ABSTRACT
The differentiation and specificity of human CD4+ T follicular helper cells (TFH cells) after influenza vaccination have been poorly defined. Here we profiled blood and draining lymph node (LN) samples from human volunteers for over 2 years after two influenza vaccines were administered 1 year apart to define the evolution of the CD4+ TFH cell response. The first vaccination induced an increase in the frequency of circulating TFH (cTFH) and LN TFH cells at week 1 postvaccination. This increase was transient for cTFH cells, whereas the LN TFH cells further expanded during week 2 and remained elevated in frequency for at least 3 months. We observed several distinct subsets of TFH cells in the LN, including pre-TFH cells, memory TFH cells, germinal center (GC) TFH cells and interleukin-10+ TFH cell subsets beginning at baseline and at all time points postvaccination. The shift toward a GC TFH cell phenotype occurred with faster kinetics after the second vaccine compared to the first vaccine. We identified several influenza-specific TFH cell clonal lineages, including multiple responses targeting internal influenza virus proteins, and found that each TFH cell state was attainable within a clonal lineage. Thus, human TFH cells form a durable and dynamic multitissue network.
Subject(s)
Cell Differentiation , Germinal Center , Influenza Vaccines , Influenza, Human , T Follicular Helper Cells , Vaccination , Humans , Influenza Vaccines/immunology , T Follicular Helper Cells/immunology , Influenza, Human/immunology , Influenza, Human/prevention & control , Germinal Center/immunology , Cell Differentiation/immunology , Lymph Nodes/immunology , Adult , Female , Male , Middle Aged , Interleukin-10/immunology , Interleukin-10/metabolism , Immunologic Memory/immunology , T-Lymphocytes, Helper-Inducer/immunology , Young AdultABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mRNA vaccination induce robust CD4+ T cell responses. Using single-cell transcriptomics, here, we evaluated CD4+ T cells specific for the SARS-CoV-2 spike protein in the blood and draining lymph nodes (dLNs) of individuals 3 months and 6 months after vaccination with the BNT162b2 mRNA vaccine. We analyzed 1,277 spike-specific CD4+ T cells, including 238 defined using Trex, a deep learning-based reverse epitope mapping method to predict antigen specificity. Human dLN spike-specific CD4+ follicular helper T (TFH) cells exhibited heterogeneous phenotypes, including germinal center CD4+ TFH cells and CD4+IL-10+ TFH cells. Analysis of an independent cohort of SARS-CoV-2-infected individuals 3 months and 6 months after infection found spike-specific CD4+ T cell profiles in blood that were distinct from those detected in blood 3 months and 6 months after BNT162b2 vaccination. Our findings provide an atlas of human spike-specific CD4+ T cell transcriptional phenotypes in the dLNs and blood following SARS-CoV-2 vaccination or infection.
Subject(s)
BNT162 Vaccine , CD4-Positive T-Lymphocytes , COVID-19 , Lymph Nodes , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Humans , COVID-19/immunology , COVID-19/prevention & control , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , BNT162 Vaccine/immunology , CD4-Positive T-Lymphocytes/immunology , Lymph Nodes/immunology , COVID-19 Vaccines/immunology , Vaccination , Phenotype , Female , Male , Adult , Middle Aged , mRNA Vaccines/immunologyABSTRACT
Long intergenic noncoding RNAs (lincRNAs) are important regulators of gene expression. Although lincRNAs are expressed in immune cells, their functions in immunity are largely unexplored. Here, we identify an immunoregulatory lincRNA, lincRNA-EPS, that is precisely regulated in macrophages to control the expression of immune response genes (IRGs). Transcriptome analysis of macrophages from lincRNA-EPS-deficient mice, combined with gain-of-function and rescue experiments, revealed a specific role for this lincRNA in restraining IRG expression. Consistently, lincRNA-EPS-deficient mice manifest enhanced inflammation and lethality following endotoxin challenge in vivo. lincRNA-EPS localizes at regulatory regions of IRGs to control nucleosome positioning and repress transcription. Further, lincRNA-EPS mediates these effects by interacting with heterogeneous nuclear ribonucleoprotein L via a CANACA motif located in its 3' end. Together, these findings identify lincRNA-EPS as a repressor of inflammatory responses, highlighting the importance of lincRNAs in the immune system.
Subject(s)
Gene Expression Regulation , Inflammation/genetics , Macrophages/immunology , RNA, Long Noncoding/metabolism , Animals , Chromatids/metabolism , Gene Deletion , Humans , Listeria monocytogenes/physiology , Listeriosis/immunology , Macrophages/metabolism , Macrophages/microbiology , Macrophages/virology , Mice , Mice, Inbred C57BL , RNA, Long Noncoding/genetics , Respirovirus Infections/immunology , Sendai virus/physiology , Toll-Like Receptors/metabolism , TranscriptomeABSTRACT
Chimeric antigen receptor (CAR) T-cell therapy targeting T-cell acute lymphoblastic leukemia (T-ALL) faces limitations such as antigen selection and limited T-cell persistence. CD7 is an attractive antigen for targeting T-ALL, but overlapping expression on healthy T cells leads to fratricide of CD7-CAR T cells, requiring additional genetic modification. We took advantage of naturally occurring CD7- T cells to generate CD7-CAR (CD7-CARCD7-) T cells. CD7-CARCD7- T cells exhibited a predominantly CD4+ memory phenotype and had significant antitumor activity upon chronic antigen exposure in vitro and in xenograft mouse models. Based on these encouraging results, we next explored the utility of CD7- T cells for the immunotherapy of CD19+ hematological malignancies. Direct comparison of nonselected (bulk) CD19-CAR and CD19-CARCD7- T cells revealed that CD19-CARCD7- T cells had enhanced antitumor activity compared with their bulk counterparts in vitro and in vivo. Lastly, to gain insight into the behavior of CD19-CAR T cells with low levels of CD7 gene expression (CD7lo) in humans, we mined single-cell gene and T-cell receptor (TCR) expression data sets from our institutional CD19-CAR T-cell clinical study. CD19-CARCD7lo T cells were present in the initial CD19-CAR T-cell product and could be detected postinfusion. Intriguingly, the only functional CD4+ CD19-CAR T-cell cluster observed postinfusion exhibited CD7lo expression. Additionally, samples from patients responsive to therapy had a higher proportion of CD7lo T cells than nonresponders (NCT03573700). Thus, CARCD7- T cells have favorable biological characteristics and may present a promising T-cell subset for adoptive cell therapy of T-ALL and other hematological malignancies.
Subject(s)
Hematologic Neoplasms , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma , Humans , Mice , Animals , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology , Receptors, Antigen, T-Cell , Immunotherapy, Adoptive , Hematologic Neoplasms/therapy , Immunotherapy , Antigens, CD19ABSTRACT
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult but important task. Current methods of TCR repertoire comparison can incur a high loss of distributional information by considering overly simplistic sequence- or repertoire-level characteristics. Optimal transport methods form a suitable approach for such comparison given some distance or metric between values in the sample space, with appealing theoretical and computational properties. In this paper we introduce a nonparametric approach to comparing empirical TCR repertoires that applies the Sinkhorn distance, a fast, contemporary optimal transport method, and a recently-created distance between TCRs called TCRdist. We show that our methods identify meaningful differences between samples from distinct TCR distributions for several case studies, and compete with more complicated methods despite minimal modeling assumptions and a simpler pipeline.
ABSTRACT
Over the last several decades, novel populations of unconventional T cells have been identified; defined by an invariant (or nearly invariant) T cell receptor (TCR) with a fixed specificity to non-canonical antigens and major histocompatibility (MHC) molecules, they form large, functionally monoclonal populations tasked with surveying for their specific antigens. With residence in both lymphoid and non-lymphoid tissues coupled with their ability to rapidly produce a spectrum of cytokines and effector molecules, the unconventional T cells are poised as some of the first responders to infection/damage and are thought to provide critical coverage before more focused, conventional T cell responses are mobilized. However, new technologies for the measurement and characterization of TCR repertoires have identified an underappreciated amount of TCR diversity in the unconventional T cells. In many cases, the specificities of these diverse TCRs converge on the same or similar antigens as their invariant counterparts, while others have yet to be defined. Here, we will review the current knowledge of the TCR repertoires of unconventional T cells and discuss how repertoires might be used as a framework for their organization, and further our understanding of their role not only during an immune response, but also their contribution in maintaining homeostasis.
Subject(s)
Natural Killer T-Cells/immunology , Receptors, Antigen, T-Cell, gamma-delta/immunology , T-Lymphocyte Subsets/immunology , Adaptive Immunity/immunology , Animals , Genetic Variation/immunology , Humans , MiceABSTRACT
Innate sensing of nucleic acids lies at the heart of antiviral immunity. During viral infection, dying cells may also release nucleic acids into the tissue microenvironment. It is unknown what effect such host signals have on the quality or duration of the immune response to viruses. In this study, we uncovered an immune-regulatory pathway that tempers the intensity of the host response to influenza A virus (IAV) infection. We found that host-derived DNA accumulates in the lung microenvironment during IAV infection. Ablation of DNA in the lung resulted in increased mortality, increased cellular recruitment, and increased inflammation following IAV challenge. The released DNA, in turn, was sensed by the DNA receptor absent in melanoma 2. Aim2(-/-) mice showed similarly exaggerated immune responses to IAV. Taken together, our results identify a novel mechanism of cross-talk between pathogen- and damage-associated molecular pattern-sensing pathways, wherein sensing of host-derived DNA limits immune-mediated damage to infected tissues.
Subject(s)
DNA-Binding Proteins/genetics , DNA-Binding Proteins/immunology , DNA/immunology , Influenza A Virus, H1N1 Subtype/immunology , Orthomyxoviridae Infections/immunology , Animals , Cellular Microenvironment/immunology , Host-Pathogen Interactions/immunology , Immunity, Innate/immunology , Inflammation/immunology , Lung/immunology , Mice , Mice, Inbred C57BL , Mice, KnockoutABSTRACT
Cytosolic DNA-sensing pathways that signal via Stimulator of interferon genes (STING) mediate immunity to pathogens and also promote autoimmune pathology in DNaseII- and DNaseIII-deficient mice. In contrast, we report here that STING potently suppresses inflammation in a model of systemic lupus erythematosus (SLE). Lymphoid hypertrophy, autoantibody production, serum cytokine levels, and other indicators of immune activation were markedly increased in STING-deficient autoimmune-prone mice compared with STING-sufficient littermates. As a result, STING-deficient autoimmune-prone mice had significantly shorter lifespans than controls. Importantly, Toll-like receptor (TLR)-dependent systemic inflammation during 2,6,10,14-tetramethylpentadecane (TMPD)-mediated peritonitis was similarly aggravated in STING-deficient mice. Mechanistically, STING-deficient macrophages failed to express negative regulators of immune activation and thus were hyperresponsive to TLR ligands, producing abnormally high levels of proinflammatory cytokines. This hyperreactivity corresponds to dramatically elevated numbers of inflammatory macrophages and granulocytes in vivo. Collectively these findings reveal an unexpected negative regulatory role for STING, having important implications for STING-directed therapies.
Subject(s)
Autoimmunity/physiology , Membrane Proteins/physiology , Animals , Autoantibodies/biosynthesis , Dendritic Cells/immunology , Gene Expression Regulation/physiology , Interferon Regulatory Factor-3/genetics , Interferon Regulatory Factor-3/physiology , Interferons/physiology , Lymphocyte Activation , Membrane Proteins/genetics , MiceABSTRACT
Herpesviruses are DNA viruses harboring the capacity to establish lifelong latent-recurrent infections. There is limited knowledge about viruses targeting the innate DNA-sensing pathway, as well as how the innate system impacts on the latent reservoir of herpesvirus infections. In this article, we report that murine gammaherpesvirus 68 (MHV68), in contrast to α- and ß-herpesviruses, induces very limited innate immune responses through DNA-stimulated pathways, which correspondingly played only a minor role in the control of MHV68 infections in vivo. Similarly, Kaposi's sarcoma-associated herpesvirus also did not stimulate immune signaling through the DNA-sensing pathways. Interestingly, an MHV68 mutant lacking deubiquitinase (DUB) activity, embedded within the large tegument protein open reading frame (ORF)64, gained the capacity to stimulate the DNA-activated stimulator of IFN genes (STING) pathway. We found that ORF64 targeted a step in the DNA-activated pathways upstream of the bifurcation into the STING and absent in melanoma 2 pathways, and lack of the ORF64 DUB was associated with impaired delivery of viral DNA to the nucleus, which, instead, localized to the cytoplasm. Correspondingly, the ORF64 DUB active site mutant virus exhibited impaired ability to establish latent infection in wild-type, but not STING-deficient, mice. Thus, gammaherpesviruses evade immune activation by the cytosolic DNA-sensing pathway, which, in the MHV68 model, facilitates establishment of infections.
Subject(s)
DNA, Viral/immunology , Gammaherpesvirinae/immunology , Herpesviridae Infections/immunology , Immunity, Innate/immunology , Virus Latency/immunology , Animals , Cytosol/immunology , Disease Models, Animal , Enzyme-Linked Immunosorbent Assay , Flow Cytometry , Humans , Macrophages/immunology , Macrophages/virology , Mice , Mice, Inbred C57BL , Mice, Knockout , Microscopy, Confocal , Real-Time Polymerase Chain ReactionABSTRACT
Aspartoacylase (AspA) gene mutations cause the pediatric lethal neurodegenerative Canavan disease (CD). There is emerging promise of successful gene therapy for CD using recombinant adeno-associated viruses (rAAVs). Here, we report an intracerebroventricularly delivered AspA gene therapy regime using three serotypes of rAAVs at a 20-fold reduced dose than previously described in AspA(-/-) mice, a bona-fide mouse model of CD. Interestingly, central nervous system (CNS)-restricted therapy prolonged survival over systemic therapy in CD mice but failed to sustain motor functions seen in systemically treated mice. Importantly, we reveal through histological and functional examination of untreated CD mice that AspA deficiency in peripheral tissues causes morphological and functional abnormalities in this heretofore CNS-defined disorder. We demonstrate for the first time that AspA deficiency, possibly through excessive N-acetyl aspartic acid accumulation, elicits both a peripheral and CNS immune response in CD mice. Our data establish a role for peripheral tissues in CD pathology and serve to aid the development of more efficacious and sustained gene therapy for this disease.
Subject(s)
Amidohydrolases/genetics , Canavan Disease/therapy , Central Nervous System/pathology , Genetic Therapy/methods , Animals , Canavan Disease/genetics , Canavan Disease/pathology , Central Nervous System/metabolism , Dependovirus/genetics , Disease Models, Animal , Genetic Vectors/administration & dosage , Humans , Mice , Organ Specificity , Survival Analysis , Treatment OutcomeABSTRACT
The four Toll/IL-1R domain-containing adaptor proteins MyD88, MAL, TRIF, and TRAM are well established as essential mediators of TLR signaling and gene induction following microbial detection. In contrast, the function of the fifth, most evolutionarily conserved Toll/IL-1R adaptor, sterile α and HEAT/Armadillo motif-containing protein (SARM), has remained more elusive. Recent studies of Sarm(-/-) mice have highlighted a role for SARM in stress-induced neuronal cell death and immune responses in the CNS. However, whether SARM has a role in immune responses in peripheral myeloid immune cells is less clear. Thus, we characterized TLR-induced cytokine responses in SARM-deficient murine macrophages and discovered a requirement for SARM in CCL5 production, whereas gene induction of TNF, IL-1ß, CCL2, and CXCL10 were SARM-independent. SARM was not required for TLR-induced activation of MAPKs or of transcription factors implicated in CCL5 induction, namely NF-κB and IFN regulatory factors, nor for Ccl5 mRNA stability or splicing. However, SARM was critical for the recruitment of transcription factors and of RNA polymerase II to the Ccl5 promoter. Strikingly, the requirement of SARM for CCL5 induction was not restricted to TLR pathways, as it was also apparent in cytosolic RNA and DNA responses. Thus, this study identifies a new role for SARM in CCL5 expression in macrophages.
Subject(s)
Armadillo Domain Proteins/immunology , Chemokine CCL5/immunology , Cytoskeletal Proteins/immunology , Interferon Regulatory Factors/immunology , Macrophages, Peritoneal/immunology , NF-kappa B/immunology , Promoter Regions, Genetic/immunology , RNA Polymerase II/immunology , Animals , Armadillo Domain Proteins/genetics , Armadillo Domain Proteins/metabolism , Chemokine CCL2/genetics , Chemokine CCL2/immunology , Chemokine CCL2/metabolism , Chemokine CCL5/biosynthesis , Chemokine CCL5/genetics , Chemokine CXCL10/genetics , Chemokine CXCL10/immunology , Chemokine CXCL10/metabolism , Cytoskeletal Proteins/genetics , Cytoskeletal Proteins/metabolism , Gene Expression Regulation/physiology , Interferon Regulatory Factors/genetics , Interferon Regulatory Factors/metabolism , Interleukin-1beta/genetics , Interleukin-1beta/immunology , Interleukin-1beta/metabolism , Macrophages, Peritoneal/cytology , Macrophages, Peritoneal/metabolism , Mice , Mice, Knockout , NF-kappa B/genetics , NF-kappa B/metabolism , RNA Polymerase II/genetics , RNA Polymerase II/metabolism , Tumor Necrosis Factor-alpha/genetics , Tumor Necrosis Factor-alpha/immunology , Tumor Necrosis Factor-alpha/metabolismABSTRACT
TLR4 interactor with leucine-rich repeats (TRIL) is a brain-enriched accessory protein that is important in TLR3 and TLR4 signaling. In this study, we generated Tril(-/-) mice and examined TLR responses in vitro and in vivo. We found a role for TRIL in both TLR4 and TLR3 signaling in mixed glial cells, consistent with the high level of expression of TRIL in these cells. We also found that TRIL is a modulator of the innate immune response to LPS challenge and Escherichia coli infection in vivo. Tril(-/-) mice produce lower levels of multiple proinflammatory cytokines and chemokines specifically within the brain after E. coli and LPS challenge. Collectively, these data uncover TRIL as a mediator of innate immune responses within the brain, where it enhances neuronal cytokine responses to infection.
Subject(s)
Brain/immunology , Carrier Proteins/immunology , Immunity, Innate/immunology , Membrane Proteins/immunology , Toll-Like Receptor 3/immunology , Toll-Like Receptor 4/immunology , Animals , Carrier Proteins/biosynthesis , Carrier Proteins/genetics , Cells, Cultured , Chemokine CCL5/biosynthesis , Escherichia coli/immunology , Escherichia coli Infections/immunology , Intercellular Signaling Peptides and Proteins , Interleukin-6/biosynthesis , Lipopolysaccharides , Membrane Glycoproteins/immunology , Membrane Proteins/biosynthesis , Membrane Proteins/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , Neuroglia/immunology , Poly I-C/pharmacology , Signal Transduction/immunology , Toll-Like Receptor 2/immunology , Toll-Like Receptor 7/immunology , Toll-Like Receptor 8/immunology , Tumor Necrosis Factor-alpha/biosynthesisABSTRACT
Synthetic oligodeoxynucleotides (ODNs) comprised of the immunosuppressive motif TTAGGG block TLR9 signaling, prevent STAT1 and STAT4 phosphorylation and attenuate a variety of inflammatory responses in vivo. In this study, we demonstrate that such suppressive ODN abrogate activation of cytosolic nucleic acid-sensing pathways. Pretreatment of dendritic cells and macrophages with the suppressive ODN-A151 abrogated type I IFN, TNF-α, and ISG induction in response to cytosolic dsDNA. In addition, A151 abrogated caspase-1-dependent IL-1ß and IL-18 maturation in dendritic cells stimulated with dsDNA and murine CMV. Inhibition was dependent on A151's phosphorothioate backbone, whereas substitution of the guanosine residues for adenosine negatively affected potency. A151 mediates these effects by binding to AIM2 in a manner that is competitive with immune-stimulatory DNA and as a consequence prevents AIM2 inflammasome complex formation. Collectively, these findings reveal a new route by which suppressive ODNs modulate the immune system and unveil novel applications for suppressive ODNs in the treatment of infectious and autoimmune diseases.
Subject(s)
Inflammasomes/antagonists & inhibitors , Nuclear Proteins/metabolism , Nucleotide Motifs , Oligodeoxyribonucleotides/chemistry , Oligodeoxyribonucleotides/pharmacology , Animals , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacology , Cell Line , Cluster Analysis , Cytoskeletal Proteins/chemistry , Cytoskeletal Proteins/metabolism , Cytosol/metabolism , DNA/metabolism , DNA-Binding Proteins , Gene Expression Profiling , Gene Expression Regulation/drug effects , Humans , Inflammasomes/chemistry , Inflammasomes/metabolism , Mice , Oligodeoxyribonucleotides/metabolism , Protein Binding , Protein Multimerization/drug effects , Signal Transduction/drug effects , Thionucleotides/chemistryABSTRACT
The innate immune response is the first line of defense against infection and relies on the ability of immune cells to detect the presence of infection through germline-encoded pattern recognition receptors. These include the Toll-like receptors, the retinoic acid inducible gene-like receptors, the nucleotide oligomerization domain-like receptors, and a number of DNA-sensing molecules. Members of the PYHIN protein family have recently emerged as sensors of microbial DNA. PYHIN proteins bind microbial DNA and form caspase-1-activating inflammasomes (AIM2) or drive type I IFN gene transcription (IFI16). Here, we review these discoveries and highlight the emerging role of the PYHIN protein family in mammalian host defenses.
Subject(s)
Infections/immunology , Inflammasomes/immunology , Nuclear Proteins/immunology , Receptors, Pattern Recognition/immunology , Animals , DNA, Bacterial/immunology , DNA, Viral/immunology , Humans , Immunity, Innate , Interferon Type I/immunology , Mammals , Transcriptional Activation/immunologyABSTRACT
Virus-specific T cells (VST) from partially-HLA matched donors have been effective for treatment of refractory viral infections in immunocompromised patients in prior studies with a good safety profile, but rare adverse events have been described. Here we describe a unique and severe adverse event of VST therapy in an infant with severe combined immunodeficiency, who receives, as part of a clinical trial (NCT03475212), third party VSTs for treating cytomegalovirus viremia following bone marrow transplantation. At one-month post-VST infusion, rejection of graft and reversal of chimerism is observed, as is an expansion of T cells exclusively from the VST donor. Single-cell gene expression and T cell receptor profiling demonstrate a narrow repertoire of predominantly activated CD4+ T cells in the recipient at the time of rejection, with the repertoire overlapping more with that of peripheral blood from VST donor than the infused VST product. This case thus demonstrates a rare but serious side effect of VST therapy.
Subject(s)
Hematopoietic Stem Cell Transplantation , Virus Diseases , Infant , Humans , Bone Marrow Transplantation/adverse effects , Bone Marrow , Immunotherapy, Adoptive , T-Lymphocytes/transplantation , Hematopoietic Stem Cell Transplantation/adverse effectsABSTRACT
We profiled blood and draining lymph node (LN) samples from human volunteers after influenza vaccination over two years to define evolution in the T follicular helper cell (TFH) response. We show LN TFH cells expanded in a clonal-manner during the first two weeks after vaccination and persisted within the LN for up to six months. LN and circulating TFH (cTFH) clonotypes overlapped but had distinct kinetics. LN TFH cell phenotypes were heterogeneous and mutable, first differentiating into pre-TFH during the month after vaccination before maturing into GC and IL-10+ TFH cells. TFH expansion, upregulation of glucose metabolism, and redifferentiation into GC TFH cells occurred with faster kinetics after re-vaccination in the second year. We identified several influenza-specific TFH clonal lineages, including multiple responses targeting internal influenza proteins, and show each TFH state is attainable within a lineage. This study demonstrates that human TFH cells form a durable and dynamic multi-tissue network.
ABSTRACT
Advances in single-cell technologies have made it possible to simultaneously quantify gene expression and immune receptor sequence across thousands of individual T or B cells in a single experiment. Data from such experiments are advancing our understanding of the relationship between adaptive immune receptor sequence and transcriptional profile. We recently reported a software tool, CoNGA, specifically developed to detect correlation between receptor sequence and transcriptional profile. Here we describe in detail how CoNGA can be applied to analyze a large and diverse T cell dataset featuring multiple donors and batch annotations. Our workflow illustrates new analysis modes for the detection of TCR sequence convergence into similarity clusters and of matches to literature-derived TCR databases, as well as processing of gamma-delta T cells.
Subject(s)
Receptors, Antigen, T-Cell, gamma-delta , Software , Receptors, Antigen, T-Cell, gamma-delta/geneticsABSTRACT
Links between T cell clonotypes, as defined by T cell receptor (TCR) sequences, and phenotype, as reflected in gene expression (GEX) profiles, surface protein expression and peptide:major histocompatibility complex binding, can reveal functional relationships beyond the features shared by clonally related cells. Here we present clonotype neighbor graph analysis (CoNGA), a graph theoretic approach that identifies correlations between GEX profile and TCR sequence through statistical analysis of GEX and TCR similarity graphs. Using CoNGA, we uncovered associations between TCR sequence and GEX profiles that include a previously undescribed 'natural lymphocyte' population of human circulating CD8+ T cells and a set of TCR sequence determinants of differentiation in thymocytes. These examples show that CoNGA might help elucidate complex relationships between TCR sequence and T cell phenotype in large, heterogeneous, single-cell datasets.
Subject(s)
CD8-Positive T-Lymphocytes , Receptors, Antigen, T-Cell, alpha-beta , CD8-Positive T-Lymphocytes/metabolism , Cell Differentiation , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , Receptors, Antigen, T-Cell, alpha-beta/geneticsABSTRACT
Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual's genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.
Subject(s)
Genome-Wide Association Study , V(D)J Recombination , Genetic Loci , Genotype , Humans , Probability , Receptors, Antigen, T-Cell/genetics , V(D)J Recombination/geneticsABSTRACT
T resident helper cells (TRH), a T cell subset with follicular helper and resident memory properties, regulate B cell responses in nonlymphoid organs (see the related Research Articles by Swarnalekha et al. and Son et al.).