Defining Housekeeping Genes Suitable for RNA-seq Analysis of the Human Allograft Kidney Biopsy Tissue
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE120495 | GEO | 2019/07/10
REPOSITORIES: GEO
Similar Datasets
Project description:BACKGROUND:RNA-seq is poised to play a major role in the management of kidney transplant patients. Rigorous definition of housekeeping genes (HKG) is essential for further progress in this field. Using single genes or a limited set HKG is inherently problematic since their expression might be altered by specific diseases in the patients being studied. METHODS:To generate a HKG set specific for kidney transplantation, we performed RNA-sequencing from renal allograft biopsies collected in a variety of clinical settings. Various normalization methods were applied to identify transcripts that had a coefficient of variation of expression that was below the 2nd percentile across all samples, and the corresponding genes were designated as housekeeping genes. Comparison with transcriptomic data from the Gene Expression Omnibus (GEO) database, pathway analysis and molecular biological functions were utilized to validate the housekeeping genes set. RESULTS:We have developed a bioinformatics solution to this problem by using nine different normalization methods to derive large HKG gene sets from a RNA-seq data set of 47,611 transcripts derived from 30 biopsies. These biopsies were collected in a variety of clinical settings, including normal function, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy and polyomavirus nephropathy. Transcripts with coefficient of variation below the 2nd percentile were designated as HKG, and validated by showing their virtual absence in diseased allograft derived transcriptomic data sets available in the GEO. Pathway analysis indicated a role for these genes in maintenance of cell morphology, pyrimidine metabolism, and intracellular protein signaling. CONCLUSIONS:Utilization of these objectively defined HKG data sets will guard against errors resulting from focusing on individual genes like 18S RNA, actin & tubulin, which do not maintain constant expression across the known spectrum of renal allograft pathology.
| S-EPMC6580566 | biostudies-literature
Project description:Defining Housekeeping Genes Suitable for RNA-seq Analysis of the Human Allograft Kidney Biopsy Tissue
| PRJNA493201 | ENA
Project description:COVID-19 has been associated with acute kidney injury and published reports of native kidney biopsies have reported diverse pathologies. Case series directed specifically to kidney allograft biopsy findings in the setting of COVID-19 are lacking. We evaluated 18 kidney transplant recipients who were infected with SARS-CoV-2 and underwent allograft biopsy. Patients had a median age of 55 years, six were female, and five were Black. Fifteen patients developed COVID-19 pneumonia, of which five required mechanical ventilation. Notably, five of 11 (45%) biopsies obtained within 1 month of positive SARS-CoV-2 PCR showed acute rejection (four with arteritis, three of which were not associated with reduced immunosuppression). The remaining six biopsies revealed podocytopathy (n = 2, collapsing glomerulopathy and lupus podocytopathy), acute tubular injury (n = 2), infarction (n = 1), and transplant glomerulopathy (n = 1). Biopsies performed >1 month after positive SARS-CoV-2 PCR revealed collapsing glomerulopathy (n = 1), acute tubular injury (n = 1), and nonspecific histologic findings (n = 5). No direct viral infection of the kidney allograft was detected by immunohistochemistry, in situ hybridization, or electron microscopy. On follow-up, two patients died and most patients showed persistent allograft dysfunction. In conclusion, we demonstrate diverse causes of kidney allograft dysfunction after COVID-19, the most common being acute rejection with arteritis.
| S-EPMC8441660 | biostudies-literature
Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters M-bM-^@M-^S one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genesM-bM-^@M-^Y core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.
2014-12-10 | E-GEOD-57876 | biostudies-arrayexpress
Project description:BackgroundEfforts to maximize transplantation by matching organ quality to recipient longevity require reliable tools. The US kidney allocation system uses the Kidney Donor Risk Index (KDRI) for this purpose, and many centers additionally rely on donor biopsies. The Leuven score combines donor age with procurement histology (glomerulosclerosis and interstitial fibrosis/tubular atrophy) to predict allograft survival.MethodsWe compared KDRI with Leuven scores for associations with kidney discard, delayed graft function, and allograft function and survival. We used Cox, modified Poisson, and linear regression to calculate risks based on KDRI and (separately) Leuven scores, adjusting for important transplant and recipient variables.ResultsFrom 890 donors, 1729 kidneys were procured and biopsied. Five hundred eighty-five (34%) kidneys were discarded. Median donor age was 53 years (interquartile range [IQR], 44-61 years). Median KDRI and Leuven scores were 1.56 (IQR, 1.28-1.90) and 59 (IQR, 49-69). Relative risk for discard was 1.21 (95% confidence interval [CI], 1.17-1.24) per 0.2-unit increase in KDRI and 1.38 (1.31-1.46) per 10-unit increase in Leuven score. Adjusted relative risks for delayed graft function were 0.98 (95% CI, 0.94-1.02) and 0.94 (95% CI, 0.90-0.99), adjusted hazard ratios for graft failure were 1.10 (95% CI, 1.04-1.16) and 1.11 (95% CI, 1.02-1.21), and adjusted linear regression coefficients for 3-year estimated glomerular filtration rate were -3.88 (-4.63 to -3.13) and -5.18 (-6.19 to -4.18).ConclusionsIn kidneys clinically selected for procurement biopsy, the Leuven score was more strongly associated with discard but performed similarly to KDRI for predicting transplant outcomes, suggesting the need to reevaluate current procurement biopsy practices. Given modest associations for both tools; however, neither KDRI nor the Leuven score should be used in isolation for individual organ acceptance decisions.
| S-EPMC6092182 | biostudies-literature
Project description: Not available
| S-EPMC6365308 | biostudies-literature
Project description:67 kidney allograft biopsy samples against common reference. Both tissue samples and reference samples were double amplified according to Wang et al, and hybridized to lymphochip.
2004-01-18 | E-SMDB-1 | biostudies-arrayexpress
Project description:Background Single-cell genomics techniques are revolutionizing our ability to characterize complex tissues. By contrast, the techniques used to analyze renal biopsy specimens have changed little over several decades. We tested the hypothesis that single-cell RNA-sequencing can comprehensively describe cell types and states in a human kidney biopsy specimen.Methods We generated 8746 single-cell transcriptomes from a healthy adult kidney and a single kidney transplant biopsy core by single-cell RNA-sequencing. Unsupervised clustering analysis of the biopsy specimen was performed to identify 16 distinct cell types, including all of the major immune cell types and most native kidney cell types, in this biopsy specimen, for which the histologic read was mixed rejection.Results Monocytes formed two subclusters representing a nonclassical CD16+ group and a classic CD16- group expressing dendritic cell maturation markers. The presence of both monocyte cell subtypes was validated by staining of independent transplant biopsy specimens. Comparison of healthy kidney epithelial transcriptomes with biopsy specimen counterparts identified novel segment-specific proinflammatory responses in rejection. Endothelial cells formed three distinct subclusters: resting cells and two activated endothelial cell groups. One activated endothelial cell group expressed Fc receptor pathway activation and Ig internalization genes, consistent with the pathologic diagnosis of antibody-mediated rejection. We mapped previously defined genes that associate with rejection outcomes to single cell types and generated a searchable online gene expression database.Conclusions We present the first step toward incorporation of single-cell transcriptomics into kidney biopsy specimen interpretation, describe a heterogeneous immune response in mixed rejection, and provide a searchable resource for the scientific community.
| S-EPMC6065085 | biostudies-literature
Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters – one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genes’ core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.
2014-12-10 | GSE57876 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30989: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (ChIP-chip dataset) GSE30990: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (expression dataset) Refer to individual Series
2011-10-28 | E-GEOD-30991 | biostudies-arrayexpress