The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

Bin Zhu, Maria Luana Poeta, Manuela Costantini, Tongwu Zhang, Jianxin Shi, Steno Sentinelli, Wei Zhao, Vincenzo Pompeo, Maurizio Cardelli, Boian S. Alexandrov, Burcak Otlu, Xing Hua, Kristine Jones, Seth Brodie, Malgorzata Ewa Dabrowska, Jorge R. Toro, Meredith Yeager, Mingyi Wang, Belynda Hicks, Ludmil B. Alexandrov, Kevin M. Brown, David C. Wedge (), Stephen Chanock, Vito Michele Fazio, Michele Gallucci and Maria Teresa Landi ()
Additional contact information
Bin Zhu: National Cancer Institute, NIH, DHHS
Maria Luana Poeta: Biotechnology and Biopharmaceutics, University of Bari
Manuela Costantini: Biotechnology and Biopharmaceutics, University of Bari
Tongwu Zhang: National Cancer Institute, NIH, DHHS
Jianxin Shi: National Cancer Institute, NIH, DHHS
Steno Sentinelli: “Regina Elena” National Cancer Institute
Wei Zhao: National Cancer Institute, NIH, DHHS
Vincenzo Pompeo: “Regina Elena” National Cancer Institute
Maurizio Cardelli: Advanced Technology Center for Aging Research, IRCCS INRCA
Boian S. Alexandrov: Los Alamos National Laboratory
Burcak Otlu: University of California, San Diego
Xing Hua: National Cancer Institute, NIH, DHHS
Kristine Jones: Frederick National Laboratory for Cancer Research
Seth Brodie: Frederick National Laboratory for Cancer Research
Malgorzata Ewa Dabrowska: “Regina Elena” National Cancer Institute
Jorge R. Toro: Washington, DC Veteran Affairs Medical Center
Meredith Yeager: Frederick National Laboratory for Cancer Research
Mingyi Wang: Frederick National Laboratory for Cancer Research
Belynda Hicks: Frederick National Laboratory for Cancer Research
Ludmil B. Alexandrov: University of California, San Diego
Kevin M. Brown: National Cancer Institute, NIH, DHHS
David C. Wedge: Big Data Institute
Stephen Chanock: National Cancer Institute, NIH, DHHS
Vito Michele Fazio: University Campus Bio-Medico of Rome
Michele Gallucci: “Regina Elena” National Cancer Institute
Maria Teresa Landi: National Cancer Institute, NIH, DHHS

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: Abstract Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC, driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and that targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.

Date: 2020
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DOI: 10.1038/s41467-020-16546-5

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