Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Virus-specific TRM cells of both donor and recipient origin reside in human kidney transplants

ABSTRACT: Tissue-resident lymphocytes (TRLs) are critical for local protection against viral pathogens in peripheral tissue. However, it is unclear if TRLs perform a similar role in transplanted organs under chronic immunosuppressed conditions. The present study aimed to characterize the TRL compartment in human kidney transplant nephrectomies and examine its potential role in antiviral immunity. Paired single-cell transcriptome and T-cell receptor (TCR) sequencing showed that donor and recipient tissue-resident memory T (TRM) cells exhibit striking similarities in their transcriptomic profiles and share numerous TCR clonotypes predicted to target viral pathogens.

ORGANISM(S): Homo sapiens

PROVIDER: GSE242909 | GEO | 2023/09/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Tissue-Resident Memory T Cells in Human Kidney Transplants have alloreactive potential

Project description:The extent to which tissue-resident memory T (TRM) cells in transplanted organs possess alloreactivity is uncertain. This study investigates the alloreactive potential of TRM cells in kidney explants from four patients who experienced severe acute rejection leading to graft loss. Alloreactive T-cell receptors (TCRs) clones were identified in pre-transplant blood samples through mixed lymphocyte reactions, followed by single-cell RNA and TCR sequencing of the proliferated recipient T cells. Subsequently, these TCR clones were traced in the TRM cells of kidney explants, which were also subjected to single-cell RNA and TCR sequencing. The proportion of TRM cells expressing an alloreactive TCR in the four kidney explants varied from 0% to 9%. Notably, these alloreactive TCRs were predominantly found among CD4+ and CD8+ TRM cells with an effector phenotype. Intriguingly, alloreactive clones were present not only in recipient-derived TRM cells but also in donor-derived TRM cells, constituting up to 4% of the donor population, suggesting the presence of self-reactive TRM cells. Overall, our study demonstrates that T cells with alloreactive potential present in the peripheral blood prior to transplantation can infiltrate the kidney transplant and adopt a TRM phenotype.

2024-03-01 | GSE249197 | GEO

Potential impact of microarray diagnosis of T cell-mediated rejection in kidney transplants: the INTERCOM study

Project description:The authors report that in INTERCOM, a prospective international study of 300 kidney transplant biopsies, a microarray-based molecular score for T cell-mediated rejection changed the assessment of 26% of all biopsies, illustrating the potential of precision diagnostics to impact practice. Microarray analysis of 300 kidney transplant biopsies (non-TCMR, TCMR) and 6 nephrectomies.

2013-09-15 | E-GEOD-48581 | biostudies-arrayexpress

Single Cell Transcriptomics identifies Focal Segmental Glomerulosclerosis Remission Endothelial Biomarker

Project description:Intrinsic nephron cell types and tissue resident immune cells were recovered from renal biopsy specimens using a scRNAseq protocol for the Kidney Precision Medicine Project (KPMP), designed for deployment in a multicenter research network. Combined processing of 24 samples including 16 tumor-nephrectomy, 5 surveillance and 3 pre-perfusion biopsies using the scRNAseq protocol yielded 22,268 cells (4690 from surveillance biopsies, 16,491 from tumor-nephrectomies and 2834 cells from pre-perfusion biopsies) .

2020-03-03 | GSE140989 | GEO

Neoantigen-Specific CD8 T Cells with High Structural Avidity Preferentially Reside in and Eliminate Tumors (VDJ)

Project description:The success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. We characterized the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy subjects. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCRs biophysicochemical properties, we derived and applied an in silico model predicting TCR structural avidity and validated the enrichment in high avidity T cells in patients’ tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.

2023-05-18 | GSE232446 | GEO

Neoantigen-Specific CD8 T Cells with High Structural Avidity Preferentially Reside in and Eliminate Tumors (GEX)

2023-05-18 | GSE232444 | GEO

Analysis of transcriptomic profile of iNKT cells

Project description:The maintenance of tissue homeostasis is critically dependent on the function of tissue-resident lymphocytes, including lipid-reactive invariant natural killer T (iNKT) cells. iNKT cells have unique properties according to their tissues of residency, but if and how the tissue environment shapes their antigen specificity remains unknown. By analysing iNKT cells from tissues of mice and humans we demonstrate that their T cell receptor (TCR) repertoire is highly diverse and is distinct for iNKT cells resident in individual tissues resulting in differential lipid-antigen recognition. Within peripheral tissues, the TCR repertoire of iNKT cell recent thymic emigrants is different from that of mature cells, indicating that the iNKT population is shaped after their arrival to the tissues. Accordingly, in homeostatic conditions the repertoire of iNKT cells is modulated by tissue-specific signals that control iNKT cell activation and proliferation resulting in differential clonal expansion found for cells resident in various organs. Moreover, the iNKT cell TCR repertoire changes in response to lipid immunization and is shaped by age and by environmental changes. Thus, post-thymic modification of the iNKT cell TCR repertoire underpins the distinct antigen specificity of iNKT cells residing in peripheral tissues

2019-12-17 | GSE131420 | GEO

B cells and their progenitors reside in homeostatic meninges

Project description:The central nervous system (CNS) is ensheathed by the meninges and cerebrospinal fluid. Recent findings suggest complex immunological functions of these CNS-associated border tissues. Unlike myeloid lineage cells, lymphocytes in border compartments have been largely disregarded in previous studies. Based on single cell transcriptomics, we here identified a highly location-specific composition and expression profile of tissue-resident leukocytes in every border compartment. Only the dura layer of the meninges contained a large population of B cells under homeostatic conditions in multiple species. Murine dura B cells exhibited slow turnover, long-term tissue residency and matured in experimental neuroinflammation. The dura also contained B lineage progenitors at the pro-B cell stage unexpected outside of bone marrow, without direct influx from the periphery or the skull bone marrow. This identifies the dura as an unexpected site of B cell residence and potentially development in homeostasis and neuroinflammation.

2021-05-01 | GSE165153 | GEO

Clear-cell renal cell carcinomas tumors

Project description:Whole genome expression of 39 clear-cell renal cell carcinomas tumors 39 frozen tissue from recent nephrectomies for clear-cell renal cell carcinoma; association with clinical characteristics

2011-05-28 | E-GEOD-29609 | biostudies-arrayexpress

Expression data from NP366-374/Db and PA224-233/Db CD103 positive and negative T-cells

Project description:To investigate the role of TCR-pMHC interaction in regulating lung tissue-resident CD8 T cell differentiation, polyclonal responses were compared against NP366-374/Db and PA224-233/Db, two immunodominant epitopes that arise during influenza A infection. To characterize the molecular programs associated with the lung tissue-resident CD8 T cell subpopulations, we measured by microarray the global gene transcriptional profile of NP366-374/Db CD103+ and NP366-374/Db CD103-, PA224-233/Db CD103+, PA224-233/Db CD103- lung resident T cells.

2017-11-29 | GSE107448 | GEO

Comparison of F4/80 high and low peritoneal macrophages in H.polygyrus - Salmonella Typhimurium co-infected mice

Project description:Macrophages are involved in many different biological processes (e.g. tissue homeostasis, embryonic development, immune defence against invading pathogens). To be able to deal with these different tasks macrophages adopt distinct activation phenotypes tailored to the situation. However, macrophages show a remarkable degree of plasticity and can change their activation phenotype in response to new environmental triggers. Macrophages recruited to the site of infection can be derived from two main sources, blood monocytes and tissue resident macrophages. Of note, different types of pathogens lead to the accumulation of different types of macrophages. Thus, we have asked here whether helminth expanded, tissue resident derived macrophages will change their activation phenotype in vivo in response to consecutive bacterial co-infection.types of macrophages.

2017-02-14 | GSE85805 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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