ArticleJournal of the American Society of Nephrology : JASN2015
Functional genomic annotation of genetic risk loci highlights inflammation and epithelial biology networks in CKD.
Article in Journal of the American Society of Nephrology : JASN, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- Fluid-electrolyte homeostasis requires histone deacetylase function.JCI insight · 2020Pooled it
- The effects of elevated phosphate on the kidney - damaging the gatekeeper.Pflugers Archiv : European journal of physiology · 2026Review
- Association of ALDH2 rs671 Polymorphism with chronic kidney disease incidence in a population-based Korean cohort.Scientific reports · 2026Article
- Updates on renal phosphate transport.Current opinion in nephrology and hypertension · 2025Review
- Advances in uromodulin biology and potential clinical applications.Nature reviews. Nephrology · 2024Review
- 5-Hydroxytryptamine 1F Receptor Agonist Lasmiditan Differentially Regulates Successful Repair and Failed Repair Genes in a Mouse Model of Acute Kidney Injury.ACS pharmacology & translational science · 2024Article
- Integration of artificial intelligence and multi-omics in kidney diseases.Fundamental research · 2023Review
- Non-diabetic urine glucose in idiopathic membranous nephropathy.Renal failure · 2022Article
- UMOD and the architecture of kidney disease.Pflugers Archiv : European journal of physiology · 2022Review
- Comprehensive Network-Based Analyses Reveal Novel Renal Function-Related Targets in Acute Kidney Injury.Frontiers in genetics · 2022Article
- Procollagen C-proteinase enhancer-1 (PCPE-1), a potential biomarker and therapeutic target for fibrosis.Matrix biology plus · 2021Article
- Article
- Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.International journal of molecular sciences · 2021Review
- The uncharacterized protein FAM47E interacts with PRMT5 and regulates its functions.Life science alliance · 2021Article
- Expression ofAmerican journal of physiology. Renal physiology · 2020Article
- It Takes Two to Tango: The Role of Dysregulated Metabolism and Inflammation in Kidney Disease Development.Seminars in nephrology · 2020Review
- Uromodulin (Tamm-Horsfall protein): guardian of urinary and systemic homeostasis.Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association · 2020Review
- A journey from microenvironment to macroenvironment: the role of metaflammation and epigenetic changes in cardiorenal disease.Clinical kidney journal · 2019Article
- The kidney transcriptome, from single cells to whole organs and back.Current opinion in nephrology and hypertension · 2019Review
- Renal phosphate handling and inherited disorders of phosphate reabsorption: an update.Pediatric nephrology (Berlin, Germany) · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Genome-wide association studies (GWASs) have identified multiple loci associated with the risk of CKD. Almost all risk variants are localized to the noncoding region of the genome; therefore, the role of these variants in CKD development is largely unknown. We hypothesized that polymorphisms alter transcription factor binding, thereby influencing the expression of nearby genes. Here, we examined the regulation of transcripts in the vicinity of CKD-associated polymorphisms in control and diseased human kidney samples and used systems biology approaches to identify potentially causal genes for prioritization. We interrogated the expression and regulation of 226 transcripts in the vicinity of 44 single nucleotide polymorphisms using RNA sequencing and gene expression arrays from 95 microdissected control and diseased tubule samples and 51 glomerular samples. Gene expression analysis from 41 tubule samples served for external validation. 92 transcripts in the tubule compartment and 34 transcripts in glomeruli showed statistically significant correlation with eGFR. Many novel genes, including ACSM2A/2B, FAM47E, and PLXDC1, were identified. We observed that the expression of multiple genes in the vicinity of any single CKD risk allele correlated with renal function, potentially indicating that genetic variants influence multiple transcripts. Network analysis of GFR-correlating transcripts highlighted two major clusters; a positive correlation with epithelial and vascular functions and an inverse correlation with inflammatory gene cluster. In summary, our functional genomics analysis highlighted novel genes and critical pathways associated with kidney function for future analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.