology methods, Epitopes, T-Lymphocyte genetics, Epitopes, T-Lymphocyte immunology, High-Throughput Nucleotide Sequencing instrumentation, Humans, Neoplasms genetics, Neoplasms pathology, Receptors, Antigen, T-Cell immunology, Receptors, Antigen, T-Cell metabolism, Sequence Analysis, DNA instrumentation, Sequence Analysis, DNA methods, Sequence Analysis, RNA instrumentation, Sequence Analysis, RNA methods, T-Lymphocytes metabolism, High-Throughput Nucleotide Sequencing methods, Neoplasms immunology, Receptors, Antigen, T-Cell genetics, T-Lymphocytes immunology
- Abstract
Anti-tumor T cells are the soldiers in the body's war against cancer. Effector T cells can detect and eliminate cells expressing their cognate antigen via activation through engagement of the T cell receptor (TCR) with its cognate peptide:MHC complex. Owing to the recent success of immunotherapy in the treatment of many different cancer types, research efforts have shifted toward identifying and tracking anti-tumor T cell responses upon treatment in cancer patients. While traditional methods, such as ELISpot and flow cytometric intracellular staining have had limited success, likely owing to the inability to get viable biospecimens or the lower magnitude of tumor-specific T cell responses relative to virus-specific responses, new techniques that utilize next generation sequencing enable T cell response tracking independent of cytokine production or cell viability. The TCR, which confers T cell antigen-specificity, can be used as a molecular barcode to track T cell clonotypic dynamics across biological compartments and over time in cancer patients undergoing treatment. Because this method does not require viable cells, these T cell clonotypes can also be tracked in archival tumor tissue and flash frozen cell pellets. While exciting, quantitative TCR sequencing (TCRseq) technologies have been met with the conundrum of how to properly analyze and interpret the data. Here we provide a comprehensive guide on how to acquire, analyze, and interpret TCRseq data, as well as special considerations that should be taken prior to experimental setup., (© 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
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- View/download PDF
98. Complimentary mechanisms of dual checkpoint blockade expand unique T-cell repertoires and activate adaptive anti-tumor immunity in triple-negative breast tumors.
- Author
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Crosby, Erika J., Wei, Junping, Yang, Xiao Yi, Lei, Gangjun, Wang, Tao, Liu, Cong-Xiao, Agarwal, Pankaj, Korman, Alan J., Morse, Michael A., Gouin, Kenneth, Knott, Simon R. V., Lyerly, H. Kim, and Hartman, Zachary C.
- Subjects
- *
T cells , *TRIPLE-negative breast cancer - Abstract
Triple-negative breast cancer (TNBC) is an aggressive and molecularly diverse breast cancer subtype typified by the presence of p53 mutations (∼80%), elevated immune gene signatures and neoantigen expression, as well as the presence of tumor infiltrating lymphocytes (TILs). As these factors are hypothesized to be strong immunologic prerequisites for the use of immune checkpoint blockade (ICB) antibodies, multiple clinical trials testing single ICBs have advanced to Phase III, with early indications of heterogeneous response rates of <20% to anti-PD1 and anti-PDL1 ICB. While promising, these modest response rates highlight the need for mechanistic studies to understand how different ICBs function, how their combination impacts functionality and efficacy, as well as what immunologic parameters predict efficacy to different ICBs regimens in TNBC. To address these issues, we tested anti-PD1 and anti-CTLA4 in multiple models of TNBC and found that their combination profoundly enhanced the efficacy of either treatment alone. We demonstrate that this efficacy is due to anti-CTLA4-driven expansion of an individually unique T-cell receptor (TCR) repertoire whose functionality is enhanced by both intratumoral Treg suppression and anti-PD1 blockade of tumor expressed PDL1. Notably, the individuality of the TCR repertoire was observed regardless of whether the tumor cells expressed a nonself antigen (ovalbumin) or if tumor-specific transgenic T-cells were transferred prior to sequencing. However, responsiveness was strongly correlated with systemic measures of tumor-specific T-cell and B-cell responses, which along with systemic assessment of TCR expansion, may serve as the most useful predictors for clinical responsiveness in future clinical trials of TNBC utilizing anti-PD1/anti-CTLA4 ICB. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
99. Blocking CTLA-4 while priming with a whole cell vaccine reshapes the oligoclonal T cell infiltrate and eradicates tumors in an orthotopic glioma model.
- Author
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Field, Cameron S., Hunn, Martin K., Ferguson, Peter M., Ruedl, Christiane, Ancelet, Lindsay R., and Hermans, Ian F.
- Subjects
- *
CANCER cells , *CANCER treatment , *INTRACRANIAL tumors , *TUMOR treatment - Abstract
Vaccine-mediated cancer treatment is unlikely to induce long-term survival unless suppressive mechanisms are overcome. Given the success of antibody-mediated immune checkpoint blockade in relieving regulation of endogenous anti-tumor T cell responses in tumor-burdened hosts, we investigated whether checkpoint blockade could improve the efficacy of responses induced with a whole tumor-cell vaccine. We show that administration of a single dose of blocking antibody was sufficient to significantly enhance antitumor activity of the vaccine, inducing complete radiological regression of established intracranial tumors. The antibody or vaccine alone were ineffective in this setting. The antibody had to be administered before, or close to, vaccine administration, suggesting CTLA-4 blockade had an impact on early priming events. The combined treatment resulted in enhanced trapping of leukocytes in the lymphoid tissues, including T cells that had undergone significant proliferation. There were no obvious changes in the stimulatory function of antigen-presenting cells or the number and function of regulatory T cells, suggesting T cells were the targets of the checkpoint blockade. While tumors regressing under combined treatment were highly infiltrated with a variety of leukocytes, tumor eradication was dependent on CD4+T cells. Analysis of the TCR repertoire showed that the addition of anti-CTLA-4 at priming reshaped the repertoire of tumor infiltrating T cells. In particular, the oligoclonal populations became greater in magnitude and more diverse in specificity. Using anti-CTLA-4 in a restricted way to promote the priming phase of an anti-cancer vaccine may offer a useful way of harnessing clinical benefit from this powerful agent. [ABSTRACT FROM PUBLISHER]
- Published
- 2018
- Full Text
- View/download PDF
100. Blocking CTLA-4 while priming with a whole cell vaccine reshapes the oligoclonal T cell infiltrate and eradicates tumors in an orthotopic glioma model.
- Author
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Field CS, Hunn MK, Ferguson PM, Ruedl C, Ancelet LR, and Hermans IF
- Abstract
Vaccine-mediated cancer treatment is unlikely to induce long-term survival unless suppressive mechanisms are overcome. Given the success of antibody-mediated immune checkpoint blockade in relieving regulation of endogenous anti-tumor T cell responses in tumor-burdened hosts, we investigated whether checkpoint blockade could improve the efficacy of responses induced with a whole tumor-cell vaccine. We show that administration of a single dose of blocking antibody was sufficient to significantly enhance antitumor activity of the vaccine, inducing complete radiological regression of established intracranial tumors. The antibody or vaccine alone were ineffective in this setting. The antibody had to be administered before, or close to, vaccine administration, suggesting CTLA-4 blockade had an impact on early priming events. The combined treatment resulted in enhanced trapping of leukocytes in the lymphoid tissues, including T cells that had undergone significant proliferation. There were no obvious changes in the stimulatory function of antigen-presenting cells or the number and function of regulatory T cells, suggesting T cells were the targets of the checkpoint blockade. While tumors regressing under combined treatment were highly infiltrated with a variety of leukocytes, tumor eradication was dependent on CD4
+ T cells. Analysis of the TCR repertoire showed that the addition of anti-CTLA-4 at priming reshaped the repertoire of tumor infiltrating T cells. In particular, the oligoclonal populations became greater in magnitude and more diverse in specificity. Using anti-CTLA-4 in a restricted way to promote the priming phase of an anti-cancer vaccine may offer a useful way of harnessing clinical benefit from this powerful agent.- Published
- 2017
- Full Text
- View/download PDF
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