Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNAseq of immune cells from human palatine tonsils

ABSTRACT: Palatine tonsils are secondary lymphoid organs that are strategically positioned in the oropharynx to secure a first line of defense against oral pathogens. Specialized immune-interacting fibroblasts, generally termed fibroblastic reticular cells (FRC), underpin distinct microenvironments within lymphoid organs to compartmentalize and direct the efficient interaction and activation of immune cells. As a particular anatomical property, palatine tonsils harbor a reticular-shaped lymphoepithelium that generates an antigen sampling zone in the crypts. Here, we have employed single cell transcriptomics to unveil the molecular identity of tonsillar immune cells. We found that PI16+ RCs interact with activated macrophages via the OSM-OSMR pathway and thereby shape particular immune cell environments of inflamed lymphoid tissues.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Lisa Kurz

PROVIDER: E-MTAB-14987 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNAseq of immune and stromal cells from human palatine tonsils

Project description:Palatine tonsils are secondary lymphoid organs that are strategically positioned in the oropharynx to secure a first line of defense against oral pathogens. Specialized immune-interacting fibroblasts, generally termed fibroblastic reticular cells (FRC), underpin distinct microenvironments within lymphoid organs to compartmentalize and direct the efficient interaction and activation of immune cells. As a particular anatomical property, palatine tonsils harbor a reticular-shaped lymphoepithelium that generates an antigen sampling zone in the crypts. While the histological ultrastructure and the immune cell composition of human palatine tonsils has been elaborated in detail, the molecular identity of the diverse stromal cell compartments including FRC and the specialized lymphoepithelium remains largely unknown. Here, we have employed single cell transcriptomics and extensive flow cytometric analyses to unveil the molecular identity of tonsillar cells and to disentangle the heterogeneity of fibroblast and epithelial cell subsets in palatine tonsils. Our results reveal a remarkable conservation of stromal cell organization and molecularly-defined subsets in infant and adult human palatine tonsils.

2023-03-30 | E-MTAB-11715 | biostudies-arrayexpress

Single cell RNAseq of immune and stromal cells from human lymph nodes

Project description:B cell-interacting reticular cells (BRC) form transcriptionally and topologically stable immune-interacting microenvironments that direct efficient humoral immunity. While several immune niche factors have been elucidated, the cues sustaining BRC function and topology across activation states remain unclear. Here, we employed single cell RNA-sequencing of human lymph node stromal cells and immune cells to analyse local BRC-immune cell interactions and compare them across SLOs and species from additional datasets. Shared BRC subsets were imprinted by tissue-specific gene signatures, but also expressed functionally convergent niche factors that directed regionalized leukocyte composition. Local BRC-immune cell interactions sustained BRC subset identity via immune cell-provided maturation factors. Bidirectional signalling programs were independent of activation state and mirrored across murine and human tissues. Collectively, our data reveal a conserved set of feedforward BRC-immune cell circuits that sustain topologically-organized, functional niches across inflammatory states, lymphoid organs and species.

2023-03-30 | E-MTAB-11710 | biostudies-arrayexpress

Transcriptomic profiling of immune and stromal cells from the non small cell lung cancer (NSCLC) environment

Project description:T lymphocytes can efficiently counteract the growth of tumors within the tumor microenvironment. Specialized immune-interacting fibroblasts, termed fibroblastic reticular cells (FRC) are responsible for the formation of specialized niches promoting immune cell activation in secondary lymphoid organs and originate from embryonic progenitors. FRCs have also been identified in tertiary lymphoid structures (TLS) in tumor tissues. However, the identity and differentiation of TLS-associated FRC subsets that promote intra-tumoral T cell activity have remained unexplored. Here, we employed single cell RNA-sequencing of fibroblasts and immune cells, sampled from subpleural margin, central margin and unaffected lung tissue in non small cell lung cancer (NSCLC), demonstrating the formation of specific tumor T cell environments (TTEs) underpinned by CCL19-expressing FRCs. We detected tumor-specific FRC subsets namely CCL19-expressing TRCs and perivascular reticular cells (PRCs) interacting with intratumoral T cells, and thus regulating FRC differentiation and T cell activation. Our results highlight a remarkable functionality of FRCs to efficiently determine protective antitumoral T cell responses in NSCLC.

2024-11-19 | E-MTAB-13710 | biostudies-arrayexpress

Single cell RNAseq of immune and stromal cells from clinically inflammed and non inflammed human lymph nodes

Project description:Because of their central role in inflammatory processes pathological alterations in lymph nodes can affect innate and adaptive immunity. However, interpretation of lymph node pathology in humans is hampered by the lack of a reference under homeostatic conditions and a limited understanding of the molecular processes that occur during inflammatory activation. Using a combination of confocal microscopy, flow cytometry, and single cell and spatial transcriptome analysis, our study provides an in-depth characterization of the immunoanatomy of clinically inflammed and non-inflamed human lymph nodes.

2025-03-31 | E-MTAB-13857 | biostudies-arrayexpress

Type I interferon signaling in fibroblastic reticular cells prevents exhaustive activation of antiviral CD8+ T cells

Project description:Fibroblastic reticular cells (FRC) shape the organization of secondary lymphoid organs and actively promote the induction of immune responses by coordinating the interaction of innate and adaptive immune cells. However, the mechanisms underlying FRC functions during viral infections have remained largely unexplored. In the study, we combined FRC-specific genetic ablation of the type 1 IFN-alpha receptor (IFNAR) with high-dimensional transcriptomics analyses to elaborate the phenotypical alterations and functional consequences of impaired innate immunological sensing in FRC during lymph node-restricted viral infection

2020-09-01 | E-MTAB-8906 | biostudies-arrayexpress

Single cell RNAseq analysis of fibroblastic reticular cells from murine brachial lymph nodes during inflamed and resting states

Project description:The lymph node is home to resident macrophage populations that are essential for healthy immune function and homeostasis. They are involved in multiple processes including the initiation of the local response to pathogens, halting viral and bacterial spread, and clearance of apoptotic cells, but the macrophage niche and factors that create it are largely undefined. Here we analyse fibroblastic reticular cells (FRCs) as an essential component of the lymph node macrophage niche using single-cell RNA-sequencing. Our analysis revealed that most reticular cell subsets within lymph nodes expressed master macrophage regulator CSF1. We further show that signalling through CSF1R was sufficient to support macrophage development, while in the presence of LPS, FRCs underwent a mechanistic switch and maintained support through CSF1R-independent mechanisms. Our data reveal a critically important role for FRCs in the creation of the parenchymal macrophage niche within LNs.

2023-05-01 | E-MTAB-10908 | biostudies-arrayexpress

Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp - single cell RNAseq dataset 1

Project description:Splenic white pulp (WP) structures are underpinned by fibroblastic stromal cells (FSCs) to facilitate splenic compartmentalization and execute efficient immune responses. Although distinct WP FSCs exhibit various molecular traits, the origin and the hierarchical differentiation of different cell subsets are not characterized. Here we showed, the organization of splenic WP and the differentiation of WP FSCs were governed by lymphotoxin beta receptor (LTβR) signaling pathway. Cell fate mapping analysis revealed that different WP fibroblastic stromal cells descend from a common perivascular LTβR-sensitive mesenchymal lymphoid organizer cells (mLTo) at prenatal stage. Moreover, embryonic mLTo cells required LTβR signaling to give rise to different WP stromal cell subsets, while the proliferation of these cells was devoid of LTβR signaling but followed the development of WP during ontogeny. Moreover, cell fate mapping from different time point indicated a consecutive commitment of mLTo cells initiated from the proximal region around the splenic artery. RNAseq and differentiation trajectory analysis of distinct FSCs showed that Ltbr-deficient cells and perivascular reticular cells (PRCs) from adult spleen exhibited a progenitor phenotype and revealed a closer hierarchical lineage with embryonic mLTo cells. Taken together, our results unveil that embryonic mLTo cells residing in the perivascular niches can give rise to different FSC populations in a LTβR-dependent manner during development.

2019-03-27 | E-MTAB-7094 | biostudies-arrayexpress

Fibroblastic reticular cells in the spleen - total splenic Stroma cells - single cell RNAseq dataset 2

2019-03-27 | E-MTAB-7703 | biostudies-arrayexpress

Single cell RNAseq of B cell interacting reticular cells and immune cells from murine secondary lymphoid organs

Project description:B cell-interacting reticular cells (BRC) form transcriptionally and topologically stable immune-interacting microenvironments that direct efficient humoral immunity. While several immune niche factors have been elucidated, the cues sustaining BRC function and topology across activation states remain unclear. Here, we employed single cell RNA-sequencing of stromal cells and immune cells from murine lymph nodes, Peyer’spatches and spleens to analyse local BRC-immune cell interactions and compare them across SLOs and species. Shared BRC subsets were imprinted by tissue-specific gene signatures, but also expressed functionally convergent niche factors that directed regionalized leukocyte composition. Local BRC-immune cell interactions sustained BRC subset identity via immune cell-provided maturation factors. Bidirectional signalling programs were independent of activation state and mirrored across murine and human tissues. Collectively, our data reveal a conserved set of feedforward BRC-immune cell circuits that sustain topologically-organized, functional niches across inflammatory states, lymphoid organs and species.

2023-03-30 | E-MTAB-11738 | biostudies-arrayexpress

Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function - Intestinal fibroblasts

Project description:Innate lymphoid cells (ILC) in the small intestine govern immune homeostasis and protect the host against gut pathogens. While distinct cell-intrinsic signals have been identified that determine ILC development and differentiation, it has remained unclear which cell population regulates ILC sustenance. Using unbiased single cell RNA transcriptomic analysis of intestinal fibroblasts, we have identified a specialized Ccl19-expressing fibroblastic reticular cell (FRC) population that underpins solitary intestinal lymphoid tissue (SILT) structures including cryptopatches and isolated lymphoid follicles. Conditional ablation of lymphotoxin-β receptor (LTβR) signalling in SILT FRC impeded the maturation of isolated lymphoid follicles and blocked ILC maintenance through the downregulation of IL-7, consequently resulting in the elevated susceptibility to bacterial infection. Moreover, specific Ltbr ablation in FRC during adulthood revealed that constant LTβR-dependent FRC-ILC interaction is required to maintain SILT structures and ILC populations. Taken together, our study unveils a critical intestinal FRC niche that secures protective gut immunity.

2022-02-12 | E-MTAB-10638 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data