GEO DataSets

(Submitter supplied) We performed total RNA-Seq and compared expression levels of genes of whole blood cells isolated from patients after kidney transplantation with stable graft function, antibody mediated- and t cell mediated graft rejection.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: TXT

(Submitter supplied) The enigmatic natural killer (NK) cells mediate spontaneous cell-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity via cell surface Fc receptors. The dual functionality of NK cells may enable their participation in chronic active antibody-mediated rejection (CA-ABMR), wherein evidence for complement activation is inconsistent. We RNA sequenced 57 human kidney allograft biopsies to determine whether NK cell cytotoxicity pathway gene set enrichment is an attribute of CA-ABMR. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

57 Samples

Download data: TXT

(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 recipients with biopsy-proven microvascular injury (MVI) have increased risk for allograft failure. MVI is often caused by antibody-mediated injury that is resistant to available treatments. Current diagnostic methods are also inadequate, with interobserver variability in traditional pathology reads, variable assessment of circulating donor-specific antibody between HLA laboratories, and peritubular capillary C4d staining. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25197

95 Samples

Download data: RCC

(Submitter supplied) We previously reported a system for assessing rejection in kidney transplant biopsies using microarray-based gene expression data, the Molecular Microscope® Diagnostic System (MMDx). Ensembles generated diagnoses that were both more accurate than the best individual classifiers, and nearly as stable as the best, consistent with expectations from the machine learning literature. Human experts had ~93% agreement (balanced accuracy) signing out the reports, and random forest-based automated sign-outs showed similar levels of agreement with the human experts (92% and 94% for predicting the expert MMDx sign-outs for T cell-mediated (TCMR) and antibody-mediated rejection (ABMR) respectively). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

1745 Samples

Download data: CEL

(Submitter supplied) Circulating anti-HLA donor-specific antibodies (HLA-DSA) are often absent in serum of kidney allograft recipients with biopsies demonstrating histology of antibody-mediated rejection (ABMRh). In this multicenter study, we aimed to elucidate whether the transcriptional profile of biopsies with HLA-DSA negative ABMRh can indicate an undetected humoral etiology, or whether HLA-DSA negative ABMRh should be considered as a distinct histomolecular entity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

224 Samples

Download data: CEL

(Submitter supplied) Chronic antibody-mediated rejection (CAMR) represents the main cause of kidney graft loss, but its pathogenesis is unclear. In order to uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of circulating peripheral blood mononuclear cells and, separately, of CD4+ T lymphocytes isolated from CAMR patients compared to kidney transplant recipients with normal graft function and histology. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

10 Samples

Download data: TXT

(Submitter supplied) Chronic antibody-mediated rejection (CAMR) represents the main cause of kidney graft loss, but its pathogenesis is unclear. In order to uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of circulating peripheral blood mononuclear cells and, separately, of CD4+ T lymphocytes isolated from CAMR patients compared to kidney transplant recipients with normal graft function and histology. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL16770

9 Samples

Download data: TXT

(Submitter supplied) Chronic antibody-mediated rejection (CAMR) represents the main cause of kidney graft loss, but its pathogenesis is unclear. In order to uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of circulating peripheral blood mononuclear cells and, separately, of CD4+ T lymphocytes isolated from CAMR patients compared to kidney transplant recipients with normal graft function and histology. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

18 Samples

Download data: TXT

(Submitter supplied) The first-generation Molecular Microscope® (MMDx) system for heart transplant endomyocardial biopsies used expression of rejection-associated transcripts (RATs) to diagnose T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) but also detected acute injury. However, the ideal system should detect rejection without being influenced by injury, to permit analysis of the relationship between rejection and parenchymal injury. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16043

3230 Samples

Download data: CEL, TXT

(Submitter supplied) Cancer stem cells (CSCs) represent a population of cells within the tumor able to drive tumorigenesis and known to be highly resistant to conventional chemotherapy and radiotherapy. In this work, we show a new role for ETV7, a transcriptional repressor member of the ETS family, in promoting breast cancer stem-like cells plasticity and resistance to chemo- and radiotherapy in breast cancer (BC) cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Histologic assessment of kidney transplant biopsies relies on cortex rather than medulla, but for microarray studies, the proportion cortex in a biopsy is typically unknown and could affect the molecular readings. The present study aimed to develop a molecular estimate of proportion cortex in biopsies and examine its effect on molecular diagnoses. Microarrays from 26 kidney transplant biopsies divided into cortex and medulla components and processed separately showed that many of the most significant differences were in glomerular genes e.g. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

154 Samples

Download data: CEL, TXT

(Submitter supplied) We compared the transcriptomic profile between patients without donor-specific antibodies (DSA-), patients with donor-specific antibodies without antibody-mediated rejection (DSA+ ABMR-) and patients with donor-specific antibodies and antibody-mediated rejection (DSA+ ABMR+). We found that patients with DSA+ ABMR+ had a distinct transcriptomic profile compared to DSA- and DSA+ ABMR- patients, characterized by upregulation of genes related to B cell activation and B cell effector functions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: TXT

(Submitter supplied) Molecular diagnosis of rejection is emerging in kidney, heart, and lung transplant biopsies and could offer insights for liver transplant biopsies. Groups differed in median time post-transplant e.g. R3injury 99 days vs. R4late 3117 days. R2TCMR biopsies expressed typical TCMR-related transcripts e.g. intense IFNG-induced effects. R3injury displayed increased expression of parenchymal injury transcripts (e.g. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

235 Samples

Download data: CEL, TXT

(Submitter supplied) In the present work, we have used whole genome expression profiling of peripheral blood samples from 51 patients with biopsy-proven acute kidney transplant rejection and 24 patients with excellent function and biopsy-proven normal transplant histology. The results demonstrate that there are 1738 probesets on the Affymetrix HG-U133 Plus 2.0 GeneChip representing 1472 unique genes which are differentially expressed in the peripheral blood during an acute kidney transplant rejection. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

75 Samples

Download data: CEL