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

¹ Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
² Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
³ Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. dm@hms.harvard.edu.
⁴ Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. cbdm@hms.harvard.edu.

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.

Other Links

Free PMC article
Full text on Nature immunology

References
Cited By

References
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Jernej Godec, Yan Tan, +5 authors, W Nicholas Haining. less Immunity, 2016 Jan 23; 44(1). PMID: 26795250 Free PMC article. Highly Cited.
Transcriptional control of regulatory T cell development and function. Chong T Luo, Ming O Li. Trends Immunol, 2013 Sep 11; 34(11). PMID: 24016547 Free PMC article. Review.
Plasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells. Takahisa Miyao, Stefan Floess, +5 authors, Shohei Hori. less Immunity, 2012 Feb 14; 36(2). PMID: 22326580 Highly Cited.
T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. Amy E Moran, Keli L Holzapfel, +4 authors, Kristin A Hogquist. less J Exp Med, 2011 May 25; 208(6). PMID: 21606508 Free PMC article. Highly Cited.
Foxp3+ regulatory T cells: differentiation, specification, subphenotypes. Markus Feuerer, Jonathan A Hill, Diane Mathis, Christophe Benoist. Nat Immunol, 2009 Jun 19; 10(7). PMID: 19536194 Highly Cited. Review.
Restricted islet-cell reactive T cell repertoire of early pancreatic islet infiltrates in NOD mice. Felix J Baker, Mark Lee, Yueh-hsiu Chien, Mark M Davis. Proc Natl Acad Sci U S A, 2002 Jun 26; 99(14). PMID: 12082183 Free PMC article.
Apoptotic signals delivered through the T-cell receptor of a T-cell hybrid require the immediate-early gene nur77. Z G Liu, S W Smith, +2 authors, K A McLaughlin, L M Schwartz, B A Osborne. less Nature, 1994 Jan 20; 367(6460). PMID: 8121494 Highly Cited.
Continuous T cell receptor signals maintain a functional regulatory T cell pool. J Christoph Vahl, Christoph Drees, +19 authors, Marc Schmidt-Supprian. less Immunity, 2014 Dec 04; 41(5). PMID: 25464853 Highly Cited.
Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. Graham Heimberg, Rajat Bhatnagar, Hana El-Samad, Matt Thomson. Cell Syst, 2016 May 03; 2(4). PMID: 27135536 Free PMC article.
MiXCR: software for comprehensive adaptive immunity profiling. Dmitriy A Bolotin, Stanislav Poslavsky, +4 authors, Dmitriy M Chudakov. less Nat Methods, 2015 Apr 30; 12(5). PMID: 25924071 Highly Cited.
CCR6 expression defines regulatory effector/memory-like cells within the CD25(+)CD4+ T-cell subset. Markus Kleinewietfeld, Fabiola Puentes, +3 authors, Kirsten Falk. less Blood, 2004 Dec 23; 105(7). PMID: 15613550 Highly Cited.
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Weiming Ouyang, Will Liao, +13 authors, Ming O Li. less Nature, 2012 Nov 09; 491(7425). PMID: 23135404 Free PMC article. Highly Cited.
A Regulatory T-Cell Gene Signature Is a Specific and Sensitive Biomarker to Identify Children With New-Onset Type 1 Diabetes. Anne M Pesenacker, Adele Y Wang, +8 authors, Megan K Levings. less Diabetes, 2016 Jan 21; 65(4). PMID: 26786322
CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai. Cell Rep, 2012 Sep 04; 2(3). PMID: 22939981 Highly Cited.
Once a Treg, always a Treg? Deepali V Sawant, Dario A A Vignali. Immunol Rev, 2014 Apr 10; 259(1). PMID: 24712466 Free PMC article. Highly Cited. Review.
MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. Esen Sefik, Naama Geva-Zatorsky, +14 authors, Christophe Benoist. less Science, 2015 Aug 15; 349(6251). PMID: 26272906 Free PMC article. Highly Cited.
MUCOSAL IMMUNOLOGY. The microbiota regulates type 2 immunity through RORγt⁺ T cells. Caspar Ohnmacht, Joo-Hong Park, +15 authors, Gérard Eberl. less Science, 2015 Jul 15; 349(6251). PMID: 26160380 Highly Cited.
Bayesian approach to single-cell differential expression analysis. Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods, 2014 May 20; 11(7). PMID: 24836921 Free PMC article. Highly Cited.
Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Sanjay M Prakadan, Alex K Shalek, David A Weitz. Nat Rev Genet, 2017 Apr 11; 18(6). PMID: 28392571 Free PMC article. Highly Cited. Review.
BACH2 represses effector programs to stabilize T(reg)-mediated immune homeostasis. Rahul Roychoudhuri, Kiyoshi Hirahara, +27 authors, Nicholas P Restifo. less Nature, 2013 Jun 04; 498(7455). PMID: 23728300 Free PMC article. Highly Cited.
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Wenxian Fu, Ayla Ergun, +12 authors, Christophe Benoist. less Nat Immunol, 2012 Sep 11; 13(10). PMID: 22961053 Free PMC article. Highly Cited.
Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells. Estelle Bettelli, Yijun Carrier, +5 authors, Vijay K Kuchroo. less Nature, 2006 May 02; 441(7090). PMID: 16648838 Highly Cited.
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Diego Adhemar Jaitin, Ephraim Kenigsberg, +8 authors, Ido Amit. less Science, 2014 Feb 18; 343(6172). PMID: 24531970 Free PMC article. Highly Cited.
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Daehwan Kim, Geo Pertea, +3 authors, Steven L Salzberg. less Genome Biol, 2013 Apr 27; 14(4). PMID: 23618408 Free PMC article. Highly Cited.
T follicular regulatory cells. Peter T Sage, Arlene H Sharpe. Immunol Rev, 2016 Apr 19; 271(1). PMID: 27088919 Highly Cited. Review.
Stable inhibitory activity of regulatory T cells requires the transcription factor Helios. Hye-Jung Kim, R Anthony Barnitz, +10 authors, Harvey Cantor. less Science, 2015 Oct 17; 350(6258). PMID: 26472910 Free PMC article. Highly Cited.
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Alex K Shalek, Rahul Satija, +19 authors, Aviv Regev. less Nature, 2014 Jun 12; 510(7505). PMID: 24919153 Free PMC article. Highly Cited.
A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Yongqiang Feng, Joris van der Veeken, +10 authors, Alexander Y Rudensky. less Nature, 2015 Nov 26; 528(7580). PMID: 26605529 Free PMC article. Highly Cited.
Inhibition of p300 impairs Foxp3⁺ T regulatory cell function and promotes antitumor immunity. Yujie Liu, Liqing Wang, +11 authors, Wayne W Hancock. less Nat Med, 2013 Aug 21; 19(9). PMID: 23955711 Free PMC article.
Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity. David Zemmour, Alvin Pratama, +2 authors, Scott M Loughhead, Diane Mathis, Christophe Benoist. less Proc Natl Acad Sci U S A, 2017 Apr 12; 114(17). PMID: 28396406 Free PMC article. Highly Cited.
Differentiation and function of Foxp3(+) effector regulatory T cells. Erika Cretney, Axel Kallies, Stephen L Nutt. Trends Immunol, 2012 Dec 12; 34(2). PMID: 23219401 Review.
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Daniel Ramsköld, Shujun Luo, +9 authors, Rickard Sandberg. less Nat Biotechnol, 2012 Jul 24; 30(8). PMID: 22820318 Free PMC article. Highly Cited.
Costimulation via the tumor-necrosis factor receptor superfamily couples TCR signal strength to the thymic differentiation of regulatory T cells. Shawn A Mahmud, Luke S Manlove, +10 authors, Michael A Farrar. less Nat Immunol, 2014 Mar 19; 15(5). PMID: 24633226 Free PMC article. Highly Cited.
How regulatory T cells work. Dario A A Vignali, Lauren W Collison, Creg J Workman. Nat Rev Immunol, 2008 Jun 21; 8(7). PMID: 18566595 Free PMC article. Highly Cited. Review.
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Evan Z Macosko, Anindita Basu, +13 authors, Steven A McCarroll. less Cell, 2015 May 23; 161(5). PMID: 26000488 Free PMC article. Highly Cited.
Single-cell analysis of normal and FOXP3-mutant human T cells: FOXP3 expression without regulatory T cell development. Marc A Gavin, Troy R Torgerson, +7 authors, Alexander Y Rudensky. less Proc Natl Acad Sci U S A, 2006 Apr 18; 103(17). PMID: 16617117 Free PMC article. Highly Cited.
Aire Enforces Immune Tolerance by Directing Autoreactive T Cells into the Regulatory T Cell Lineage. Sven Malchow, Daniel S Leventhal, +3 authors, Peter A Savage. less Immunity, 2016 May 01; 44(5). PMID: 27130899 Free PMC article. Highly Cited.
CD4+ regulatory T cells control TH17 responses in a Stat3-dependent manner. Ashutosh Chaudhry, Dipayan Rudra, +4 authors, Alexander Y Rudensky. less Science, 2009 Oct 03; 326(5955). PMID: 19797626 Free PMC article. Highly Cited.
Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation. Marc Beyer, Yasser Thabet, +32 authors, Joachim L Schultze. less Nat Immunol, 2011 Aug 16; 12(9). PMID: 21841785 Free PMC article.
Functional delineation and differentiation dynamics of human CD4+ T cells expressing the FoxP3 transcription factor. Makoto Miyara, Yumiko Yoshioka, +15 authors, Shimon Sakaguchi. less Immunity, 2009 May 26; 30(6). PMID: 19464196 Highly Cited.
Revealing the vectors of cellular identity with single-cell genomics. Allon Wagner, Aviv Regev, Nir Yosef. Nat Biotechnol, 2016 Nov 09; 34(11). PMID: 27824854 Free PMC article. Highly Cited. Review.
Phenotypical and functional specialization of FOXP3+ regulatory T cells. Daniel J Campbell, Meghan A Koch. Nat Rev Immunol, 2011 Jan 27; 11(2). PMID: 21267013 Free PMC article. Highly Cited. Review.
The cytokines interleukin 27 and interferon-γ promote distinct Treg cell populations required to limit infection-induced pathology. Aisling O'Hara Hall, Daniel P Beiting, +20 authors, Christopher A Hunter. less Immunity, 2012 Sep 18; 37(3). PMID: 22981537 Free PMC article. Highly Cited.
Instability of the transcription factor Foxp3 leads to the generation of pathogenic memory T cells in vivo. Xuyu Zhou, Samantha L Bailey-Bucktrout, +6 authors, Jeffrey A Bluestone. less Nat Immunol, 2009 Jul 28; 10(9). PMID: 19633673 Free PMC article. Highly Cited.
mRNA-Seq whole-transcriptome analysis of a single cell. Fuchou Tang, Catalin Barbacioru, +9 authors, M Azim Surani. less Nat Methods, 2009 Apr 08; 6(5). PMID: 19349980 Highly Cited.
Regulatory T-cell suppressor program co-opts transcription factor IRF4 to control T(H)2 responses. Ye Zheng, Ashutosh Chaudhry, +7 authors, Alexander Y Rudensky. less Nature, 2009 Feb 03; 458(7236). PMID: 19182775 Free PMC article. Highly Cited.
T cell receptor signalling in the control of regulatory T cell differentiation and function. Ming O Li, Alexander Y Rudensky. Nat Rev Immunol, 2016 Mar 31; 16(4). PMID: 27026074 Free PMC article. Highly Cited. Review.
Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Saiful Islam, Una Kjällquist, +4 authors, Sten Linnarsson. less Nat Protoc, 2012 Apr 07; 7(5). PMID: 22481528 Highly Cited.
Thymus-derived regulatory T cells contribute to tolerance to commensal microbiota. Anna Cebula, Michal Seweryn, +7 authors, Leszek Ignatowicz. less Nature, 2013 Apr 30; 497(7448). PMID: 23624374 Free PMC article. Highly Cited.
Foxp3+ follicular regulatory T cells control the germinal center response. Michelle A Linterman, Wim Pierson, +11 authors, Carola G Vinuesa. less Nat Med, 2011 Jul 26; 17(8). PMID: 21785433 Free PMC article. Highly Cited.
Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions. Yeonseok Chung, Shinya Tanaka, +11 authors, Chen Dong. less Nat Med, 2011 Jul 26; 17(8). PMID: 21785430 Free PMC article. Highly Cited.
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Allon M Klein, Linas Mazutis, +6 authors, Marc W Kirschner. less Cell, 2015 May 23; 161(5). PMID: 26000487 Free PMC article. Highly Cited.
A function for interleukin 2 in Foxp3-expressing regulatory T cells. Jason D Fontenot, Jeffrey P Rasmussen, Marc A Gavin, Alexander Y Rudensky. Nat Immunol, 2005 Oct 18; 6(11). PMID: 16227984 Highly Cited.
A special population of regulatory T cells potentiates muscle repair. Dalia Burzyn, Wilson Kuswanto, +8 authors, Diane Mathis. less Cell, 2013 Dec 10; 155(6). PMID: 24315098 Free PMC article. Highly Cited.
Continuous requirement for the TCR in regulatory T cell function. Andrew G Levine, Aaron Arvey, Wei Jin, Alexander Y Rudensky. Nat Immunol, 2014 Sep 30; 15(11). PMID: 25263123 Free PMC article. Highly Cited.
Early T cell activation: integrating biochemical, structural, and biophysical cues. Bernard Malissen, Pierre Bongrand. Annu Rev Immunol, 2015 Apr 12; 33. PMID: 25861978 Review.
The Immunological Genome Project: networks of gene expression in immune cells. Tracy S P Heng, Michio W Painter, Immunological Genome Project Consortium. Nat Immunol, 2008 Sep 19; 9(10). PMID: 18800157 Highly Cited.
Immune homeostasis enforced by co-localized effector and regulatory T cells. Zhiduo Liu, Michael Y Gerner, +3 authors, Ronald N Germain. less Nature, 2015 Nov 26; 528(7581). PMID: 26605524 Free PMC article. Highly Cited.
Tissue Tregs. Marisella Panduro, Christophe Benoist, Diane Mathis. Annu Rev Immunol, 2016 May 12; 34. PMID: 27168246 Free PMC article. Highly Cited. Review.
The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells. Erika Cretney, Annie Xin, +8 authors, Axel Kallies. less Nat Immunol, 2011 Mar 08; 12(4). PMID: 21378976 Highly Cited.
Homeostasis and anergy of CD4(+)CD25(+) suppressor T cells in vivo. Marc A Gavin, Sally R Clarke, +2 authors, Ella Negrou, Alena Gallegos, Alexander Rudensky. less Nat Immunol, 2001 Dec 12; 3(1). PMID: 11740498 Highly Cited.
Foxp3 transcription-factor-dependent and -independent regulation of the regulatory T cell transcriptional signature. Jonathan A Hill, Markus Feuerer, +5 authors, Christophe Benoist. less Immunity, 2007 Nov 21; 27(5). PMID: 18024188 Highly Cited.
Interindividual variation in human T regulatory cells. Alessandra Ferraro, Anna Morena D'Alise, +10 authors, Christophe Benoist. less Proc Natl Acad Sci U S A, 2014 Mar 13; 111(12). PMID: 24610777 Free PMC article.
Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Andrew J Martins, Manikandan Narayanan, +8 authors, John S Tsang. less Cell Syst, 2017 Apr 04; 4(4). PMID: 28365150 Free PMC article.
Convergent and divergent effects of costimulatory molecules in conventional and regulatory CD4+ T cells. Ei Wakamatsu, Diane Mathis, Christophe Benoist. Proc Natl Acad Sci U S A, 2013 Jan 02; 110(3). PMID: 23277554 Free PMC article.
Differentiation of regulatory Foxp3+ T cells in the thymic cortex. Adrian Liston, Katherine M Nutsch, +4 authors, Alexander Y Rudensky. less Proc Natl Acad Sci U S A, 2008 Aug 13; 105(33). PMID: 18695219 Free PMC article. Highly Cited.
Selection of regulatory T cells in the thymus. Chyi-Song Hsieh, Hyang-Mi Lee, Chan-Wang J Lio. Nat Rev Immunol, 2012 Feb 11; 12(3). PMID: 22322317 Highly Cited. Review.
Regulatory T cells: mechanisms of differentiation and function. Steven Z Josefowicz, Li-Fan Lu, Alexander Y Rudensky. Annu Rev Immunol, 2012 Jan 10; 30. PMID: 22224781 Free PMC article. Highly Cited. Review.
Single-cell barcoding and sequencing using droplet microfluidics. Rapolas Zilionis, Juozas Nainys, +4 authors, Linas Mazutis. less Nat Protoc, 2016 Dec 09; 12(1). PMID: 27929523 Highly Cited.
Stability of the regulatory T cell lineage in vivo. Yuri P Rubtsov, Rachel E Niec, +5 authors, Alexander Y Rudensky. less Science, 2010 Oct 12; 329(5999). PMID: 20929851 Free PMC article. Highly Cited.
Extrathymic generation of regulatory T cells in placental mammals mitigates maternal-fetal conflict. Robert M Samstein, Steven Z Josefowicz, +2 authors, Aaron Arvey, Piper M Treuting, Alexander Y Rudensky. less Cell, 2012 Jul 10; 150(1). PMID: 22770213 Free PMC article. Highly Cited.
CCR7 provides localized access to IL-2 and defines homeostatically distinct regulatory T cell subsets. Kate S Smigiel, Elizabeth Richards, +4 authors, Daniel J Campbell. less J Exp Med, 2014 Jan 01; 211(1). PMID: 24378538 Free PMC article. Highly Cited.
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Maayan Baron, Adrian Veres, +9 authors, Itai Yanai. less Cell Syst, 2016 Oct 28; 3(4). PMID: 27667365 Free PMC article. Highly Cited.
Endogenous Nur77 Is a Specific Indicator of Antigen Receptor Signaling in Human T and B Cells. Judith F Ashouri, Arthur Weiss. J Immunol, 2016 Dec 13; 198(2). PMID: 27940659 Free PMC article.
Single-cell messenger RNA sequencing reveals rare intestinal cell types. Dominic Grün, Anna Lyubimova, +5 authors, Alexander van Oudenaarden. less Nature, 2015 Aug 20; 525(7568). PMID: 26287467 Highly Cited.
Guidance of regulatory T cell development by Satb1-dependent super-enhancer establishment. Yohko Kitagawa, Naganari Ohkura, +10 authors, Shimon Sakaguchi. less Nat Immunol, 2016 Dec 20; 18(2). PMID: 27992401 Free PMC article. Highly Cited.
Peripheral education of the immune system by colonic commensal microbiota. Stephanie K Lathrop, Seth M Bloom, +6 authors, Chyi-Song Hsieh. less Nature, 2011 Sep 23; 478(7368). PMID: 21937990 Free PMC article. Highly Cited.
Regulatory T cell lineage specification by the forkhead transcription factor foxp3. Jason D Fontenot, Jeffrey P Rasmussen, +3 authors, Alexander Y Rudensky. less Immunity, 2005 Mar 23; 22(3). PMID: 15780990 Highly Cited.
Scaling single-cell genomics from phenomenology to mechanism. Amos Tanay, Aviv Regev. Nature, 2017 Jan 20; 541(7637). PMID: 28102262 Free PMC article. Highly Cited. Review.
Aire controls gene expression in the thymic epithelium with ordered stochasticity. Matthew Meredith, David Zemmour, Diane Mathis, Christophe Benoist. Nat Immunol, 2015 Aug 04; 16(9). PMID: 26237550 Free PMC article. Highly Cited.
The transcription factor T-bet controls regulatory T cell homeostasis and function during type 1 inflammation. Meghan A Koch, Glady's Tucker-Heard, +3 authors, Daniel J Campbell. less Nat Immunol, 2009 May 05; 10(6). PMID: 19412181 Free PMC article. Highly Cited.
Homeostatic maintenance of natural Foxp3(+) CD25(+) CD4(+) regulatory T cells by interleukin (IL)-2 and induction of autoimmune disease by IL-2 neutralization. Ruka Setoguchi, Shohei Hori, Takeshi Takahashi, Shimon Sakaguchi. J Exp Med, 2005 Mar 09; 201(5). PMID: 15753206 Free PMC article. Highly Cited.
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol, 2014 Dec 18; 15(12). PMID: 25516281 Free PMC article. Highly Cited.
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Robert M Samstein, Aaron Arvey, +11 authors, Alexander Y Rudensky. less Cell, 2012 Oct 02; 151(1). PMID: 23021222 Free PMC article. Highly Cited.
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Alexandra-Chloé Villani, Rahul Satija, +21 authors, Nir Hacohen. less Science, 2017 Apr 22; 356(6335). PMID: 28428369 Free PMC article. Highly Cited.
Singular role for T-BET+CXCR3+ regulatory T cells in protection from autoimmune diabetes. Tze Guan Tan, Diane Mathis, Christophe Benoist. Proc Natl Acad Sci U S A, 2016 Nov 23; 113(49). PMID: 27872297 Free PMC article.

Citedby
Method for identification of condition-associated public antigen receptor sequences. Mikhail V Pogorelyy, Anastasia A Minervina, +4 authors, Aleksandra M Walczak. less Elife, 2018 Mar 14; 7. PMID: 29533178 Free PMC article.
Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis. Alla Bradley, Tetsuo Hashimoto, Masahiro Ono. Front Immunol, 2018 Aug 01; 9. PMID: 30061879 Free PMC article.
Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges. Marco De Simone, Grazisa Rossetti, Massimiliano Pagani. Front Immunol, 2018 Aug 04; 9. PMID: 30072991 Free PMC article. Review.
Clonally Expanded Decidual Effector Regulatory T Cells Increase in Late Gestation of Normal Pregnancy, but Not in Preeclampsia, in Humans. Sayaka Tsuda, Xiaoxin Zhang, +6 authors, Shigeru Saito. less Front Immunol, 2018 Sep 11; 9. PMID: 30197648 Free PMC article.
Molecular diversification of regulatory T cells in nonlymphoid tissues. Joanna R DiSpirito, David Zemmour, +5 authors, Diane Mathis. less Sci Immunol, 2018 Sep 16; 3(27). PMID: 30217811 Free PMC article. Highly Cited.
Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges. Siddhartha Sharma, Louis Gioia, +5 authors, Luc Teyton. less Mol Immunol, 2018 Oct 10; 103. PMID: 30300798 Free PMC article. Review.
Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types. Angela M Magnuson, Evgeny Kiner, +8 authors, Christophe Benoist. less Proc Natl Acad Sci U S A, 2018 Oct 24; 115(45). PMID: 30348759 Free PMC article.
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Sonya A MacParland, Jeff C Liu, +30 authors, Ian D McGilvray. less Nat Commun, 2018 Oct 24; 9(1). PMID: 30348985 Free PMC article. Highly Cited.
Differential gene expression in human tissue resident regulatory T cells from lung, colon, and blood. Magdalena Niedzielska, Elisabeth Israelsson, +5 authors, Céline Dumont. less Oncotarget, 2018 Dec 14; 9(90). PMID: 30546835 Free PMC article.
Helper T cell differentiation. Jordy Saravia, Nicole M Chapman, Hongbo Chi. Cell Mol Immunol, 2019 Mar 15; 16(7). PMID: 30867582 Free PMC article. Review.
IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus. Saskia Hemmers, Michail Schizas, +5 authors, Alexander Y Rudensky. less J Exp Med, 2019 Aug 23; 216(11). PMID: 31434685 Free PMC article.
Helios: still behind the clouds. Angela M Thornton, Ethan M Shevach. Immunology, 2019 Sep 14; 158(3). PMID: 31517385 Free PMC article. Review.
Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Peter A Szabo, Hanna Mendes Levitin, +9 authors, Peter A Sims. less Nat Commun, 2019 Oct 19; 10(1). PMID: 31624246 Free PMC article.
Dormant pathogenic CD4+ T cells are prevalent in the peripheral repertoire of healthy mice. Anna Cebula, Michal Kuczma, +6 authors, Leszek Ignatowicz. less Nat Commun, 2019 Oct 28; 10(1). PMID: 31653839 Free PMC article.
Digitaldlsorter: Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data. Carlos Torroja, Fatima Sanchez-Cabo. Front Genet, 2019 Nov 12; 10. PMID: 31708961 Free PMC article.
The NF-κB RelA Transcription Factor Is Critical for Regulatory T Cell Activation and Stability. Emilie Ronin, Martina Lubrano di Ricco, +8 authors, Benoit L Salomon. less Front Immunol, 2019 Nov 22; 10. PMID: 31749798 Free PMC article.
A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage. Amnon Sharir, Pauline Marangoni, +12 authors, Ophir D Klein. less Nat Cell Biol, 2019 Sep 05; 21(9). PMID: 31481792 Free PMC article.
Homeostasis and transitional activation of regulatory T cells require c-Myc. Jordy Saravia, Hu Zeng, +11 authors, Hongbo Chi. less Sci Adv, 2020 Jan 09; 6(1). PMID: 31911938 Free PMC article.
Treg Heterogeneity, Function, and Homeostasis. Daniil Shevyrev, Valeriy Tereshchenko. Front Immunol, 2020 Jan 30; 10. PMID: 31993063 Free PMC article. Review.
Very rapid cloning, expression and identifying specificity of T-cell receptors for T-cell engineering. Shan Zong, Tiejuan Mi, +7 authors, Hiroki Torikai. less PLoS One, 2020 Feb 11; 15(2). PMID: 32040512 Free PMC article.
Future prospects for CD8+ regulatory T cells in immune tolerance. Léa Flippe, Séverine Bézie, Ignacio Anegon, Carole Guillonneau. 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. less 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, Guy Gorochov, Ye Htun Oo, Makoto Miyara. less 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. less 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. less 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, Achia Khatun, David M Schauder, Weiguo Cui. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Chamith Y Fonseka, Jessica I Beynor, Soumya Raychaudhuri. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Jie Wang, Xiaojun Wu, Indrani Datta, Qing-Sheng Mi. less 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. less 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. less 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, Ashutosh Chaudhry, Aaron S Rapaport, Wenjun Ouyang. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Anjun Ma, Jian Zhu, Dong Xu, Qin Ma. less 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. less 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, Hiroyoshi Nishikawa, F Stephen Hodi, Rakesh K Jain. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Tiago B R Castro, Tomohisa Sujino, Daniel Mucida. less 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. less 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. less 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. less 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. less 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, Suk Woo Nam, Kyoung Bun Lee, Jin-Wu Nam. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Juliane Schweizer, Mira Katan, Jean-Charles Sanchez. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Knut E A Lundin, Geir Kjetil Sandve, Shuo-Wang Qiao. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less Methods Mol Biol, 2022 May 28; 2453. PMID: 35622331

BioKDE: Biomedical Knowledge Discovery Engine

Abstract

Other Links