Cited by 1,173Renal cell carcinoma treatmentChromatin Remodeling and CancerCancer Genomics and Diagnostics

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Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

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Dalgliesh, Gillian L., Furge, Kyle, Greenman, Chris, Chen, Lina, Bignell, Graham, Butler, Adam, Davies, Helen, Edkins, Sarah, Hardy, Claire, Latimer, Calli, Teague, Jon, Andrews, Jenny, Barthorpe, Syd, Beare, Dave, Buck, Gemma, Campbell, Peter J., Forbes, Simon, Jia, Mingming, Jones, David, Knott, Henry, Kok, Chai Yin, Lau, King Wai, Leroy, Catherine, Lin, Meng-Lay, McBride, David J., Maddison, Mark, Maguire, Simon, McLay, Kirsten, Menzies, Andrew, Mironenko, Tatiana, Mulderrig, Lee, Mudie, Laura, O’Meara, Sarah, Pleasance, Erin, Rajasingham, Arjunan, Shepherd, Rebecca, Smith, Raffaella, Stebbings, Lucy, Stephens, Philip, Tang, Gurpreet, Tarpey, Patrick S., Turrell, Kelly, Dykema, Karl J., Khoo, Sok Kean, Petillo, David, Wondergem, Bill, Anema, John, Kahnoski, Richard J., Teh, Bin Tean, Stratton, Michael R., Futreal, P. Andrew·2010·Nature

DOI 10.1038/nature08672PMC PMC2820242

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Abstract

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

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“[8–11].”
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Background
Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex
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Influential
RETRACTED ARTICLE: Significant directed walk framework to increase the accuracy of cancer classification using gene expression data
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Background
Retracted
Biomarkers for Renal Cell Carcinoma
Li, M., & Rathmell, W. K. (2011) · Springer eBooks · doi:10.1007/978-3-642-21858-3_4 · Cited by 3
“protein 1 ) have also recently been described, in addition to several other less commonly mutated genes [ 40 , 41 ].”
Background
Histone Demethylases in Prostate Cancer
Wang, L., Guo, W., Kim, K., Pochampalli, M. R., Hung, C.-L., Izumiya, Y., & Kung, H.-J. (2013) · Cancer drug discovery and develogment/Cancer drug discovery and development · doi:10.1007/978-1-4614-8039-6_15 · Cited by 3
Molecular Biology of Kidney Cancer
Kaelin, W. G. (2011) · Springer eBooks · doi:10.1007/978-3-642-21858-3_3 · Cited by 3
“histone tails such as SETD2, a histone H3 lysine 36 methyltransferase; JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase; and UTX (KMD6A), a histone H3 lysine 27 demethylase [ 104, 105 ] .”
Background
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes
Wittler, R., & Chauve, C. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s9-s21 · Cited by 3
“from a tissue not affected by cancer) from the same individual is available, this is not a trivial task [3,4,14-16].”
Background
Molecular Characterization of Renal Cell Carcinoma
Teh, B. T., Farber, L. J., & Furge, K. (2012) · Springer eBooks · doi:10.1007/978-1-4614-2400-0_5 · Cited by 3
Self-citation
Altered oncomodules underlie chromatin regulatory factors driver mutations
Frigola, J., Iturbide, A., López-Bigas, N., Peiró, S., & González-Pérez, A. (2016) · Oncotarget · doi:10.18632/oncotarget.8752 · Cited by 2
“com/oncotarget driver, [31] are genes in the p53 pathway (Supplementary Table S3).”
Background
Molecular Genetics of Renal Cell Carcinoma
Fukawa, T., Shannon, N. B., Huang, D., Tan, J. Y., Yao, X., Rozen, S., Tan, P., & Teh, B. T. (2017) · Springer eBooks · doi:10.1007/978-4-431-55531-5_3 · Cited by 3
Self-citation
Hereditary Renal Cell Carcinoma
Baba, M., Schmidt, L. S., & Linehan, W. M. (2017) · Springer eBooks · doi:10.1007/978-4-431-55531-5_2 · Cited by 4
Misregulation of Histone Methylation Regulators in Cancer
Ooi, W. F., Yao, X., Tan, P. B. O., & Teh, B. T. (2017) · Cancer drug discovery and develogment/Cancer drug discovery and development · doi:10.1007/978-3-319-59786-7_8 · Cited by 3
Self-citation
Cancer of the Kidney
Пили, Р., KAUFFMAN, E. C., & Rodríguez, R. (2014) · Elsevier eBooks · doi:10.1016/b978-1-4557-2865-7.00082-5 · Cited by 3
“Zisman and coworkers, in an attempt to standardize RCC staging and management protocol, developed the UISS, described earlier.161 This system incorporates histologic grade, ECOG status, and TNM stage to improve prognostication for RCC.161 With this system, they created a surveillance protocol for patients grouped acco…”
BackgroundInfluential
Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients
Belikov, A. V., Otnyukov, D. V., Vyatkin, A. D., & Leonov, S. V. (2022) · PeerJ · doi:10.7717/peerj.13860 · Cited by 3
“NF2 is also mutated and deleted in mesotheliomas (Sekido et al., 1995), clear cell renal cell carcinomas (Dalgliesh et al., 2010), collecting duct Belikov et al. (2022), PeerJ, DOI 10.7717/peerj.13860 18/30 carcinomas of the kidney (Pal et al., 2016), and renal cell carcinomas with sarcomatoid…”
BackgroundInfluential
New Insights into von Hippel-Lindau Function Highlighted by Investigation of the Trichloroethylene-Induced p.P81S Hotspot Mutation
Neckers, L., Ricketts, C. J., & Linehan, W. M. (2013) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djt240 · Cited by 3
Multi-regional characterisation of renal cell carcinoma and microenvironment at single cell resolutionPreprint
Li, R., Ferdinand, J. R., Loudon, K. W., Bowyer, G., Mamanova, L., Neves, J. B., Bolt, L., Fasouli, E. S., Lawson, A. R. J., Young, M. D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.12.468373 · Cited by 2
Self-citation
Upregulation of Pole2 Promotes Clear Cell Renal Cell Carcinoma Progression via AKT/mTOR Pathway and Predicts a Poor PrognosisPreprint
Su, Y., Li, C., Liu, K., Wei, L., Li, D., Wang, W., Xu, Y., Pan, H., & Teng, L. L. (2020) · doi:10.21203/rs.3.rs-35733/v1 · Cited by 3
The SLC1A1 /EAAT3 Dicarboxylic Amino Acid Transporter is an Epigenetically Dysregulated Nutrient Carrier that Sustains Oncogenic Metabolic ProgramsPreprint
Grubb, T. M., Khatun, J., Matar, S., Ghandour, F., Dubasik, N., Salem, C., Orlando, D. A., Guenther, M. G., Martinez, S. R., Koochaki, P., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.04.556240 · Cited by 2
“HIF-dependent mechanisms include the transcriptional activation of several JumonjiC-family histone demethylases (KDMs) (14), whereas HIF-independent mechanisms include the genetic inactivation of SWI/SNF-family chromatin modifiers, such as PBRM1 (15); or inactivation of histone modifiers, such as SETD2, MLL3, KDM5C, a…”
Background
Canonical and Non‐Canonical Functions of Histone H3K4 Methylation Modifiers in Cancer
Hoshii, T. (2025) · Cancer Science · doi:10.1111/cas.70190 · Cited by 2
“Similarly, KDM5C is oncogenic in some cancers but suppressive in others, including clear cell renal carcinoma [70, 71].”
Chromatin Regulatory Targets for Anticancer Therapeutics
Barta, P. A., Carter, T. R., & Erb, M. A. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.5c00231 · Cited by 2
Integrating whole-exome sequencing and scRNA-seq reveal the characteristic in one clear cell renal cell carcinoma sample arising in the setting of VHL disease
Lu, W., Jin, T., Yu, X., Liu, Y., Zheng, L., Huang, S., Zheng, W., Yan, H.-B., Su, C., Ye, Y., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-27699-y · Cited by 2
“As a pervious study reported, TAMs could induce T cells exhaustion and CD8 + exhausted T would release factors to encourage polarization 34 .”
Metabolic and epigenetic interplay in HSPC specification: A balance between extrinsic and intrinsic cues
Kalogeraki, M., Rondeau, V., Nader, Z. A., Espéli, M., & Balabanian, K. (2026) · iScience · doi:10.1016/j.isci.2026.114921 · Cited by 2
“125 Knocking out Setd2 disrupts hematopoietic differentiation, decreases the number of MPPs and alters the composition of this compartment.”
Structural landscape of H3K27me3 recognition by protein domains and their potential for inhibition
Rosas, R., Baracaldo-Lancheros, L. F., Dykhuizen, E. C., & Musselman, C. A. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.111344 · Cited by 2
The Development of Cancer Genome Research and its Clinical Opportunity brought by Next Generation Sequencing
Li, J., & Wang, B. (2012) · Journal of Health & Medical Informatics · doi:10.4172/2157-7420.s1-002 · Cited by 2
Evolutionary History of Oncogenes and Tumor Suppressor Genes Families: The Ancestral Origin in Mammals and Duplication Patterns
Nawaz, Y., Khan, A. Z., Tanvir, F., Ambreen, S., Zafar, J., Umar, A., Majeed, I., & Tariq, H. (2023) · Letters in Drug Design & Discovery · doi:10.2174/1570180820666230227114821 · Cited by 2
Correctly identifying the cells of origin is essential for tailoring treatment and understanding the emergence of cancer stem cells and late metastases
Waldum, H. L., & Slupphaug, G. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1369907 · Cited by 2
“Lack of VHL factor function is also central in CCRCCs in general (37, 38), but the cancers not being a part of inherent VHL disease manifest themselves a few decades later.”
Background
Inherited KDM6AA649T facilitates tumor-immune escape and exacerbates colorectal signet-ring cell carcinoma outcomes
Feng, M., Chai, C., Hao, X., Lai, X., Luo, Y., Zhang, H., Tang, W., Gao, N., Pan, G., Liu, X., et al. (2024) · Oncogene · doi:10.1038/s41388-024-03029-w · Cited by 2
“Numerous loss-of-function mutations of KDM6A were frequently discovered in a variety of human solid tumors and leukemias [10, 12, 37 – 42].”
TNFSF9 Is Associated with Favorable Tumor Immune Microenvironment in Patients with Renal Cell Carcinoma Who Are Treated with the Combination Therapy of Nivolumab and Ipilimumab
Isoda, B., Kandori, S., Sazuka, T., Kojima, T., Nitta, S., Shiga, M., Nagumo, Y., Fujimoto, A., Arai, T., Sato, H., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137444 · Cited by 2
“In terms of the percentage of these gene mutations, they are slightly more common in SETD2 , but the rest are comparable to those reported in the past [3–6].”
Result
Ankrd1 Promotes Lamellipodia Formation and Cell Motility via Interaction with Talin-1 in Clear Cell Renal Cell Carcinoma
Takai, Y., Naito, S., Ito, H., Horie, S., Ushijima, M., Narisawa, T., Yagi, M., Ichiyanagi, O., & Tsuchiya, N. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26094232 · Cited by 2
“NF2 mutations were found in ccRCC [37].”
The epigenetic landscape of innate immunity
Luca, M. D., Pels, K., Moleirinho, S., & Curtale, G. (2017) · AIMS molecular science · doi:10.3934/molsci.2017.1.110 · Cited by 2
Novel germline mutation in lung cancer pedigrees establishes BCAR1 as a human cancer susceptibility gene: a case report
Zhu, K., Zhao, Y., Zhang, S., Wu, L. Y., Zong, Y., Li, Z., Li, Q., Cheng, F., & Meng, R. (2022) · Annals of Translational Medicine · doi:10.21037/atm-21-7017 · Cited by 2
“There are also several studies that have attempted to identify driver mutations of cancer including leukemias, myelomas and solid tumors (34-36).”
Background
Renal Cell Carcinoma: Overview
Ricketts, C. J., & Maher, E. R. (2014) · Springer eBooks · doi:10.1007/978-0-85729-482-1_17 · Cited by 2
“In addition SETD2 , JARID1C , UTX and MLL2 have each been reported to be mutated in up to 5 % of clear cell RCC [ 24 ].”
Background
Molecular Biology of Clear Cell Renal Carcinoma
Kaelin, W. G. (2012) · Springer eBooks · doi:10.1007/978-1-4614-2400-0_2 · Cited by 2
Thyrosinkinaseinhibitoren in der Onkologie
Zander, T., & Hallek, M. J. (2011) · Der Internist · doi:10.1007/s00108-011-2818-3 · Cited by 2
Insights into cancer mechanisms from genomic research on urological cancers
Schulz, W. A., & Ribarska, T. (2011) · Genome Medicine · doi:10.1186/gm234 · Cited by 2
“Renal cancer: aberrant hypoxia regulation as a primary mechanism in carcinogenesis Investigations of clearcell renal cell carcinoma (ccRCC), the major histological subtype of renal carcinoma, have highlighted the importance of hypoxia in cancer generally.”
BackgroundInfluential
Molecular Pathology of Genitourinary Cancers: Translating the Cancer Genome to the Clinic
Warrick, J. I., & Tomlins, S. A. (2014) · Springer eBooks · doi:10.1007/978-1-4939-0727-4_26 · Cited by 2
PBRM1: A Critical Subunit of the SWI/SNF Chromatin Remodeling Complex
Lee, C., Pham, C. G., & Hsieh, J. J.-D. (2014) · Springer eBooks · doi:10.1007/978-1-4939-1622-1_5 · Cited by 2
“Mutations of SETD2 were originally identifi ed by a large-scale exome sequencing of 3544 genes in tumor samples from 101 ccRCC cases [ 15 ].”
Background
System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach
Ran, J., Li, H., & Li, H. (2016) · The Scientific World JOURNAL · doi:10.1155/2016/1970904 · Cited by 2
“It is a helpful way by network approach to perform system review on a certain gene.”
Method
[Molecular biological foundation of targeted therapy for metastatic renal cell carcinoma].
Lai, C., & Teng, X. (2016) · PubMed Central · doi:10.3785/j.issn.1008-9292.2016.01.15 · Cited by 2
Malignant Transformation and Epigenetics
Han, Y., Ren, J., Yu, W., Terashima, M., & Muegge, K. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-800957-4.00007-2 · Cited by 2
Next Generation Sequencing in Renal Cell Carcinoma: Towards Precision Medicine.
Elias, R. M., Sharma, A., Singla, N., & Brugarolas, J. (2019) · PubMed · Cited by 2
Epigenetic silencing of ZBTB28 promotes renal cell carcinogenesis
Tong, X., Xu, L., Rong, R., Su, X., Xiang, T., Peng, W., & Shi, T. (2021) · Asia-Pacific Journal of Clinical Oncology · doi:10.1111/ajco.13560 · Cited by 2
Ceruloplasmin Expression in Renal Cell Carcinoma Correlates with Higher-Grade and Shortened Survival
Zimpfer, A., Glass, A. S., Bastian, M., Schuff‐Werner, P., Hakenberg, O. W., & Maruschke, M. (2021) · Biomarkers in Medicine · doi:10.2217/bmm-2020-0514 · Cited by 2
Liquid biopsy as a new tool for diagnosis, monitoring, and personalized medicine in urogenital cancers
Aghamir, S. M. K., Gholami, K., & Calvez‐Kelm, F. L. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-99884-0.00009-4 · Cited by 2
Relationship between body composition and PBRM1 mutations in clear cell renal cell carcinoma: a propensity score matching analysis
Demırel, E., & Dılek, O. (2023) · Revista da Associação Médica Brasileira · doi:10.1590/1806-9282.20220415 · Cited by 2
“2023;69(5):e20220415 Relation between body composition and PBRM1 in clear cell renal cell carcinoma”
Background
The Fundamental Role of Epigenetic Regulation in Normal and Disturbed Cell Growth, Differentiation, and Stemness
Rodríguez‐Paredes, M., & Esteller, M. (2013) · Springer eBooks · doi:10.1007/978-3-642-38404-2_1 · Cited by 2

Authors: Dalgliesh, G. L., Furge, K., Greenman, C., Chen, L., Bignell, G., Butler, A., Davies, H., Edkins, S., Hardy, C., Latimer, C., Teague, J., Andrews, J., Barthorpe, S., Beare, D., Buck, G., Campbell, P. J., Forbes, S., Jia, M., Jones, D., Knott, H., Kok, C. Y., Lau, K. W., Leroy, C., Lin, M.-L., McBride, D. J., Maddison, M., Maguire, S., McLay, K., Menzies, A., Mironenko, T., Mulderrig, L., Mudie, L., O’Meara, S., Pleasance, E., Rajasingham, A., Shepherd, R., Smith, R., Stebbings, L., Stephens, P., Tang, G., Tarpey, P. S., Turrell, K., Dykema, K. J., Khoo, S. K., Petillo, D., Wondergem, B., Anema, J., Kahnoski, R. J., Teh, B. T., Stratton, M. R., & Futreal, P. A.
Affiliations: Wellcome Sanger Institute (GB)
Van Andel Institute (US)
Spectrum Health (US)
Institute of Cancer Research (GB)
Corresponding author: Teh, Bin Tean
Stratton, Michael R.
Futreal, P. Andrew
ORCID: Dalgliesh, Gillian L.
Greenman, Chris
Chen, Lina
Davies, Helen
Edkins, Sarah
Latimer, Calli
Teague, Jon
Barthorpe, Syd
Buck, Gemma
Campbell, Peter J.
Jia, Mingming
Jones, David
Lau, King Wai
Lin, Meng-Lay
McBride, David J.
Menzies, Andrew
Mironenko, Tatiana
Pleasance, Erin
Shepherd, Rebecca
Tarpey, Patrick S.
Khoo, Sok Kean
Petillo, David
Kahnoski, Richard J.
Teh, Bin Tean
Stratton, Michael R.
Futreal, P. Andrew
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2010-01
Volume: 463
Issue: 7279
Pages: 360-363
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature08672
PMC: PMC2820242
OpenAlex: W2079212177
Cited by: 1,173
References: 28
Citations by year: 2026: 20 · 2025: 26 · 2024: 33 · 2023: 43 · 2022: 40 · 2021: 58 · 2020: 63 · 2019: 54 · 2018: 66 · 2017: 65 · 2016: 91 · 2015: 85 · 2014: 119 · 2013: 125 · 2012: 114
FWCI: 109.36
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders: Wellcome Trust (077012/Z/05/Z, 082359, 077012, 088340, 093867)
Topics: Health Sciences › Medicine › Oncology › Renal cell carcinoma treatment
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Keywords: clear cell renal cell carcinoma, somatic mutations, histone-modifying enzymes, SETD2, JARID1C, KDM6A, neurofibromatosis type 2, VHL, chromatin modification, histone H3 lysine 36 methylation, histone H3 lysine 4 demethylation, tumor suppressor, cancer gene identification
MeSH terms: Carcinoma, Renal Cell, Chromatin, Histones, Humans, Kidney Neoplasms, Mutation, Nuclear Proteins, Oxidoreductases, N-Demethylating, Histone-Lysine N-Methyltransferase, Cell Hypoxia, Gene Expression Regulation, Neoplastic, Genes, Neurofibromatosis 2, Sequence Analysis, DNA, Histone Demethylases

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Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

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