Creating a single-cell atlas of T cell state holds significant importance in the field of immunology and biomedical research. T cells play a crucial role in orchestrating immune responses and are involved in various diseases, including cancer, autoimmune disorders, and infectious diseases. Understanding the diverse states and functional heterogeneity of T cells at a single-cell resolution can provide invaluable insights into their development, activation, differentiation, and response to environmental cues.
🎉 huARdb v1 has been published on Nucleic Acid Research.
Please cite : Wu et al. (2021) huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level, Nucleic Acids Research. https://doi.org/10.1093/nar/gkab857
🎉 The CD8+ T cell atlas built on huARdb v2 has been published on Nature Methods.
Please cite : Xue et al. (2024) Integrative mapping of human CD8+ T cells in inflammation and cancer, Nature Methods. https://doi.org/10.1038/s41592-024-02530-0
Link to scAtlasVAE: Github
Cite scAtlasVAE and CD8+ T cell atlas: Xue, Z., Wu, L., Tian, R. et al. Integrative mapping of human CD8+ T cells in inflammation and cancer. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02530-0
Link to TCR-DeepInsight: Github
Cite TCR-DeepInsight and CD4/CD8 TCRαβ repertoire atlas
Abbas, H. et al. Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy, Nature Communications, 2021, 12(1). 10.1038/s41467-021-26282-z.
Abdelfatah, E. et al. Predictive and Prognostic Implications of Circulating CX3CR1+ CD8+ T Cells in Non–Small Cell Lung Cancer Patients Treated with Chemo-Immunotherapy, Cancer Research Communications, 2023, 3(3), 510-520. 10.1158/2767-9764.crc-22-0383.
Ali, L. et al. PD-1 blockade and CDK4/6 inhibition augment nonoverlapping features of T cell activation in cancer, Journal of Experimental Medicine, 2023, 220(4). 10.1084/jem.20220729.
Azizi, E. et al. Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment, Cell, 2018, 174(5), 1293-1308.e36. 10.1016/j.cell.2018.05.060.
Bacher, P. et al. Low-Avidity CD4+ T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19, Immunity, 2020, 53(6), 1258-1271.e5. 10.1016/j.immuni.2020.11.016.
Barras, D. et al. Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8(+) T-myeloid cell networks in melanoma, Science Immunology, 2024, 9(92). 10.1126/sciimmunol.adg7995.
Bieberich, F. et al. A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients, Frontiers in Immunology, 2021, 12. 10.3389/fimmu.2021.701085.
Boland, B. et al. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses, Science Immunology, 2020, 5(50). 10.1126/sciimmunol.abb4432.
Borcherding, N. et al. Mapping the immune environment in clear cell renal carcinoma by single-cell genomics, Communications Biology, 2021, 4(1). 10.1038/s42003-020-01625-6.
Buggert, M. et al. The Identity of Human Tissue-Emigrant CD8+ T Cells, Cell, 2020, 183(7), 1946-1961.e15. 10.1016/j.cell.2020.11.019.
Cheon, I. et al. Immune signatures underlying post-acute COVID-19 lung sequelae, Science Immunology, 2021, 6(65). 10.1126/sciimmunol.abk1741.
Chow, R. et al. Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma, Cancer Discovery, 2022, 13(2), 312-331. 10.1158/2159-8290.cd-22-0686.
Collora, J. et al. Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones, Immunity, 2022, 55(6), 1013-1031.e7. 10.1016/j.immuni.2022.03.004.
Corridoni, D. et al. Single-cell atlas of colonic CD8+ T cells in ulcerative colitis, Nature Medicine, 2020, 26(9), 1480-1490. 10.1038/s41591-020-1003-4.
Eberhardt, C. et al. Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer, Nature, 2021, 597(7875), 279-284. 10.1038/s41586-021-03862-z.
Friedrich, M. et al. The pre-existing T cell landscape determines the response to bispecific T cell engagers in multiple myeloma patients, Cancer Cell, 2023, 41(4), 711-725.e6. 10.1016/j.ccell.2023.02.008.
Furtado, R. et al. Cytolytic circumsporozoite-specific memory CD4+ T cell clones are expanded during Plasmodium falciparum infection, Nature Communications, 2023, 14(1). 10.1038/s41467-023-43376-y.
Gao, S. et al. Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells, Nature Communications, 2022, 13(1). 10.1038/s41467-022-29175-x.
Gate, D. et al. Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease, Nature, 2020, 577(7790), 399-404. 10.1038/s41586-019-1895-7.
He, S. et al. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs, Genome Biology, 2020, 21(1). 10.1186/s13059-020-02210-0.
Iinuma, T. et al. Single-cell immunoprofiling after immunotherapy for allergic rhinitis reveals functional suppression of pathogenic TH2 cells and clonal conversion, Journal of Allergy and Clinical Immunology, 2022, 150(4), 850-860.e5. 10.1016/j.jaci.2022.06.024.
Jiang, R. et al. Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells, JCI Insight, 2021, 6(12). 10.1172/jci.insight.148035.
Kawakami, R. et al. Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells, Immunity, 2021, 54(5), 947-961.e8. 10.1016/j.immuni.2021.04.005.
Khoo, W. et al. Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19, Clinical Immunology, 2023, 246, 109209. 10.1016/j.clim.2022.109209.
Kim, S. et al. Distinct molecular and immune hallmarks of inflammatory arthritis induced by immune checkpoint inhibitors for cancer therapy, Nature Communications, 2022, 13(1). 10.1038/s41467-022-29539-3.
Krishna, C. et al. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy, Cancer Cell, 2021, 39(5), 662-677.e6. 10.1016/j.ccell.2021.03.007.
Leader, A. et al. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification, Cancer Cell, 2021, 39(12), 1594-1609.e12. 10.1016/j.ccell.2021.10.009.
Lee, B. et al. Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis, Gut, 2021, 71(9), 1831-1842. 10.1136/gutjnl-2021-324546.
Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19, Nature Medicine, 2020, 26(6), 842-844. 10.1038/s41591-020-0901-9.
Liu, T. et al. Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients, Nature Communications, 2022, 13(1). 10.1038/s41467-022-34581-2.
Liu, Y. et al. Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution, Nature Communications, 2021, 12(1). 10.1038/s41467-021-21043-4.
Lu, Y. et al. Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy, Cancer Immunology Research, 2019, 7(11), 1824-1836. 10.1158/2326-6066.cir-19-0299.
Luo, O. et al. Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty, Nature Aging, 2022, 2(4), 348-364. 10.1038/s43587-022-00198-9.
Luoma, A. et al. Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy, Cell, 2020, 182(3), 655-671.e22. 10.1016/j.cell.2020.06.001.
Mahuron, K. et al. Layilin augments integrin activation to promote antitumor immunity, Journal of Experimental Medicine, 2020, 217(9). 10.1084/jem.20192080.
Minervina, A. et al. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells, Nature Immunology, 2022, 23(5), 781-790. 10.1038/s41590-022-01184-4.
Moon, J. et al. Cytotoxic CD8+ T cells target citrullinated antigens in rheumatoid arthritis, Nature Communications, 2023, 14(1). 10.1038/s41467-022-35264-8.
Neal, J. et al. Organoid Modeling of the Tumor Immune Microenvironment, Cell, 2018, 175(7), 1972-1988.e16. 10.1016/j.cell.2018.11.021.
Notarbartolo, S. et al. Integrated longitudinal immunophenotypic, transcriptional, and repertoire analyses delineate immune responses in patients with COVID-19, Science Immunology, 2021, 6(62). 10.1126/sciimmunol.abg5021.
Ogino, H. et al. Randomized trial of neoadjuvant vaccination with tumor-cell lysate induces T cell response in low-grade gliomas, Journal of Clinical Investigation, 2022, 132(3). 10.1172/jci151239.
Pai, J. et al. Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade, Cancer Cell, 2023, 41(4), 776-790.e7. 10.1016/j.ccell.2023.03.009.
Park, J. et al. A cell atlas of human thymic development defines T cell repertoire formation, Science, 2020, 367(6480). 10.1126/science.aay3224.
Penkava, F. et al. Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis, Nature Communications, 2020, 11(1). 10.1038/s41467-020-18513-6.
Phan, J. et al. Cytotoxic T Cells Targeting Spike Glycoprotein Are Associated with Hybrid Immunity to SARS-CoV-2, The Journal of Immunology, 2023, 210(9), 1236-1246. 10.4049/jimmunol.2200815.
Poon, M. et al. Tissue adaptation and clonal segregation of human memory T cells in barrier sites, Nature Immunology, 2023, 24(2), 309-319. 10.1038/s41590-022-01395-9.
Rahim, M. et al. Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes, Cell, 2023, 186(6), 1127-1143.e18. 10.1016/j.cell.2023.02.021.
Ramaswamy, A. et al. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children, Immunity, 2021, 54(5), 1083-1095.e7. 10.1016/j.immuni.2021.04.003.
Ren, Y. et al. Single-cell sequencing reveals effects of chemotherapy on the immune landscape and TCR/BCR clonal expansion in a relapsed ovarian cancer patient, Frontiers in Immunology, 2022, 13. 10.3389/fimmu.2022.985187.
Roider, T. et al. Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities, Nature Cell Biology, 2024, 26(3), 478-489. 10.1038/s41556-024-01358-2.
Schalck, A. et al. Single-Cell Sequencing Reveals Trajectory of Tumor-Infiltrating Lymphocyte States in Pancreatic Cancer, Cancer Discovery, 2022, 12(10), 2330-2349. 10.1158/2159-8290.cd-21-1248.
Shi, X. et al. Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment, npj Precision Oncology, 2022, 6(1). 10.1038/s41698-022-00300-9.
Simone, D. et al. Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates, Communications Biology, 2021, 4(1). 10.1038/s42003-021-02931-3.
Sonigra, A. et al. Randomized phase I trial of antigen-specific tolerizing immunotherapy with peptide/calcitriol liposomes in ACPA+ rheumatoid arthritis, JCI Insight, 2022, 7(20). 10.1172/jci.insight.160964.
Sun, K. et al. scRNA-seq of gastric tumor shows complex intercellular interaction with an alternative T cell exhaustion trajectory, Nature Communications, 2022, 13(1). 10.1038/s41467-022-32627-z.
Suo, C. et al. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins, Nature Biotechnology, 2023, 42(1), 40-51. 10.1038/s41587-023-01734-7.
Suo, C. et al. Mapping the developing human immune system across organs, Science, 2022, 376(6597). 10.1126/science.abo0510.
Wang, R. et al. Clonally expanded CD38hi cytotoxic CD8 T cells define the T cell infiltrate in checkpoint inhibitor–associated arthritis, Science Immunology, 2023, 8(85).
Wang, X. et al. Identification of Distinct Immune Cell Subsets Associated With Asymptomatic Infection, Disease Severity, and Viral Persistence in COVID-19 Patients, Frontiers in Immunology, 2022, 13. 10.3389/fimmu.2022.812514.
Wang, X. et al. Single‐Cell RNA‐Seq of T Cells in B‐ALL Patients Reveals an Exhausted Subset with Remarkable Heterogeneity, Advanced Science, 2021, 8(19). 10.1002/advs.202101447.
Wang, Z. et al. Single-cell RNA sequencing of peripheral blood mononuclear cells from acute Kawasaki disease patients, Nature Communications, 2021, 12(1). 10.1038/s41467-021-25771-5.
Wen, T. et al. NKG7 Is a T-cell–Intrinsic Therapeutic Target for Improving Antitumor Cytotoxicity and Cancer Immunotherapy, *Cancer Immunology Research*, 2021, 10(2), 162-181. 10.1158/2326-6066.cir-21-0539.
Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing, *Cell Discovery*, 2020, 6(1). 10.1038/s41421-020-0168-9.
Wong, H. et al. Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease, *Nature Communications*, 2022, 13(1). 10.1038/s41467-022-33780-1.
Xiao, C. et al. Insufficient epitope-specific T cell clones are responsible for impaired cellular immunity to inactivated SARS-CoV-2 vaccine in older adults, *Nature Aging*, 2023, 3(4), 418-435. 10.1038/s43587-023-00379-0.
Xin, Z. et al. The immune landscape of human thymic epithelial tumors, *Nature Communications*, 2022, 13(1). 10.1038/s41467-022-33170-7.
Yost, K. et al. Clonal replacement of tumor-specific T cells following PD-1 blockade, Nature Medicine, 2019, 25(8), 1251-1259. 10.1038/s41591-019-0522-3.
Zeng, S. et al. Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease, Cell Host & Microbe, 2023, 31(3), 389-404.e7. 10.1016/j.chom.2023.02.001.
Zhang, W. et al. CMV Status Drives Distinct Trajectories of CD4+ T Cell Differentiation, Frontiers in Immunology, 2021, 12. 10.3389/fimmu.2021.620386.
Zheng, Y. et al. Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment, Nature Communications, 2020, 11(1). 10.1038/s41467-020-20019-0.