Project description:Human γδ T cells take a small but important part in the immune system. Human γδ T cells are usually categorized by the V gene of their T cell receptor (TCR) δ chain; most of which are Vδ1+ or Vδ2+. Naive γδ T cells are often found from neonates and cytotoxic γδ T cells (γδCTLs) are frequent in adults. However, phenotypes and the developmental programs of human γδ T cells are not fully clear. Here, by single-cell RNA sequencing (sc-RNAseq) of transcriptome and T cell receptor (sc-TCRseq) on γδ T cells from neonates and adults, we revealed human γδ T cells can be divided as naïve T cells, γδCTLs, and γδNKT cells which are featured by pro-Vδ1, Vδ1, and Vδ2 TCR repertoire, respectively. γδNKT cells can be further described as γδNKT-1, γδNKT-2, and γδNKT-17 cells.
Project description:Developmental thymic waves of innate-like and adaptive-like gd T cells have been described, but the current understanding of γδ T cell development is mainly limited to mouse models. Here, we combined single cell (sc) RNA gene expression and sc γδ T cell receptor (TCR) sequencing on fetal and pediatric γδ thymocytes in order to understand the ontogeny of human γδ T cells. Mature fetal γδ thymocytes were committed to either a type 1, a type 3 or type 2-like effector fate, independent from γδ T cell subset type (Vγ9Vδ2 vs nonVγ9Vδ2), and were enriched for public CDR3 features upon maturation. Strikingly, type 1, type 3 and type 2 cells expressed different CDR3 sequences and followed distinct developmental trajectories. In contrast, the pediatric thymus generated only a small effector subset that was highly biased towards Vγ9Vδ2 TCR usage and showed a mixed type 1/type 3 effector profile. Thus, our combined dataset of gene expression and detailed TCR information at the single-cell level defines γδ thymocyte development in human and provides a resource for further study.
Project description:γδ T cells perform heterogeneous functions in homeostasis and disease across tissues. However, it is unclear whether these roles correspond to distinct γδ subsets or to a homogeneous population of cells exerting context-dependent functions. Here, by cross-organ multimodal single-cell profiling, we reveal that various mouse tissues harbor unique site-adapted γδ subsets. Epidermal and intestinal intraepithelial γδ T cells are transcriptionally homogeneous and exhibit epigenetic hallmarks of functional diversity. Through parabiosis experiments, we uncovered cellular states associated with cytotoxicity, innate-like rapid IFN-γ production and tissue repair functions displaying tissue residency hallmarks. Notably, our observations nuance the link between IL-17-producing γδ T cells and tissue residency. Moreover, transcriptional programs associated with tissue-resident γδ T cells are analogous to those of CD8+ tissue-resident memory T cells. Altogether, this study provides the first multimodal landscape of tissue-adapted γδ T cells, revealing heterogeneity, lineage relationships and their tissue residency program.
Project description:Hepatosplenic T-cell lymphoma (HSTCL) is a rare but very aggressive lymphoma mostly derived from γδ T cells. The molecular pathogenesis driving HSTCL is largely unknown while only limited treatment options are available with poor outcomes. In this study, we performed paired single cell RNA-seq and T cell receptor (TCR) sequencing on biopsies collected from a HSTCL patient pre- and post- chemotherapy treatments. We characterized unique gene expressing signatures of malignant γδ T cells with a set of marker genes were newly identified in HSTCL (AREG, PLEKHA5, VCAM1 etc.). Although the malignant cells were expanded from a single TCR clonotype according to their TCR sequences, they evolved into two transcriptional distinct tumor subtypes during the disease progression. The Tumor_1 subtype was dominant in pre-treatment samples with highly aggressive phenotypes. The Tumor_2 had relative mild cancer hallmark signatures but expressed genes associated with survival and drug resistance (IL32, TOX2, AIF1, AKAP12 etc.), and finally became the major tumor subtype post-treatment. We further dissected the tumor microenvironment of the HSTCL and found CD8 memory T cells were clonal expanded post-treatment. In addition, we discovered dynamically rewiring cell-cell interaction networks during the treatment. The tumor cells had reduced interactions with the microenvironment post-treatment. Our study reveals heterogenous and dynamic tumor and microenvironment underlying pathogenesis of HSTCL and may contribute to identify novel targets for diagnosis and cure of HSTCL in the future.
Project description:We combined the Single-probe single cell MS(SCMS) experimental technique with a bioinformatics software package, SinCHet-MS (Single Cell Heterogeneity for Mass Spectrometry), to characterize changes of tumor heterogeneity, quantify cell subpopulations, and prioritize the metabolite biomarkers of each subpopulation.
Project description:Background: Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity, but is difficult to detect and assess functionally. Results: We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify the cell surface marker CD24 as co-varying with chromatin accessibility changes linked to GATA transcription factors in single cells. Fluorescence-activated cell sorting of CD24 high vs. low cells prospectively isolated GATA1 and GATA2 high vs. low cells. GATA high vs. low cells express differential gene regulatory networks, differential sensitivity to the drug imatinib mesylate, and differential self-renewal capacity. Lineage tracing experiments show that GATA/CD24hi cells have the capability to rapidly reconstitute the heterogeneity within the entire starting population, suggesting that GATA expression levels drive a phenotypically relevant source of epigenomic plasticity. Conclusion: Single-cell chromatin accessibility can guide prospective characterization of cancer heterogeneity. Epigenomic subpopulations in cancer impact drug sensitivity and the clonal dynamics of cancer evolution.