Which dataset
would you like to
analyze in BBrowser?

Species: human
Number of cells: 68627
Study size: 1GB

Immunology 
ulcerative colitis 

Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

Boland, Brigid S and He, Zhaoren and Tsai, Matthew S and Olvera, Jocelyn G and Omilusik, Kyla D and Duong, Han G and Kim, Eleanor S and Limary, Abigail E and Jin, Wenhao and Milner, J Justin and others

Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal mucosal immune systems in health and ulcerative colitis (UC). UC was associated with an increase in IgG1+ plasma cells in colonic tissue, increased colonic regulatory T cells characterized by elevated expression of the transcription factor ZEB2, and an enrichment of a γδ T cell subset in the peripheral blood. Moreover, we observed heterogeneity in CD8+ tissue-resident memory T (TRM) cells in colonic tissue, with four transcriptionally distinct states of differentiation observed across health and disease. In the setting of UC, there was a marked shift of clonally related CD8+ TRM cells toward an inflammatory state, mediated, in part, by increased expression of the T-box transcription factor Eomesodermin. Together, these results provide a detailed atlas of transcriptional changes occurring in adaptive immune cells in the context of UC and suggest a role for CD8+ TRM cells in IBD.

Download bbrowser to analyze now

Species: human
Number of cells: 10005
Study size: 860MB

Immunology 
colon 
ulcerative colitis 

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

Corridoni, Daniele and Antanaviciute, Agne and Gupta, Tarun and Fawkner-Corbett, David and Aulicino, Anna and Jagielowicz, Marta and Parikh, Kaushal and Repapi, Emmanouela and Taylor, Steve and Ishikawa, Dai and others

Colonic antigen-experienced lymphocytes such as tissue-resident memory CD8+ T cells can respond rapidly to repeated antigen exposure. However, their cellular phenotypes and the mechanisms by which they drive immune regulation and inflammation remain unclear. Here we compiled an unbiased atlas of human colonic CD8+ T cells in health and ulcerative colitis (UC) using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry. We reveal extensive heterogeneity in CD8+ T-cell composition, including expanded effector and post-effector terminally differentiated CD8+ T cells. While UC-associated CD8+ effector T cells can trigger tissue destruction and produce tumor necrosis factor (TNF)-α, post-effector cells acquire innate signatures to adopt regulatory functions that may mitigate excessive inflammation. Thus, we identify colonic CD8+ T-cell phenotypes in health and UC, define their clonal relationships and characterize terminally differentiated dysfunctional UC CD8+ T cells expressing IL-26, which attenuate acute colitis in a humanized IL-26 transgenic mouse model.

Download bbrowser to analyze now

Species: human
Number of cells: 11704
Study size: 184MB

Immunology 
colon 
ulcerative colitis 

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis (cite-seq)

Corridoni, Daniele and Antanaviciute, Agne and Gupta, Tarun and Fawkner-Corbett, David and Aulicino, Anna and Jagielowicz, Marta and Parikh, Kaushal and Repapi, Emmanouela and Taylor, Steve and Ishikawa, Dai and others

Colonic antigen-experienced lymphocytes such as tissue-resident memory CD8+ T cells can respond rapidly to repeated antigen exposure. However, their cellular phenotypes and the mechanisms by which they drive immune regulation and inflammation remain unclear. Here we compiled an unbiased atlas of human colonic CD8+ T cells in health and ulcerative colitis (UC) using single-cell transcriptomics with T-cell receptor repertoire analysis and mass cytometry. We reveal extensive heterogeneity in CD8+ T-cell composition, including expanded effector and post-effector terminally differentiated CD8+ T cells. While UC-associated CD8+ effector T cells can trigger tissue destruction and produce tumor necrosis factor (TNF)-α, post-effector cells acquire innate signatures to adopt regulatory functions that may mitigate excessive inflammation. Thus, we identify colonic CD8+ T-cell phenotypes in health and UC, define their clonal relationships and characterize terminally differentiated dysfunctional UC CD8+ T cells expressing IL-26, which attenuate acute colitis in a humanized IL-26 transgenic mouse model.

Download bbrowser to analyze now

About 3 datasets