HIV-1 permanently disrupts homeostatic ILCs and expands inflammatory TCF7-dependent memory NK cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504630 | ENA |
REPOSITORIES: ENA
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Project description:This SuperSeries is composed of the SubSeries listed below.
2018-11-09 | GSE122326 | GEO
Project description:T cell factor 1 (Tcf1, encoded by Tcf7) promotes the central memory CD8+ T cell (TCM) differentiation and homeostatic proliferation in lymphoid tissues. It remains unclear if and how Tcf1 regulates the CD103high tissue-resident memory CD8+ T cell (TRM) formation in non-lymphoid tissues. Using an influenza A infection mouse model, we collected Tcf7-deficient and -sufficient lung CD8+ TRM cells for RNA sequencing analysis.
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Project description:We set out to identify differences in the transcriptome influenced by knockout of the transcription factor T-cell factor 7 (Tcf7) in mouse islets. Furthermore, we wanted to determine if metabolic stress (age,diet) influences these changes. Therefore, we compared the islet transcriptome from WT and Tcf7-/- mice both at a young age (8 weeks old) fed a low fat (10%) diet, versus WT and Tcf7-/- mice at an old age (20 weeks old) on a high-fat (45%) diet. Tcf7-/- mice and littermate wildtype mice were compared. Mice were placed on either a low-fat (10%) or high-fat (45%) diet at weeks of age. For the low fat group, islets from 8 week old mice were isolated and total RNA was extracted with Trizol. For the high fat group, islets from 20 week old mice were isolated and total RNA was extracted with Trizol.
2015-11-21 | E-GEOD-65361 | biostudies-arrayexpress
Project description:Innate lymphoid cells (ILCs) are highly plastic and predominantly mucosal tissue-resident cells that contribute to both homeostasis and inflammation depending on the microenvironment. The recent discovery of naïve-like tissue-resident ILCs suggests an ILC differentiation process that is akin to naïve T cell differentiation. Delineating the naïve-like ILC heterogeneity and the transcriptional, epigenetic and functional mechanisms that underlie ILC differentiation in tissues is crucial for understanding ILC biology in health and disease. Here we show that CD62L distinguishes two subsets of naïve-like CD45RA+ ILCs in tonsil tissue. While both subsets contain uni- and multipotent precursors of ILC1/NK cells and ILC3, CD62L+ ILCs resemble bona fide naïve ILCs with metabolism reminiscent of naïve T cells, lacking transcriptional and epigenetic signatures of mature ILCs. CD62L- ILCs are epigenetically similar to, but transcriptionally distinct from CD62L+ naïve-like ILCs including transcripts of cytokine signaling and metabolic pathways related to mature ILCs. A similar population of CD62L- quiescent ILCs with preferential differentiation capacity towards IL-22-producing ILC3 accumulate in the inflamed mucosa of patients with inflammatory bowel disease (IBD). These data suggest that naïve-like and quiescent ILCs are imprinted by their tissue microenvironment that poises their differentiation potential. Our findings identify restoration of homeostatic IL-22-producing ILC3 from CD62L- quiescent ILCs as a potential approach to improve tissue healing in IBD.
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Project description:Bulk RNA-seq, and single cell RNA-Seq using inDrops methodology, were used to compare two populations of cells that had been sorted by flow cytometry from human peripheral blood mononuclear cells (PBMCs) from two donors, G27 and G33. To sort the cells, PBMCs were stained with antibodies to 11 lineage markers (FITC), anti-CD56 (PE), and anti-CD94 (APC). The 11 lineage marker positive cells were excluded to identify the innate lymphocyte cell (ILC) population. Then we sorted the Lin-CD56+CD94- cells (CD127-ILC1s, 'neg') from the Lin-CD56+CD94+ cells (NK cells, 'pos') with a BD FACSAria IIu. Libraries were generated from each of these two populations.
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Project description:We set out to identify differences in the transcriptome influenced by knockout of the transcription factor T-cell factor 7 (Tcf7) in mouse islets. Furthermore, we wanted to determine if metabolic stress (age,diet) influences these changes. Therefore, we compared the islet transcriptome from WT and Tcf7-/- mice both at a young age (8 weeks old) fed a low fat (10%) diet, versus WT and Tcf7-/- mice at an old age (20 weeks old) on a high-fat (45%) diet.
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Project description:HIV-1 perturbs homeostatic ILCs, unmasks ILC1 plasticity, and boosts TCF7+ memory NK cells
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Project description:A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a key regulator in this self-renewal/differentiation switch, and it operates in the absence of canonical Wnt signaling. We found that TCF7 is the most downregulated transcription factor when CD34+ cells switch into CD34- cells using RNA-Seq. We subsequently identified the target genes bound by TCF7 using ChIP-Seq. We show that TCF7 binds to Runx1 (Aml1) promoter region, and RUNX1 and TCF7 co-regulate. Gene Set Enrichment Analysis suggests that TCF7 primarily acts as a positive regulator of genes preferentially expressed in CD34+ cells. Consistent with this possibility, knocking-down TCF7 represses many up-regulated genes in Lin-CD34+ cells. Finally a network of up-regulated transcription factors of CD34+ cells which defines the self-renewing state was constructed. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems. Examining the transcription factor binding targets of TCF7 and RUNX1.
2012-03-29 | E-GEOD-31221 | biostudies-arrayexpress
Project description:Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) from three independent tonsil donors. Sequencing libraries were prepared from FACS sorted individual ILCs with the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013)
2016-01-27 | E-GEOD-70580 | biostudies-arrayexpress
Project description:A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a key regulator in this self-renewal/differentiation switch, and it operates in the absence of canonical Wnt signaling. We found that TCF7 is the most downregulated transcription factor when CD34+ cells switch into CD34- cells using RNA-Seq. We subsequently identified the target genes bound by TCF7 using ChIP-Seq. We show that TCF7 binds to Runx1 (Aml1) promoter region, and RUNX1 and TCF7 co-regulate. Gene Set Enrichment Analysis suggests that TCF7 primarily acts as a positive regulator of genes preferentially expressed in CD34+ cells. Consistent with this possibility, knocking-down TCF7 represses many up-regulated genes in Lin-CD34+ cells. Finally a network of up-regulated transcription factors of CD34+ cells which defines the self-renewing state was constructed. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems. The gene expression changes when TCF7 is knocked-down by shRNA in Lin-SCA+CD34+ cells were identified by microarray analysis of one control and two experimental samples.
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