Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Impact of tissue source type on gene expression profiles of normal human kidney

ABSTRACT: Normal human tissue is critical as a reference control in biomedical research. Yet access to high quality human tissue can be challenging due to clinical, logistical and ethical issues. Possible human normal tissue source types include non-transplantable tissues from organ donors (OD), post-mortem cadaveric tissues (CAD), and surgical resections of normal adjacent tissues (NAT) in cancer patients. But few studies have comprehensively explored the impact of these source types on the biological profile of the tissue. We assembled a panel of human normal kidney tissue from 91 donors representing OD, CAD, and NAT, as well as the matching kidney tumor. Histopathologic and molecular profiles by RNASeq analysis revealed clear differences between tumor and normal samples, regardless of the source type. Among the normal samples, there was a general similarity between source types, with little evidence of a field cancerization effect in the NAT. Differential gene expression and enrichment analyses indicated differences among source types in immune system and inflammatory processes, response to extracellular stimuli, ion transport and metabolic pathways. We conclude that all three normal source types are suitable for reference kidney control samples, but important differences are to be noted for particular research areas and tissue banking strategies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE191261 | GEO | 2023/05/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma

Project description:Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients is commonly used as a control in thyroid cancer studies, but the molecular characteristics of NAT tissue are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed RNA sequencing of three categories of thyroid tissue samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex and the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 247 coding genes and 6 noncoding genes have been reported as cancer genes, being involved in cell proliferation, apoptosis, and tumorigenesis. In addition, dysregulated expression of ribosomal and small RNAs was identified in NAT. IPA analyses revealed that “Cellular Response to Therapeutics, Cardiovascular Disease, Organismal Injury and Abnormalities, Cancer, and Cellular Movement” appeared as major dysregulated pathways in the NAT tissues. This study provides a comprehensive study of the PTC transcriptome, which provides improved insight into the complexity of gene expression changes during PTC tumorigenesis.

2021-01-29 | GSE165724 | GEO

Genome-wide profiling of 5-hydroxymethylcytosine in renal cell carcinoma tissue, urine and cell line samples.

Project description:We performed genome-wide 5hmC Methylated DNA Capture (5hMethylCap-seq) on one pooled RCC tissue sample (n=3) and the corresponding matched normal kidney tissue (NAT) (n=3), and we also performed 5hMethylCap-seq on one pooled urine sample obtained from RCC patients (n=52) along with another pooled urine sample obtained from control patients without malignancy (n=65). Global 5hmC levels were dramatically reduced in RCC tissues compared to matched normal adjacent kidney tissues, and although we detected low levels of 5hmC in urine samples, we also observed reduction of 5hmC in urine samples compared to tissue samples. Through assessing histone marked regions we found that 5hmC levels were enriched in H3K9me3 marked repressive genomic regions of normal adjacent kidney compared to RCC tissue tissues. Given the lower 5hmC signal in other genomic regions in cancer tissues, this upregulated 5hmC levels in H3K9me3 marked regions were also clearly identified comparing urine samples from RCC patients to control patients without RCC. We used Caki1 and Caki2 RCC cells to established stable cells with low H3K9me3 expression by knocking down the SUV39H1 gene. We found that low global H3K9me3 causes major upregulation of 5hmC at H3K9me3 marked regions and minor downregulation of 5hmC at genebody regions without change global 5mC and 5hmC levels.

2019-12-31 | GSE118922 | GEO

Single Nuclei Transcriptomics Delineates Complex Interactions Between Immune and Renal Cells Contributing to Kidney Graft Fibrosis

Project description: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.

2023-03-06 | GSE195718 | GEO

Homo sapiens

Project description:Renal Cell Carcinoma - Papillary types 1, and 2b, Normal Kidney Tissue

| PRJNA98373 | ENA

Molecular Profiles Associated with Calcineurin Inhibitor Toxicity Post-Kidney Transplant: Input to Chronic Allograft Dysfunction

Project description:The molecular basis of calcineurin inhibitor toxicity (CNIT) in kidney transplantation (KT) and its contribution to chronic allograft dysfunction (CAD) with interstitial fibrosis (IF) and tubular atrophy (TA) were evaluated. Molecular signatures characterizing CNIT samples were identified. The recognized CNIT gene signature was most common in patients with decreased graft function and histological evidence of IF/TA. To test CNIT contribution to CAD progression, kidney biopsies from transplant recipients with histological diagnosis of CNIT (n=14), acute rejection (ACR, n=13), and CAD with IF/TA (n=10), including 18 Normal allografts, were analyzed using gene expression microarrays.

2014-06-01 | E-GEOD-53605 | biostudies-arrayexpress

A survey of gene expression in adult chicken tissues using a chicken 20K oligonucleotide microarray

Project description:Transcriptional profiling of eight normal adult chicken tissues in 10-week old brown (lohmann brown) hens, the eight tissues include brain, bursa of Fabricius, jejunum, kidney, liver, lung, spleen, thymus. Keywords: normal chicken tissues, transcriptional profiling. eight different normal chicken adult tissue types, five biological replicates per tissue, each individual sample was hybridized with a common reference pool (pool of RNA samples from all individual samples). All individual samples were labeled with Cy3, common reference was labeled with Cy5.

2010-09-09 | E-GEOD-17108 | biostudies-arrayexpress

Whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients

Project description:Full title: Expression data from whole blood gene expression analysis of stable and acute rejection pediatric kidney transplant patients Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases. Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations. Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive. This dataset is the validation dataset used to test the csSAM gene expression deconvolution algorithm as reported in the accompanying paper.

2010-03-08 | GSE20300 | GEO

Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.

2015-10-26 | GSE61441 | GEO

Novel endogenous antisense transcripts (data for the mouse normal tissues)

Project description:Recent transcriptomic analyses have uncovered widespread occurrence of natural antisense transcripts (NATs), which are transcribed from the opposite strand of another discrete transcribed region. We describe a novel probe-design technique for DNA microarray analysis that specifically targets the complementary strand of annotated genes, and show that this technique can successfully identify novel NAT expression in normal and tumor samples. Northern and in situ hybridization analyses of selected examples (Acaa1, Aard, and Thbd) confirmed their transcription and dynamic expression in a tissue- and cell-type-specific manner. Our data highlight the importance of NAT expression in the regulation of cellular processes and in oncogenesis. The fundamental basis of the technology described in this paper is applicable to all genes and sample types for the identification of NAT expression that is not possible by conventional cDNA/EST/CAGE information. Total RNA for the mouse (C57BL/6J) microarray experiments was isolated from SL10 cells (fibroblast cell line), brain, heart, intestine, kidney, liver, lung, placenta (d.p.c. 10.5 and 13.5), spleen, stomach, testis, and thymus. Testis was from C57BL/6J males (8 to 10 weeks), placenta was from pregnant mice, and the other tissue was from both male and female mice. Unpublished data has been masked in the supplementary feature extraction files.

2010-05-06 | E-GEOD-14372 | biostudies-arrayexpress

Cell-type specific gene programs of the normal human nephron define kidney cancer subtypes

Project description:Comprehensive transcriptome studies of cancers often rely on corresponding normal tissue samples to serve as a transcriptional reference. In this study we performed in-depth analyses of normal kidney tissue transcriptomes from TCGA and demonstrate that the histological variability in cellularity, inherent in the kidney architecture, lead to considerable transcriptional differences between samples. This should be considered when comparing expression profiles of normal and cancerous kidney tissues. We exploited these differences to define renal cell-specific gene signatures and used these as framework to analyze renal cell carcinoma (RCC) ontogeny. Chromophobe RCCs express FOXI1-driven genes that define collecting duct intercalated cells whereas HNF-regulated genes, specific for proximal tubule cells, are an integral part of clear cell and papillary RCC transcriptomes. These networks may be used as framework for understanding the interplay between genomic changes in RCC subtypes and the lineage-defining regulatory machinery of their non-neoplastic counterparts.

2017-08-07 | GSE95425 | 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