GEO DataSets

(Submitter supplied) Kidney transplant recipients are currently treated with nonspecific immunosuppressants that cause severe systemic side effects. Current immunosuppressants were developed based on their effect on T-cell activation rather than the underlying mechanisms driving alloimmune responses. Thus, understanding the role of the intragraft microenvironment will help us identify more directed therapies with lower side effects. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

3 Samples

Download data: MTX, TSV

(Submitter supplied) RNA-sequencing (RNA-Seq) is a precise tool to analyze global transcriptional changes, develop biomarkers, and decipher pathogenic mechanisms. We performed RNA-Seq of urinary cells to investigate gene expression patterns and pathways and whether urinary cell mRNA transcriptional profiles are enriched for biopsy transcriptional profiles.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

57 Samples

Download data: TXT

(Submitter supplied) Acute rejection of human allografts has been viewed mostly through the lens of adaptive immunity, and the intragraft landscape of innate immunity genes has not been characterized in an unbiased fashion. We did RNA sequencing of 34 kidney allograft biopsy specimens from 34 adult recipients; 16 were categorized as Banff acute T-cell mediated rejection (TCMR) and 18 as normal. Computational analysis of intragraft mRNA transcriptome identified significantly higher abundance of mRNA for pattern recognition receptors in TCMR compared to normal biopsies, as well as increased expression of mRNAs for cytokines, chemokines, interferons, and caspases. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

34 Samples

Download data: TXT

(Submitter supplied) Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. All kidney sections were from paraffin blocks. Overall, inflammatory genes were significantly upregulated in the tubular areas of the TCMR biopsy and showed an enrichment for gene-ontology terms associated with T-cell activation, differentiation, and proliferation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

19 Samples

Download data: CSV, DCC

(Submitter supplied) Early acute rejection of human allografts is mediated by circulating alloreactive host effector memory T cells (TEM). TEM infiltration typically occurs across graft post-capillary venules and involves sequential interactions with graft-derived endothelial cells (ECs) and pericytes (PCs). While the role of ECs in allograft rejection has been extensively studied, contributions of PCs to this process are largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: DIFF

(Submitter supplied) 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.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

306 Samples

Download data: CEL

(Submitter supplied) Histologic diagnosis of T cell-mediated rejection in kidney transplant biopsies has limited reproducibility because it is based on non-specific lesions using arbitrary rules that are subject to differing interpretations. We used microarray results from 403 indication biopsies previously given histologic diagnoses to develop a molecular classifier that assigned a molecular T cell-mediated rejection score to each biopsy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

411 Samples

Download data: CEL

(Submitter supplied) Kidney transplant injury processes are associated with molecular changes in renal tissue, primarily related to immune cell activation and infiltration. How these processes are reflected by molecular alterations in circulating immune cells is poorly understood. We performed RNA-sequencing on 384 biobanked blood samples from four transplant centers, taken at time of a kidney allograft biopsy, selected for their phenotype (acute T cell- and antibody-mediated rejection, polyomavirus-associated nephropathy, and control). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

384 Samples

Download data: CSV

(Submitter supplied) To unveil the molecular mechanisms underlying TCMR, we utilized spatial transcriptomics on post-transplant TCMR and non-TCMR patients. Contrary to the prevailing T cell-centric view, our findings reveal uniform inflammatory responses across glomerular and tubulointerstitial regions in TCMR.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

12 Samples

Download data: DCC

(Submitter supplied) Intimal arteritis is known to be a negative prognostic factor for kidney allograft survival. Although Banff classification assesses isolated v-lesion (IV) as a T-cell mediated rejection, its origin and significance remain unclear. To help resolve if IV truly represents acute rejection, molecular study was performed. Transcriptome of early IV, T cell-mediated vascular rejection (TCMRV) and nonrejection histologic findings was compared using microarrays (Illumina Human HT-12 v4 Expression BeadChips). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 Samples

Download data: TXT

(Submitter supplied) Banff 2019 update of kidney allograft pathology excluded isolated tubulitis without interstitial inflammation (ISO-T) from category of borderline (suspicious) for acute T cell-mediated rejection due to its proposed benign clinical outcome. However, molecular assessment of ISO-T has not been explored yet. ISO-T or interstitial inflammation with tubulitis (I+T) were diagnosed in indication biopsies within first 14 postoperative days. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) Purpose: Chronic allograft dysfunction (CAD) remains a major obstacle in kidney transplantation. However, the molecular pathogenesis of human CAD is unknown. Herein, we tested the hypothesis that single nuclei transcriptomics of human kidney allograft fibrosis will reveal diverse cell types, deconvolve complex fibrosis-driving pathways, and provide deeper insights into the progression of kidney allograft dysfunction.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: MTX, TSV

(Submitter supplied) We sequenced the transriptomes of 31203 cells from 11 human kidney transplant biopsies. We used the CITE-seq approach to generate these single cell multiomics data. We then used a computational pipeline called PIC-seq to deconvolute the transcriptional signatures of each contributing cell in a PIC by comparing PIC gene expression to a theoretical PIC.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

32 Samples

Download data: MTX, TSV