Journal Article
. 2018 Feb; 19(3):291-301.
doi: 10.1038/s41590-018-0051-0.

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

David Zemmour 1 Rapolas Zilionis 2 Evgeny Kiner 1 Allon M Klein 2 Diane Mathis 3 Christophe Benoist 4 
Affiliations
  • PMID: 29434354
  •     86 References
  •     142 citations

Abstract

CD4+ T regulatory cells (Treg) are central to immune homeostasis, their phenotypic heterogeneity reflecting the diverse environments and target cells that they regulate. To understand this heterogeneity, we combined single-cell RNA-seq, activation reporter and T cell receptor (TCR) analysis to profile thousands of Treg or conventional CD4+FoxP3- T cells (Tconv) from mouse lymphoid organs and human blood. Treg and Tconv pools showed areas of overlap, as resting 'furtive' Tregs with overall similarity to Tconvs or as a convergence of activated states. All Tregs expressed a small core of FoxP3-dependent transcripts, onto which additional programs were added less uniformly. Among suppressive functions, Il2ra and Ctla4 were quasiconstant, inhibitory cytokines being more sparsely distributed. TCR signal intensity did not affect resting/activated Treg proportions but molded activated Treg programs. The main lines of Treg heterogeneity in mice were strikingly conserved in human blood. These results reveal unexpected TCR-shaped states of activation, providing a framework to synthesize previous observations of Treg heterogeneity.

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Immunol Rev, 2019 Oct 09; 292(1). PMID: 31593314    Free PMC article.
Review.
Developmental and cellular age direct conversion of CD4+ T cells into RORγ+ or Helios+ colon Treg cells.
Alvin Pratama, Alexandra Schnell, Diane Mathis, Christophe Benoist.
J Exp Med, 2019 Nov 07; 217(1). PMID: 31685531    Free PMC article.
Helios+ and Helios- Treg subpopulations are phenotypically and functionally distinct and express dissimilar TCR repertoires.
Angela M Thornton, Jinghua Lu, +4 authors, Ethan M Shevach.
Eur J Immunol, 2019 Jan 09; 49(3). PMID: 30620397    Free PMC article.
Highly Cited.
Regulatory T cells in solid organ transplantation.
Muhammad Atif, Filomena Conti, +2 authors, Makoto Miyara.
Clin Transl Immunology, 2020 Feb 28; 9(2). PMID: 32104579    Free PMC article.
Review.
The epigenetic regulator ATF7ip inhibits Il2 expression, regulating Th17 responses.
Jun Hyung Sin, Cassandra Zuckerman, +4 authors, Michael R Waterfield.
J Exp Med, 2019 Jun 21; 216(9). PMID: 31217192    Free PMC article.
Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice.
Ying Wu, Yu-Mei Chang, +6 authors, Oliver A Garden.
Sci Rep, 2019 Sep 19; 9(1). PMID: 31530890    Free PMC article.
Transcriptional and Epigenetic Regulation of Effector and Memory CD8 T Cell Differentiation.
Yao Chen, Ryan Zander, +2 authors, Weiguo Cui.
Front Immunol, 2018 Dec 26; 9. PMID: 30581433    Free PMC article.
Review.
Transcriptional analysis of Foxp3+ Tregs and functions of two identified molecules during resolution of ALI.
Jason R Mock, Catherine F Dial, +6 authors, Claire M Doerschuk.
JCI Insight, 2019 Feb 13; 4(6). PMID: 30753170    Free PMC article.
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.
Leif S Ludwig, Caleb A Lareau, +17 authors, Vijay G Sankaran.
Cell, 2019 Mar 05; 176(6). PMID: 30827679    Free PMC article.
Highly Cited.
Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species.
Rapolas Zilionis, Camilla Engblom, +15 authors, Allon M Klein.
Immunity, 2019 Apr 14; 50(5). PMID: 30979687    Free PMC article.
Highly Cited.
Distinct immunocyte-promoting and adipocyte-generating stromal components coordinate adipose tissue immune and metabolic tenors.
Raul German Spallanzani, David Zemmour, +5 authors, Diane Mathis.
Sci Immunol, 2019 May 06; 4(35). PMID: 31053654    Free PMC article.
Highly Cited.
CTLA-4-mediated transendocytosis of costimulatory molecules primarily targets migratory dendritic cells.
Vitalijs Ovcinnikovs, Ellen M Ross, +9 authors, Lucy S K Walker.
Sci Immunol, 2019 Jun 04; 4(35). PMID: 31152091    Free PMC article.
Comparative analysis of CDR3 regions in paired human αβ CD8 T cells.
Kun Yu, Ji Shi, Dan Lu, Qiong Yang.
FEBS Open Bio, 2019 Jun 27; 9(8). PMID: 31237075    Free PMC article.
Clonal replacement of tumor-specific T cells following PD-1 blockade.
Kathryn E Yost, Ansuman T Satpathy, +13 authors, Howard Y Chang.
Nat Med, 2019 Jul 31; 25(8). PMID: 31359002    Free PMC article.
Highly Cited.
Multimodal single-cell approaches shed light on T cell heterogeneity.
Aparna Nathan, Yuriy Baglaenko, +2 authors, Soumya Raychaudhuri.
Curr Opin Immunol, 2019 Aug 21; 61. PMID: 31430664    Free PMC article.
Review.
Transcriptional Regulation of Differentiation and Functions of Effector T Regulatory Cells.
Shin-Ichi Koizumi, Hiroki Ishikawa.
Cells, 2019 Aug 23; 8(8). PMID: 31434282    Free PMC article.
Review.
Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes.
Yehezqel Elyahu, Idan Hekselman, +12 authors, Alon Monsonego.
Sci Adv, 2019 Aug 29; 5(8). PMID: 31457092    Free PMC article.
Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy.
Jerome C Martin, Christie Chang, +28 authors, Ephraim Kenigsberg.
Cell, 2019 Sep 03; 178(6). PMID: 31474370    Free PMC article.
Highly Cited.
scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data.
Ruoxin Li, Gerald Quon.
Genome Biol, 2019 Sep 11; 20(1). PMID: 31500668    Free PMC article.
From stability to dynamics: understanding molecular mechanisms of regulatory T cells through Foxp3 transcriptional dynamics.
D Bending, M Ono.
Clin Exp Immunol, 2018 Aug 05; 197(1). PMID: 30076771    Free PMC article.
Review.
Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)-driven pulmonary immunopathogenesis.
Junsong Zhang, Jun Liu, +14 authors, Hui Zhang.
PLoS Pathog, 2020 Feb 27; 16(2). PMID: 32101596    Free PMC article.
Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis.
Fernanda do Valle Duraes, Armelle Lafont, +12 authors, Max Warncke.
JCI Insight, 2020 Feb 14; 5(3). PMID: 32051345    Free PMC article.
Opposing T cell responses in experimental autoimmune encephalomyelitis.
Naresha Saligrama, Fan Zhao, +13 authors, Mark M Davis.
Nature, 2019 Aug 09; 572(7770). PMID: 31391585    Free PMC article.
Dynamic changes in the regulatory T-cell heterogeneity and function by murine IL-2 mutein.
Daniel R Lu, Hao Wu, +5 authors, Hyewon Phee.
Life Sci Alliance, 2020 Apr 10; 3(5). PMID: 32269069    Free PMC article.
Single Cell RNA Sequencing in Atherosclerosis Research.
Jesse W Williams, Holger Winkels, +3 authors, Klaus Ley.
Circ Res, 2020 Apr 24; 126(9). PMID: 32324494    Free PMC article.
Review.
IL-2 enhances ex vivo-expanded regulatory T-cell persistence after adoptive transfer.
Scott N Furlan, Karnail Singh, +7 authors, Leslie S Kean.
Blood Adv, 2020 Apr 21; 4(8). PMID: 32311015    Free PMC article.
CD4+ teff cell heterogeneity: the perspective from single-cell transcriptomics.
David Zemmour, Evgeny Kiner, Christophe Benoist.
Curr Opin Immunol, 2020 Apr 08; 63. PMID: 32259715    Free PMC article.
Review.
Tracking the immune response with single-cell genomics.
Kathryn E Yost, Howard Y Chang, Ansuman T Satpathy.
Vaccine, 2019 Dec 21; 38(28). PMID: 31859202    Free PMC article.
Single-Cell RNA-Seq Analysis Uncovers Distinct Functional Human NKT Cell Sub-Populations in Peripheral Blood.
Li Zhou, Indra Adrianto, +3 authors, Qing-Sheng Mi.
Front Cell Dev Biol, 2020 Jun 13; 8. PMID: 32528956    Free PMC article.
In situ conversion of defective Treg into SuperTreg cells to treat advanced IPEX-like disorders in mice.
Yongqin Li, Yuxin Chen, +9 authors, Tian Chi.
Nat Commun, 2020 Jun 05; 11(1). PMID: 32493900    Free PMC article.
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis.
Dominik Trzupek, Melanie Dunstan, +10 authors, Ricardo C Ferreira.
Genome Med, 2020 Jun 26; 12(1). PMID: 32580776    Free PMC article.
Unravelling the heterogeneity and dynamic relationships of tumor-infiltrating T cells by single-cell RNA sequencing analysis.
Xin Yu, Lei Zhang, +2 authors, Wenjun Ouyang.
J Leukoc Biol, 2020 Apr 10; 107(6). PMID: 32272497    Free PMC article.
Review.
Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer.
David Y Oh, Serena S Kwek, +17 authors, Lawrence Fong.
Cell, 2020 Jun 05; 181(7). PMID: 32497499    Free PMC article.
Tumor invasion in draining lymph nodes is associated with Treg accumulation in breast cancer patients.
Nicolas Gonzalo Núñez, Jimena Tosello Boari, +18 authors, Eliane Piaggio.
Nat Commun, 2020 Jul 01; 11(1). PMID: 32601304    Free PMC article.
Tumor necrosis factor receptor family costimulation increases regulatory T-cell activation and function via NF-κB.
Martina Lubrano di Ricco, Emilie Ronin, +8 authors, Benoît L Salomon.
Eur J Immunol, 2020 Feb 06; 50(7). PMID: 32012260    Free PMC article.
Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development.
Justin Le, Jeong Eun Park, +10 authors, Chintan Parekh.
Immunity, 2020 Jun 20; 52(6). PMID: 32553173    Free PMC article.
Discovery of surrogate agonists for visceral fat Treg cells that modulate metabolic indices in vivo.
Ricardo A Fernandes, Chaoran Li, +10 authors, K Christopher Garcia.
Elife, 2020 Aug 11; 9. PMID: 32773038    Free PMC article.
Single-cell analysis of tumors: Creating new value for molecular biomarker discovery of cancer stem cells and tumor-infiltrating immune cells.
Ramin Radpour, Farzad Forouharkhou.
World J Stem Cells, 2019 Jan 12; 10(11). PMID: 30631391    Free PMC article.
Review.
The expanding role of systems immunology in decoding the T cell receptor repertoire.
Vanessa Venturi, Paul G Thomas.
Curr Opin Syst Biol, 2019 May 21; 12. PMID: 31106281    Free PMC article.
Tumor-Promoting Ly-6G+ SiglecFhigh Cells Are Mature and Long-Lived Neutrophils.
Christina Pfirschke, Camilla Engblom, +11 authors, Mikael J Pittet.
Cell Rep, 2020 Sep 24; 32(12). PMID: 32966785    Free PMC article.
TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures.
Ang A Tu, Todd M Gierahn, +6 authors, J Christopher Love.
Nat Immunol, 2019 Nov 21; 20(12). PMID: 31745340    Free PMC article.
Persistent IL-2 Receptor Signaling by IL-2/CD25 Fusion Protein Controls Diabetes in NOD Mice by Multiple Mechanisms.
Natasha C Ward, Jen Bon Lui, +8 authors, Thomas R Malek.
Diabetes, 2020 Aug 28; 69(11). PMID: 32843568    Free PMC article.
Transcriptional regulation of Treg homeostasis and functional specification.
Ke Wang, Wenxian Fu.
Cell Mol Life Sci, 2020 May 01; 77(21). PMID: 32350553    Free PMC article.
Review.
A Comparison of Automated Perfusion- and Manual Diffusion-Based Human Regulatory T Cell Expansion and Functionality Using a Soluble Activator Complex.
Mark Jones, Brian Nankervis, +3 authors, Claire Coeshott.
Cell Transplant, 2020 Jul 15; 29. PMID: 32662685    Free PMC article.
Single-Cell Techniques and Deep Learning in Predicting Drug Response.
Zhenyu Wu, Patrick J Lawrence, +3 authors, Qin Ma.
Trends Pharmacol Sci, 2020 Nov 07; 41(12). PMID: 33153777    Free PMC article.
Review.
Single-Cell RNA-Sequencing Identifies Activation of TP53 and STAT1 Pathways in Human T Lymphocyte Subpopulations in Response to Ex Vivo Radiation Exposure.
Maria Moreno-Villanueva, Ye Zhang, +10 authors, Honglu Wu.
Int J Mol Sci, 2019 May 15; 20(9). PMID: 31083348    Free PMC article.
Reprogramming the Tumor Microenvironment to Improve Immunotherapy: Emerging Strategies and Combination Therapies.
Meenal Datta, Lisa M Coussens, +2 authors, Rakesh K Jain.
Am Soc Clin Oncol Educ Book, 2019 May 18; 39. PMID: 31099649    Free PMC article.
Review.
T Follicular Regulatory Cell-Derived Fibrinogen-like Protein 2 Regulates Production of Autoantibodies and Induction of Systemic Autoimmunity.
Waradon Sungnak, Allon Wagner, +11 authors, Vijay K Kuchroo.
J Immunol, 2020 Nov 11; 205(12). PMID: 33168576    Free PMC article.
Bone marrow Tregs mediate stromal cell function and support hematopoiesis via IL-10.
Virginia Camacho, Victoria R Matkins, +12 authors, Robert S Welner.
JCI Insight, 2020 Nov 20; 5(22). PMID: 33208555    Free PMC article.
TGFβ biology in cancer progression and immunotherapy.
Rik Derynck, Shannon J Turley, Rosemary J Akhurst.
Nat Rev Clin Oncol, 2020 Jul 28; 18(1). PMID: 32710082
Review.
The multifaceted functions of follicular regulatory T cells.
Peter T Sage, Arlene H Sharpe.
Curr Opin Immunol, 2020 Nov 12; 67. PMID: 33176227    Free PMC article.
Review.
Applications of Single-Cell Omics to Dissect Tumor Microenvironment.
Tingting Guo, Weimin Li, Xuyu Cai.
Front Genet, 2020 Dec 18; 11. PMID: 33329692    Free PMC article.
Review.
Regulatory T Cell Stability and Plasticity in Atherosclerosis.
Amal J Ali, Jeffrey Makings, Klaus Ley.
Cells, 2020 Dec 17; 9(12). PMID: 33322482    Free PMC article.
Review.
Efficient IL-2R signaling differentially affects the stability, function, and composition of the regulatory T-cell pool.
Marc Permanyer, Berislav Bošnjak, +10 authors, Reinhold Förster.
Cell Mol Immunol, 2021 Jan 08; 18(2). PMID: 33408345    Free PMC article.
T-regulatory cells from patients with rheumatoid arthritis retain suppressor functions in vitro.
Daniil Shevyrev, Valeriy Tereshchenko, +3 authors, Veroniсa Koksharova.
Exp Ther Med, 2021 Jan 28; 21(3). PMID: 33500700    Free PMC article.
Thymic origins of autoimmunity-lessons from inborn errors of immunity.
Rosa Bacchetta, Kenneth Weinberg.
Semin Immunopathol, 2021 Feb 04; 43(1). PMID: 33532929    Free PMC article.
Review.
T cell analysis in vaccination.
Mark M Davis.
Curr Opin Immunol, 2020 Jul 01; 65. PMID: 32604000    Free PMC article.
Review.
ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
Kenneth H Hu, John P Eichorst, +7 authors, Matthew F Krummel.
Nat Methods, 2020 Jul 08; 17(8). PMID: 32632238    Free PMC article.
Tissue Treg Secretomes and Transcription Factors Shared With Stem Cells Contribute to a Treg Niche to Maintain Treg-Ness With 80% Innate Immune Pathways, and Functions of Immunosuppression and Tissue Repair.
Ruijing Zhang, Keman Xu, +16 authors, Xiaofeng Yang.
Front Immunol, 2021 Feb 23; 11. PMID: 33613572    Free PMC article.
A LAT-Based Signaling Complex in the Immunological Synapse as Determined with Live Cell Imaging Is Less Stable in T Cells with Regulatory Capability.
Yikui Li, Helen M Tunbridge, +8 authors, Christoph Wülfing.
Cells, 2021 Mar 07; 10(2). PMID: 33671236    Free PMC article.
Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program.
Mariya London, Angelina M Bilate, +2 authors, Daniel Mucida.
Nat Immunol, 2021 Mar 10; 22(4). PMID: 33686285    Free PMC article.
Characterization and Monitoring of Antigen-Responsive T Cell Clones Using T Cell Receptor Gene Expression Analysis.
Sabrina Pollastro, Marie de Bourayne, +6 authors, Niek de Vries.
Front Immunol, 2021 Mar 09; 11. PMID: 33679697    Free PMC article.
IgG Epitopes Processed and Presented by IgG+ B Cells Induce Suppression by Human Thymic-Derived Regulatory T Cells.
Li-En Hsieh, John Sidney, +5 authors, Alessandra Franco.
J Immunol, 2021 Feb 14; 206(6). PMID: 33579724    Free PMC article.
Decreased numbers and sex-based differences of circulating regulatory T cells in patients with seropositive undifferentiated arthritis.
Hong-Qing Niu, Chenrui Yuan, +5 authors, Xiao-Feng Li.
Ther Adv Chronic Dis, 2021 Mar 16; 12. PMID: 33717426    Free PMC article.
SARS-CoV-2 infection of the oral cavity and saliva.
Ni Huang, Paola Pérez, +51 authors, Kevin M Byrd.
Nat Med, 2021 Mar 27; 27(5). PMID: 33767405    Free PMC article.
Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation.
Sang-Ho Yoon, Seo-Won Choi, +2 authors, Jin-Wu Nam.
NPJ Precis Oncol, 2021 Mar 28; 5(1). PMID: 33772139    Free PMC article.
Single-cell analysis of FOXP3 deficiencies in humans and mice unmasks intrinsic and extrinsic CD4+ T cell perturbations.
David Zemmour, Louis-Marie Charbonnier, +18 authors, Christophe Benoist.
Nat Immunol, 2021 Apr 10; 22(5). PMID: 33833438    Free PMC article.
Single-Cell Sequencing Reveals the Transcriptome and TCR Characteristics of pTregs and in vitro Expanded iTregs.
Zhenzhen Hui, Jiali Zhang, +5 authors, Xiubao Ren.
Front Immunol, 2021 Apr 20; 12. PMID: 33868236    Free PMC article.
Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas.
Zohreh Amoozgar, Jonas Kloepper, +19 authors, Rakesh K Jain.
Nat Commun, 2021 May 13; 12(1). PMID: 33976133    Free PMC article.
The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments.
Ricardo Grieshaber-Bouyer, Felix A Radtke, +8 authors, ImmGen Consortium.
Nat Commun, 2021 May 19; 12(1). PMID: 34001893    Free PMC article.
Canonical Secretomes, Innate Immune Caspase-1-, 4/11-Gasdermin D Non-Canonical Secretomes and Exosomes May Contribute to Maintain Treg-Ness for Treg Immunosuppression, Tissue Repair and Modulate Anti-Tumor Immunity via ROS Pathways.
Dong Ni, TingTing Tang, +14 authors, Xiaofeng Yang.
Front Immunol, 2021 Jun 05; 12. PMID: 34084175    Free PMC article.
Clinical and Basic Research Progress on Treg-Induced Immune Tolerance in Liver Transplantation.
Xuhao Ni, Qi Wang, Jian Gu, Ling Lu.
Front Immunol, 2021 Jun 08; 12. PMID: 34093514    Free PMC article.
Review.
A combination of cyclophosphamide and interleukin-2 allows CD4+ T cells converted to Tregs to control scurfy syndrome.
Marianne Delville, Florence Bellier, +19 authors, Emmanuelle Six.
Blood, 2021 Feb 06; 137(17). PMID: 33545713    Free PMC article.
Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human Treg compartment.
Yuechen Luo, Changlu Xu, +18 authors, Xiaoming Feng.
Nat Commun, 2021 Jun 25; 12(1). PMID: 34162888    Free PMC article.
The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss.
Pengfei Chen, Liying Zhou, +16 authors, Lisha Mou.
Front Immunol, 2021 Jun 26; 12. PMID: 34168655    Free PMC article.
Harnessing Mechanisms of Immune Tolerance to Improve Outcomes in Solid Organ Transplantation: A Review.
Priscila Ferreira Slepicka, Mahboubeh Yazdanifar, Alice Bertaina.
Front Immunol, 2021 Jun 29; 12. PMID: 34177941    Free PMC article.
Review.
A Panel Comprising Serum Amyloid A, White Blood Cells and Nihss for the Triage of Patients at Low Risk of Post-Stroke Infection.
Leire Azurmendi Gil, Laura Krattinger-Turbatu, +2 authors, Jean-Charles Sanchez.
Diagnostics (Basel), 2021 Jul 03; 11(6). PMID: 34200779    Free PMC article.
Strength and Numbers: The Role of Affinity and Avidity in the 'Quality' of T Cell Tolerance.
Sébastien This, Stefanie F Valbon, Marie-Ève Lebel, Heather J Melichar.
Cells, 2021 Jul 03; 10(6). PMID: 34204485    Free PMC article.
Review.
Insights into the biology and therapeutic implications of TNF and regulatory T cells.
Benoit L Salomon.
Nat Rev Rheumatol, 2021 Jul 07; 17(8). PMID: 34226727
Review.
Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection.
Qing Wang, Cheng Peng, +7 authors, Qiwei Qin.
PLoS Pathog, 2021 Jun 30; 17(6). PMID: 34185811    Free PMC article.
Endothelial Immunity Trained by Coronavirus Infections, DAMP Stimulations and Regulated by Anti-Oxidant NRF2 May Contribute to Inflammations, Myelopoiesis, COVID-19 Cytokine Storms and Thromboembolism.
Ying Shao, Jason Saredy, +10 authors, Xiaofeng Yang.
Front Immunol, 2021 Jul 13; 12. PMID: 34248940    Free PMC article.
Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing.
Juber Herrera-Uribe, Jayne E Wiarda, +7 authors, Christopher K Tuggle.
Front Genet, 2021 Jul 13; 12. PMID: 34249103    Free PMC article.
High-throughput and single-cell T cell receptor sequencing technologies.
Joy A Pai, Ansuman T Satpathy.
Nat Methods, 2021 Jul 21; 18(8). PMID: 34282327
Review.
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model.
Sascha Jung, Kartikeya Singh, Antonio Del Sol.
Brief Bioinform, 2020 Nov 13; 22(4). PMID: 33179736    Free PMC article.
Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'.
David S Fischer, Meshal Ansari, +27 authors, Kilian Schober.
Nat Commun, 2021 Jul 28; 12(1). PMID: 34312385    Free PMC article.
Organelle Crosstalk Regulators Are Regulated in Diseases, Tumors, and Regulatory T Cells: Novel Classification of Organelle Crosstalk Regulators.
Ming Liu, Na Wu, +19 authors, Xiaofeng Yang.
Front Cardiovasc Med, 2021 Aug 10; 8. PMID: 34368262    Free PMC article.
Peptide Allergen Immunotherapy: A New Perspective in Olive-Pollen Allergy.
David Calzada, Lucía Cremades-Jimeno, María López-Ramos, Blanca Cárdaba.
Pharmaceutics, 2021 Aug 11; 13(7). PMID: 34371699    Free PMC article.
Review.
TCF-1 controls Treg cell functions that regulate inflammation, CD8+ T cell cytotoxicity and severity of colon cancer.
Abu Osman, Bingyu Yan, +7 authors, Khashayarsha Khazaie.
Nat Immunol, 2021 Aug 14; 22(9). PMID: 34385712    Free PMC article.
Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA).
Stefan A Schattgen, Kate Guion, +5 authors, Philip Bradley.
Nat Biotechnol, 2021 Aug 25; 40(1). PMID: 34426704    Free PMC article.
Granulocyte-macrophage colony-stimulating factor mRNA and Neuroprotective Immunity in Parkinson's disease.
Katherine E Olson, Krista L Namminga, +11 authors, Howard E Gendelman.
Biomaterials, 2021 Apr 12; 272. PMID: 33839625    Free PMC article.
Insulin signaling establishes a developmental trajectory of adipose regulatory T cells.
Yangyang Li, Ying Lu, +19 authors, Bin Li.
Nat Immunol, 2021 Aug 26; 22(9). PMID: 34429546
Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity.
Yuguang Liu, Patricio Jeraldo, +3 authors, Marina Walther-Antonio.
Anal Chem, 2019 Jun 13; 91(13). PMID: 31188565    Free PMC article.
A tumor-specific mechanism of Treg enrichment mediated by the integrin αvβ8.
Robert I Seed, Kenji Kobayashi, +14 authors, Stephen L Nishimura.
Sci Immunol, 2021 Mar 28; 6(57). PMID: 33771888    Free PMC article.
Hemozoin-mediated inflammasome activation limits long-lived anti-malarial immunity.
Angela D Pack, Patrick V Schwartzhoff, +6 authors, Noah S Butler.
Cell Rep, 2021 Aug 26; 36(8). PMID: 34433049    Free PMC article.
Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing.
Amund Holte Berger, Eirik Bratland, +7 authors, Anette Susanne Bøe Wolff.
Front Immunol, 2021 Sep 17; 12. PMID: 34526996    Free PMC article.
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells.
Myung-Chul Kim, Nicholas Borcherding, +32 authors, Weizhou Zhang.
Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187    Free PMC article.
Th1 polarization defines the synovial fluid T cell compartment in oligoarticular juvenile idiopathic arthritis.
Amélie M Julé, Kacie J Hoyt, +22 authors, Lauren A Henderson.
JCI Insight, 2021 Aug 18; 6(18). PMID: 34403374    Free PMC article.
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq.
Ying Yao, Łukasz Wyrozżemski, +2 authors, Shuo-Wang Qiao.
PLoS One, 2021 Oct 08; 16(10). PMID: 34618841    Free PMC article.
Phenotypic and Functional Diversity in Regulatory T Cells.
Louisa E Sjaastad, David L Owen, Sean I Tracy, Michael A Farrar.
Front Cell Dev Biol, 2021 Oct 12; 9. PMID: 34631704    Free PMC article.
Review.
IL-35 promotes CD4+Foxp3+ Tregs and inhibits atherosclerosis via maintaining CCR5-amplified Treg-suppressive mechanisms.
Ying Shao, William Y Yang, +9 authors, Xiaofeng Yang.
JCI Insight, 2021 Oct 09; 6(19). PMID: 34622804    Free PMC article.
Transient mTOR inhibition rescues 4-1BB CAR-Tregs from tonic signal-induced dysfunction.
Baptiste Lamarthée, Armance Marchal, +20 authors, Julien Zuber.
Nat Commun, 2021 Nov 10; 12(1). PMID: 34750385    Free PMC article.
Newly Found Peacekeeper: Potential of CD8+ Tregs for Graft-Versus-Host Disease.
Weihao Wang, Tao Hong, +5 authors, Xi Zhang.
Front Immunol, 2021 Dec 14; 12. PMID: 34899714    Free PMC article.
Review.
Autoreactive T cell receptors with shared germline-like α chains in type 1 diabetes.
Peter S Linsley, Fariba Barahmand-Pour-Whitman, +16 authors, Karen Cerosaletti.
JCI Insight, 2021 Nov 23; 6(22). PMID: 34806648    Free PMC article.
Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates.
Davide Simone, Frank Penkava, +3 authors, Paul Bowness.
Commun Biol, 2021 Dec 16; 4(1). PMID: 34907325    Free PMC article.
TNF plays a crucial role in inflammation by signaling via T cell TNFR2.
Muhammad S Alam, Shizuka Otsuka, +5 authors, Jonathan D Ashwell.
Proc Natl Acad Sci U S A, 2021 Dec 08; 118(50). PMID: 34873037    Free PMC article.
Single-cell immune profiling reveals functional diversity of T cells in tuberculous pleural effusion.
Yi Cai, Yejun Wang, +13 authors, Xinchun Chen.
J Exp Med, 2022 Jan 22; 219(3). PMID: 35061012    Free PMC article.
Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target.
Nourhan Abdelfattah, Parveen Kumar, +17 authors, Kyuson Yun.
Nat Commun, 2022 Feb 11; 13(1). PMID: 35140215    Free PMC article.
Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate.
Kaitlyn A Lagattuta, Joyce B Kang, +6 authors, Soumya Raychaudhuri.
Nat Immunol, 2022 Feb 19; 23(3). PMID: 35177831    Free PMC article.
Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity.
Mathieu Uzzan, Jerome C Martin, +53 authors, Saurabh Mehandru.
Nat Med, 2022 Feb 23; 28(4). PMID: 35190725    Free PMC article.
Discovering dominant tumor immune archetypes in a pan-cancer census.
Alexis J Combes, Bushra Samad, +35 authors, Matthew F Krummel.
Cell, 2021 Dec 29; 185(1). PMID: 34963056    Free PMC article.
29 m6A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses.
Ming Liu, Keman Xu, +14 authors, Xiaofeng Yang.
J Immunol Res, 2022 Feb 26; 2022. PMID: 35211628    Free PMC article.
Absent in Melanoma 2 (AIM2) Regulates the Stability of Regulatory T Cells.
Beatriz Lozano-Ruiz, Amalia Tzoumpa, +9 authors, José M González-Navajas.
Int J Mol Sci, 2022 Feb 27; 23(4). PMID: 35216346    Free PMC article.
Fighting the SARS-CoV-2 pandemic requires a global approach to understanding the heterogeneity of vaccine responses.
Jeffrey A Tomalka, Mehul S Suthar, Steven G Deeks, Rafick Pierre Sekaly.
Nat Immunol, 2022 Feb 26; 23(3). PMID: 35210622
Review.
Regulatory T Cells: Angels or Demons in the Pathophysiology of Sepsis?
Yu-Lei Gao, Ying Yao, +8 authors, Yan-Fen Chai.
Front Immunol, 2022 Mar 15; 13. PMID: 35281010    Free PMC article.
Review.
Aorta in Pathologies May Function as an Immune Organ by Upregulating Secretomes for Immune and Vascular Cell Activation, Differentiation and Trans-Differentiation-Early Secretomes may Serve as Drivers for Trained Immunity.
Yifan Lu, Yu Sun, +13 authors, Xiaofeng Yang.
Front Immunol, 2022 Mar 25; 13. PMID: 35320939    Free PMC article.
Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells.
Shouguo Gao, Zhijie Wu, +10 authors, Neal S Young.
Nat Commun, 2022 Apr 13; 13(1). PMID: 35411048    Free PMC article.
KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.
Jing Li, Maxim Zaslavsky, +33 authors, Mark M Davis.
Science, 2022 Mar 09; 376(6590). PMID: 35258337    Free PMC article.
T cells and the skin: from protective immunity to inflammatory skin disorders.
Allen W Ho, Thomas S Kupper.
Nat Rev Immunol, 2019 Apr 18; 19(8). PMID: 30992525
Highly Cited. Review.
Cytolytic CD4+ and CD8+ Regulatory T-Cells and Implications for Developing Immunotherapies to Combat Graft-Versus-Host Disease.
Sara Bolivar-Wagers, Jemma H Larson, Sujeong Jin, Bruce R Blazar.
Front Immunol, 2022 May 03; 13. PMID: 35493508    Free PMC article.
Review.
Chronic Exposure to the Combination of Cigarette Smoke and Morphine Decreases CD4+ Regulatory T Cell Numbers by Reprogramming the Treg Cell Transcriptome.
Ying Shao, William Cornwell, +8 authors, Xiaofeng Yang.
Front Immunol, 2022 May 07; 13. PMID: 35514978    Free PMC article.
PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains Treg homeostasis during ageing.
Egle Danileviciute, Ni Zeng, +27 authors, Feng Q Hefeng.
Nat Metab, 2022 May 27; 4(5). PMID: 35618940
AIRR Community Guide to Planning and Performing AIRR-Seq Experiments.
Anne Eugster, Magnolia L Bostick, +8 authors, AIRR Community.
Methods Mol Biol, 2022 May 28; 2453. PMID: 35622331