• Campbell, P. J. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Fletcher, O. & Houlston, R. S. Architecture of inherited susceptibility to common cancer. Nat. Rev. Cancer 10, 353–361 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Purdue, M. P. et al. Genome-wide association study of renal cell carcinoma identifies two susceptibility loci on 2p21 and 11q13.3. Nat. Genet. 43, 60–65 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Scelo, G. et al. Genome-wide association study identifies multiple risk loci for renal cell carcinoma. Nat. Commun. 8, 15724 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Turajlic, S. et al. Deterministic evolutionary trajectories influence primary tumor growth: TRACERx Renal. Cell 173, 595–610 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kaelin, W. G. von Hippel-Lindau disease. Annu. Rev. Pathol. Mech. Dis. 2, 145–173 (2007).

    CAS 
    Article 

    Google Scholar
     

  • Watkins, T. B. K. et al. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 587, 126–132 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Haigis, K. M., Cichowski, K. & Elledge, S. J. Tissue-specificity in cancer: the rule, not the exception. Science 363, 1150–1151 (2019).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Shakhova, O. et al. Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma. Nat. Cell Biol. 14, 882–890 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kaufman, C. K. et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science 351, aad2197 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • McDonald, E. R. et al. Project DRIVE: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale, deep RNAi screening. Cell 170, 577–592.e10 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564–576.e16 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Vanharanta, S. et al. Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer. Nat. Med. 19, 50–56 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Jacob, L. S. et al. Metastatic competence can emerge with selection of preexisting oncogenic alleles without a need of new mutations. Cancer Res. 75, 3713–3719 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Rodrigues, P. et al. NF-κB-dependent lymphoid enhancer co-option promotes renal carcinoma metastasis. Cancer Discov. 8, 850–865 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dempster, J. M. et al. Extracting biological insights from the Project Achilles Genome-Scale CRISPR screens in cancer cell lines. Preprint at bioRxiv https://doi.org/10.1101/720243 (2019).

  • Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779–1784 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bleu, M. et al. PAX8 activates metabolic genes via enhancer elements in renal cell carcinoma. Nat. Commun. 10, 3739 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Kaminski, M. M. et al. Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors. Nat. Cell Biol. 18, 1269–1280 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Papachristou, E. K. et al. A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes. Nat. Commun. 9, 2311 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Wu, D., Potluri, N., Lu, J., Kim, Y. & Rastinejad, F. Structural integration in hypoxia-inducible factors. Nature 524, 303–308 (2015).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Corces, M. R. et al. The chromatin accessibility landscape of primary human cancers. Science 362, eaav1898 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Jolma, A. et al. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 527, 384–388 (2015).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Smith, C. C. et al. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. J. Clin. Invest. 128, 4804–4820 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zapatka, M. et al. The landscape of viral associations in human cancers. Nat. Genet. 52, 320–330 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Syafruddin, S. E. et al. A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma. Nat. Commun. 10, 1152 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Larson, M. H. et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat. Protoc. 8, 2180–2196 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Meuleman, W. et al. Index and biological spectrum of human DNase I hypersensitive sites. Nature 584, 244–251 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Schödel, J. et al. Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression. Nat. Genet. 44, 420–425 (2012).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Yao, X. et al. VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell carcinoma. Cancer Discov. 7, 1284–1305 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Musgrove, E. A., Caldon, C. E., Barraclough, J., Stone, A. & Sutherland, R. L. Cyclin D as a therapeutic target in cancer. Nat. Rev. Cancer 11, 558–572 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Wykoff, C. C. et al. Gene array of VHL mutation and hypoxia shows novel hypoxia-induced genes and that cyclin D1 is a VHL target gene. Br. J. Cancer 90, 1235–1243 (2004).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Platt, J. L. et al. Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. EMBO Rep. 17, 1410–1421 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Gordan, J. D. et al. HIF-α effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. Cancer Cell 14, 435–446 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Grampp, S. et al. Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer. Nat. Commun. 7, 13183 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hoefflin, R. et al. HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice. Nat. Commun. 11, 4111 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Gordan, J. D., Bertout, J. A., Hu, C.-J., Diehl, J. A. & Simon, M. C. HIF-2α promotes hypoxic cell proliferation by enhancing c-Myc transcriptional activity. Cancer Cell 11, 335–347 (2007).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Grampp, S. et al. Multiple renal cancer susceptibility polymorphisms modulate the HIF pathway. PLOS Genet. 13, e1006872 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • The GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318–1330 (2020).

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Bouchard, M. Nephric lineage specification by Pax2 and Pax8. Genes Dev. 16, 2958–2970 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     



  • Source link