ArticleNature communications2023
Epigenomic charting and functional annotation of risk loci in renal cell carcinoma.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions.Nature genetics · 2024Pooled it
- mTORC1 activation induces B7-H3-dependent metabolic reprogramming in renal cell carcinoma (RCC).Oncogene · 2026Article
- Generation of a comprehensive epigenomic atlas in clear cell renal cell carcinoma informs kidney cancer progression and heritability.Cell reports · 2026Article
- Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis andScience advances · 2026Article
- Cell-free DNA epigenomic profiling enables noninvasive detection and monitoring of translocation renal cell carcinoma.The Journal of clinical investigation · 2026Article
- Lactylation in cancer: molecular mechanisms and advances in clinical study.Molecular cancer · 2026Review
- Validation ofFrontiers in medicine · 2026Article
- Integrative multi-omic analysis identifies key transcription factors and target proteins in renal cell carcinoma and its subtypes.bioRxiv : the preprint server for biology · 2025Article
- Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications.Cell death & disease · 2025Article
- KIF14 plays a role in the regulation of the cell cycle and has implications for prognosis in clear cell renal cell carcinoma.BMC urology · 2025Article
- Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.Cell death discovery · 2025Review
- Oncogenic TFE3 fusions drive OXPHOS and confer metabolic vulnerabilities in translocation renal cell carcinoma.Nature metabolism · 2025Article
- Plasma Cell-Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer.Cancer research · 2025Article
- Transcriptome- and proteome-wide association studies identify genes associated with renal cell carcinoma.American journal of human genetics · 2024Article
- TFE3 fusions direct an oncogenic transcriptional program that drives OXPHOS and unveils vulnerabilities in translocation renal cell carcinoma.bioRxiv : the preprint server for biology · 2024Article
- Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma.Cell reports · 2024Article
- Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma.JCI insight · 2024Article
- The chromatin landscape of healthy and injured cell types in the human kidney.Nature communications · 2024Article
- Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort.Nature communications · 2023Article
- Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.Nucleic acids research · 2023Article
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36 authors at 4 institutions in 1 country.
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Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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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.