scholarly journals The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mohammad M. Karimi ◽  
Ya Guo ◽  
Xiaokai Cui ◽  
Husayn A. Pallikonda ◽  
Veronika Horková ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Single Cell ◽  
Signal Strength ◽  
Gene Activity ◽  
Cytotoxic T Cell ◽  
Individual Selection ◽  
Cell Lineages ◽  
Single Cell Rna Sequencing ◽  
Tcr Signals

AbstractCD4 and CD8 mark helper and cytotoxic T cell lineages, respectively, and serve as coreceptors for MHC-restricted TCR recognition. How coreceptor expression is matched with TCR specificity is central to understanding CD4/CD8 lineage choice, but visualising coreceptor gene activity in individual selection intermediates has been technically challenging. It therefore remains unclear whether the sequence of coreceptor gene expression in selection intermediates follows a stereotypic pattern, or is responsive to signaling. Here we use single cell RNA sequencing (scRNA-seq) to classify mouse thymocyte selection intermediates by coreceptor gene expression. In the unperturbed thymus, Cd4+Cd8a- selection intermediates appear before Cd4-Cd8a+ selection intermediates, but the timing of these subsets is flexible according to the strength of TCR signals. Our data show that selection intermediates discriminate MHC class prior to the loss of coreceptor expression and suggest a model where signal strength informs the timing of coreceptor gene activity and ultimately CD4/CD8 lineage choice.

scholarly journals VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data

2019 ◽  
Vol 36 (2) ◽  
pp. 546-551 ◽  
Author(s):  
Kyungsoo Kim ◽  
Sunmo Yang ◽  
Sang-Jun Ha ◽  
Insuk Lee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cell Differentiation ◽  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Signaling Molecules ◽  
Single Cell Rna Sequencing ◽  
Functional States

Abstract Motivation The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation. Results We present VirtualCytometry, a web-based computational pipeline for evaluating immune cell differentiation by exploiting cell-to-cell variation in gene expression with scRNA-seq data. Differentiating cells often show a continuous spectrum of cellular states rather than distinct populations. VirtualCytometry enables the identification of cellular subsets for different functional states of differentiation based on the expression of marker genes. Case studies have highlighted the usefulness of this subset analysis strategy for discovering signaling molecules and transcription factors for human T-cell exhaustion, a state of T-cell dysfunction, in tumor and mouse dendritic cells activated by pathogens. With more than 226 scRNA-seq datasets precompiled from public repositories covering diverse mouse and human immune cell types in normal and disease tissues, VirtualCytometry is a useful resource for the molecular dissection of immune cell differentiation. Availability and implementation www.grnpedia.org/cytometry

scholarly journals 676 Altered circulating myeloid states associated with anti-PD-1 resistance induce T cell paralysis in human biliary cancer

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A704-A704
Author(s):  
Bridget Keenan ◽  
Elizabeth McCarthy ◽  
Arielle Ilano ◽  
Hai Yang ◽  
Li Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Biliary Tract Cancer ◽  
Cd4 T Cells ◽  
Myeloid Cells ◽  
Biliary Cancer ◽  
Tract Cancer ◽  
Single Cell Rna Sequencing

BackgroundAdvanced biliary cancers (ABC) have a poor prognosis and low rates of response to immune checkpoint inhibition (CPI), with overall response rates ranging from 3–13%.1–3 Although suppressive myeloid cells have been proposed as a mechanism of resistance to immunotherapy in general, their relationship to response to CPI is unknown.MethodsWe used multiplexed simultaneous single cell RNA sequencing and cell surface proteomics (CITE-seq) to profile circulating immune cells in ABC patients receiving anti-PD-1 at longitudinal timepoints pre-immunotherapy and on treatment, as well as from healthy donors. We also performed single cell RNA sequencing on resected biliary tumors.ResultsWe identified a novel population of circulating cancer-enriched myeloid cells (CEM) characterized by chemokines and extracellular matrix digestion-related gene expression, which were present pre-treatment. Anti-PD-1 treatment drove the CEMs into two diverging states that were associated with response or resistance to treatment. CEM induced in non-responders constituted over 40% of the circulating myeloid cells and expressed immunosuppressive programs, including the upregulation of suppressive cytokines and chemokines. The frequency of these myeloid cells were correlated with the abundance of SOCS3-expressing CD4+ T cells. These SOCS3+CD4+ T cells also colocalized with tumor-infiltrating myeloid cells that share CEM gene expression signatures in the biliary cancer microenvironment. Moreover, CEM can directly induce SOCS3-expressing T cells, which despite their naïve phenotype are functionally unresponsive. Finally, expression signatures of CEM and of SOCS3+CD4+ T cells are associated with worse survival in a larger cohort of ABC patients.ConclusionsThese results demonstrate the capacity of CEM to induce T cell paralysis as an alternate mode of tumor-mediated immunosuppression. A deeper understanding of immune cell biology in ABC provides insights for developing novel therapeutics that can overcome immunotherapy resistance in biliary cancer as well as other tumor types.Trial RegistrationNCT02703714ReferencesUeno M, et al. Nivolumab alone or in combination with cisplatin plus gemcitabine in Japanese patients with unresectable or recurrent biliary tract cancer: a non-randomised, multicentre, open-label, phase 1 study. Lancet Gastroenterol Hepatol 2019;4:611–621.Piha-Paul SA, et al. Efficacy and safety of pembrolizumab for the treatment of advanced biliary cancer: results from the KEYNOTE-158 and KEYNOTE-028 studies. Int J Cancer 2020.Kim RD, et al. A Phase 2 Multi-institutional study of nivolumab for patients with advanced refractory biliary tract cancer. JAMA Oncol 2020;6:888–894.Ethics ApprovalInformed consent was obtained from all patients for participation in the listed trial and for use of blood and tumor samples in research studies.

scholarly journals Molecular determinants and heterogeneity of tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing

2020 ◽  
Author(s):  
Nadia S. Kurd ◽  
Zhaoren He ◽  
J. Justin Milner ◽  
Kyla D. Omilusik ◽  
Tiani L. Louis ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microbial Infection ◽  
Molecular Determinants ◽  
Single Cell Rna Sequencing

AbstractDuring an immune response to microbial infection, CD8+ T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of non-circulating tissue-resident memory (TRM) cells that mediate potent protection within non-lymphoid tissues. Here, we utilized single-cell RNA-sequencing to examine the gene expression patterns of individual CD8+ T cells in the spleen and small intestine intraepithelial lymphocyte (siIEL) compartment throughout the course of their differentiation in response to viral infection. These analyses revealed previously unknown transcriptional heterogeneity within the siIEL CD8+ T cell population at several states of differentiation, representing functionally distinct TRM cell subsets as well as a subset of TRM cell precursors within the tissue early in infection. Taken together, these findings may inform strategies to optimize CD8+ T cell responses to protect against microbial infection and cancer.One sentence summaryHere, we applied single-cell RNA-sequencing to elucidate the gene expression patterns of individual CD8+ T cells differentiating throughout the course of infection in the spleen and small intestinal epithelium, which revealed previously unidentified molecular determinants of tissue-resident T cell differentiation as well as functional heterogeneity within the tissue-resident CD8+ T cell population.

scholarly journals Latency Reversing Agents: Kick and Kill of HTLV-1?

2021 ◽  
Vol 22 (11) ◽  
pp. 5545
Author(s):  
Annika P. Schnell ◽  
Stephan Kohrt ◽  
Andrea K. Thoma-Kress
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Viral Gene Expression ◽  
Cytotoxic T Cell ◽  
Viral Gene ◽  
T Cell Leukemia ◽  
Cell Leukemia ◽  
Cell Leukemia Virus Type ◽  
Reversing Agents ◽  
Ctl Responses

Human T-cell leukemia virus type 1 (HTLV-1), the cause of adult T-cell leukemia/lymphoma (ATLL), is a retrovirus, which integrates into the host genome and persistently infects CD4+ T-cells. Virus propagation is stimulated by (1) clonal expansion of infected cells and (2) de novo infection. Viral gene expression is induced by the transactivator protein Tax, which recruits host factors like positive transcription elongation factor b (P-TEFb) to the viral promoter. Since HTLV-1 gene expression is repressed in vivo by viral, cellular, and epigenetic mechanisms in late phases of infection, HTLV-1 avoids an efficient CD8+ cytotoxic T-cell (CTL) response directed against the immunodominant viral Tax antigen. Hence, therapeutic strategies using latency reversing agents (LRAs) sought to transiently activate viral gene expression and antigen presentation of Tax to enhance CTL responses towards HTLV-1, and thus, to expose the latent HTLV-1 reservoir to immune destruction. Here, we review strategies that aimed at enhancing Tax expression and Tax-specific CTL responses to interfere with HTLV-1 latency. Further, we provide an overview of LRAs including (1) histone deacetylase inhibitors (HDACi) and (2) activators of P-TEFb, that have mainly been studied in context of human immunodeficiency virus (HIV), but which may also be powerful in the context of HTLV-1.

scholarly journals Evidence for the divergence of innate and adaptive T-cell precursors before commitment to the αβ and γδ lineages

Blood ◽  
2011 ◽  
Vol 118 (25) ◽  
pp. 6591-6600 ◽  
Author(s):  
Jan Kisielow ◽  
Luigi Tortola ◽  
Jacqueline Weber ◽  
Klaus Karjalainen ◽  
Manfred Kopf
Keyword(s):  
T Cells ◽  
T Cell ◽  
Natural Killer ◽  
Negative Selection ◽  
Intraepithelial Lymphocytes ◽  
Lineage Commitment ◽  
Γδt Cells ◽  
Cell Lineages ◽  
Innate T Cells ◽  
Tcr Signals

Abstract In addition to adaptive T cells, the thymus supports the development of unconventional T cells such as natural killer T (NKT) and CD8αα intraepithelial lymphocytes (IELs), which have innate functional properties, particular antigenic specificities, and tissue localization. Both conventional and innate T cells are believed to develop from common precursors undergoing instructive, TCR-mediated lineage fate decisions, but innate T cells are proposed to undergo positive instead of negative selection in response to agonistic TCR signals. In the present study, we show that, in contrast to conventional αβT cells, innate αβT cells are not selected against functional TCRγ rearrangements and express TCRγ mRNA. Likewise, in contrast to the majority of γδT cells, thymic innate γδT cells are not efficiently selected against functional TCRβ chains. In precursors of conventional T cells, autonomous TCR signals emanating from the pre-TCR or γδTCR in the absence of ligand mediate selection against the TCR of the opposite isotype and αβ/γδ lineage commitment. Our data suggest that developing innate T cells ignore such signals and rely solely on agonistic TCR interactions. Consistently, most innate T cells reacted strongly against autologous thymocytes. These results suggest that innate and adaptive T-cell lineages do not develop from the same pool of precursors and potentially diverge before αβ/γδ lineage commitment.

scholarly journals Cryopreservation of microglia enables single-cell RNA sequencing with minimal effects on disease-related gene expression patterns

iScience ◽  
2021 ◽  
Vol 24 (4) ◽  
pp. 102357
Author(s):  
Brenda Morsey ◽  
Meng Niu ◽  
Shetty Ravi Dyavar ◽  
Courtney V. Fletcher ◽  
Benjamin G. Lamberty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Related Gene ◽  
Single Cell Rna Sequencing ◽  
Disease Related Gene
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