Evidence map›Paper›PMID 41689799›Full record

ArticleCell reports2026

Generation of a comprehensive epigenomic atlas in clear cell renal cell carcinoma informs kidney cancer progression and heritability.

Sarah Abou Alaiwi, Elio Adib, Ziwei Zhang, Sandor Spisak, Aurel Prosz, Paulo Cordeiro, Talal El Zarif, Zsófia Márta Sztupinszki, Amin H Nassar, Ji-Heui Seo and 13 more

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Article in Cell reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

Sarah Abou AlaiwiDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cardiology, Yale New Haven Hospital, New Haven, CT 06510, USA.
Elio AdibDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA 02115, USA.
Ziwei ZhangDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.
Sandor SpisakDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Institute of Molecular Life Sciences, Center of Excellence of The Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary; HUN-REN-ONKOL-TTK-HCEMM Oncogenomics Research Group, Budapest, Hungary.
Aurel ProszTranslational Cancer Genomics Group, Danish Cancer Institute, Copenhagen, Denmark.
Paulo CordeiroDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA.
Talal El ZarifDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Yale New Haven Hospital, New Haven, CT 06510, USA.
Zsófia Márta SztupinszkiTranslational Cancer Genomics Group, Danish Cancer Institute, Copenhagen, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
Amin H NassarDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT 06510, USA.
Ji-Heui SeoDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Rianna CampbellDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
John A SteinharterDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.
Mitchell MachielaDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Rockville, MD 20850, USA.
Diptavo DuttaDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Rockville, MD 20850, USA.
Stephen ChanockDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Rockville, MD 20850, USA.
Mark PurdueDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Rockville, MD 20850, USA.
Mark PomerantzDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Sabina SignorettiDepartment of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
Zoltan SzallasiTranslational Cancer Genomics Group, Danish Cancer Institute, Copenhagen, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
Alexander GusevDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
Sylvan C BacaDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA. Electronic address: sylvan_baca@dfci.harvard.edu.
Toni K ChoueiriDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Electronic address: toni_choueiri@dfci.harvard.edu.
Matthew L FreedmanDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA. Electronic address: matthew_freedman@dfci.harvard.edu.

Funding

Treating the P13-Kinase/AKTP50CA101942 · NCI · BETH ISRAEL DEACONESS MEDICAL CENTER · PI David McDermott · 2003 to 2026
$53.4M
Molecular Determinants of Response and Resistance to EZH2 and PARP inhibition in Prostate CancerP50CA272390 · NCI · DANA-FARBER CANCER INST · PI Steven P. Balk, Himisha Beltran · 2023 to 2026
$12.0M
Elucidation of the genetic mechanisms driving prostate tumorigenesis through integrative computational and functional approachesR01CA251555 · NCI · DANA-FARBER CANCER INST · PI FREEDMAN, MATTHEW L, PASANIUC, BOGDAN · 2021 to 2025
$3.4M
Elucidating prostate cancer risk mechanisms through large-scale cistrome wide association studiesR01CA262577 · NCI · DANA-FARBER CANCER INST · PI FREEDMAN, MATTHEW L, GIMELBRANT, ALEXANDER · 2022 to 2025
$3.3M
NCI NIH HHS P50 CA101942NCI NIH HHS P50 CA272390NCI NIH HHS R01 CA251555NCI NIH HHS R01 CA262577
6 · The paper itself

Abstract

By generating 194 epigenomic and transcriptomic datasets from 57 human tissue samples using H3K27ac and HIF2α chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and RNA sequencing, we provide a comprehensive, integrated characterization of clear cell renal cell carcinoma (ccRCC) across normal, tumor, and metastatic states. Our analyses provide several insights into ccRCC biology. First, we demonstrate significant reprogramming of enhancer and HIF2α cistromes as well as chromatin accessibility during the normal-to-tumor transition, whereas localized and metastatic tumors show minimal epigenomic differences. Second, we show reactivation of kidney-specific developmental pathways driving malignancy. Third, we perform a cistrome-wide association study in ccRCC, validating five established RCC risk loci and identifying six novel loci, including a locus at 12q24 linked to SCARB1 that was functionally validated. These datasets provide new perspectives on the role of developmental pathways in ccRCC tumorigenesis, insights into epigenetic mechanisms of ccRCC heritability, and a comprehensive epigenomic atlas for the research community.

Indexed as

Carcinoma, Renal CellDisease ProgressionEpigenomicsKidney NeoplasmsEpigenesis, GeneticGene Expression Regulation, NeoplasticHistonesHumansHistonesATAC-seqChIP-seqCP: cancerCP: genomicsgenome-wide association studiesgermline riskkidney cancermassively parallel sequencingregulatory elementsrenal cell carcinoma

Identifiers

PMID41689799
PMCPMC13282931

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.