Punctuated evolution of prostate cancer genomes

Sylvan C. Baca; Davide Prandi; Michael S. Lawrence; Juan Miguel Mosquera; Alessandro Romanel; Yotam Drier; Kyung Park; Naoki Kitabayashi; Theresa Y. MacDonald; Mahmoud Ghandi; Eliezer Van Allen; Gregory V. Kryukov; Andrea Sboner; Jean Philippe Theurillat; T. David Soong; Elizabeth Nickerson; Daniel Auclair; Ashutosh Tewari; Himisha Beltran; Robert C. Onofrio; Gunther Boysen; Candace Guiducci; Christopher E. Barbieri; Kristian Cibulskis; Andrey Sivachenko; Scott L. Carter; Gordon Saksena; Douglas Voet; Alex H. Ramos; Wendy Winckler; Michelle Cipicchio; Kristin Ardlie; Philip W. Kantoff; Michael F. Berger; Stacey B. Gabriel; Todd R. Golub; Matthew Meyerson; Eric S. Lander; Olivier Elemento; Gad Getz; Francesca Demichelis; Mark A. Rubin; Levi A. Garraway

doi:10.1016/j.cell.2013.03.021

Punctuated evolution of prostate cancer genomes

Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V. Kryukov, Andrea Sboner, Jean Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. OnofrioGunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis^*, Mark A. Rubin, Levi A. Garraway

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1009 Scopus citations

Abstract

The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.

Original language	English
Pages (from-to)	666-677
Number of pages	12
Journal	Cell
Volume	153
Issue number	3
DOIs	https://doi.org/10.1016/j.cell.2013.03.021
State	Published - 25 Apr 2013
Externally published	Yes

Bibliographical note

Funding Information:
We thank the members of the Broad Institute Genome Sequencing Platform for their part in this work. This study was supported by the US National Human Genome Research Institute (NHGRI) Large Scale Sequencing Program (U54 HG003067 to the Broad Institute, E.S.L.), the Kohlberg Foundation (L.A.G.), the Starr Cancer Consortium (M.A.R., F.D., A.T., G.G., and L.A.G.), the Prostate Cancer Foundation (M.A.R.), US Department of Defense Synergy Awards (PC101020 to F.D., L.A.G., and M.A.R.) and a New Investigator Award (PC094516 to F.D.), the Dana-Farber/Harvard Cancer Center Prostate Cancer SPORE (US National Institutes of Health [NIH] P50 CA090381), the US National Cancer Institute, Early Detection Research Network (U01CA111275 and NCI EDRN to F.D. and M.A.R.), the US National Cancer Institute (R01 CA125612 to F.D. and M.A.R.), the Fondazione Trentina per la Ricerca sui Tumori (F.D.), the Swiss Science Foundation (PASMP3_134379/1 to J.-P.T.), the National Institute of General Medical Sciences ( T32GM007753 to S.C.B.), and a US NIH Director’s New Innovator Award (DP2OD002750 to L.A.G.). L.A.G. is an equity holder and consultant in Foundation Medicine, a consultant to Novartis and Millenium/Takeda, and a recipient of a grant from Novartis.

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10.1016/j.cell.2013.03.021

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Baca, S. C., Prandi, D., Lawrence, M. S., Mosquera, J. M., Romanel, A., Drier, Y., Park, K., Kitabayashi, N., MacDonald, T. Y., Ghandi, M., Van Allen, E., Kryukov, G. V., Sboner, A., Theurillat, J. P., Soong, T. D., Nickerson, E., Auclair, D., Tewari, A., Beltran, H., ... Garraway, L. A. (2013). Punctuated evolution of prostate cancer genomes. Cell, 153(3), 666-677. https://doi.org/10.1016/j.cell.2013.03.021

@article{e5a6f7ae55ab44698670f12ec590f61a,

title = "Punctuated evolution of prostate cancer genomes",

abstract = "The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term {"}chromoplexy,{"} frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.",

author = "Baca, {Sylvan C.} and Davide Prandi and Lawrence, {Michael S.} and Mosquera, {Juan Miguel} and Alessandro Romanel and Yotam Drier and Kyung Park and Naoki Kitabayashi and MacDonald, {Theresa Y.} and Mahmoud Ghandi and {Van Allen}, Eliezer and Kryukov, {Gregory V.} and Andrea Sboner and Theurillat, {Jean Philippe} and Soong, {T. David} and Elizabeth Nickerson and Daniel Auclair and Ashutosh Tewari and Himisha Beltran and Onofrio, {Robert C.} and Gunther Boysen and Candace Guiducci and Barbieri, {Christopher E.} and Kristian Cibulskis and Andrey Sivachenko and Carter, {Scott L.} and Gordon Saksena and Douglas Voet and Ramos, {Alex H.} and Wendy Winckler and Michelle Cipicchio and Kristin Ardlie and Kantoff, {Philip W.} and Berger, {Michael F.} and Gabriel, {Stacey B.} and Golub, {Todd R.} and Matthew Meyerson and Lander, {Eric S.} and Olivier Elemento and Gad Getz and Francesca Demichelis and Rubin, {Mark A.} and Garraway, {Levi A.}",

note = "Funding Information: We thank the members of the Broad Institute Genome Sequencing Platform for their part in this work. This study was supported by the US National Human Genome Research Institute (NHGRI) Large Scale Sequencing Program (U54 HG003067 to the Broad Institute, E.S.L.), the Kohlberg Foundation (L.A.G.), the Starr Cancer Consortium (M.A.R., F.D., A.T., G.G., and L.A.G.), the Prostate Cancer Foundation (M.A.R.), US Department of Defense Synergy Awards (PC101020 to F.D., L.A.G., and M.A.R.) and a New Investigator Award (PC094516 to F.D.), the Dana-Farber/Harvard Cancer Center Prostate Cancer SPORE (US National Institutes of Health [NIH] P50 CA090381), the US National Cancer Institute, Early Detection Research Network (U01CA111275 and NCI EDRN to F.D. and M.A.R.), the US National Cancer Institute (R01 CA125612 to F.D. and M.A.R.), the Fondazione Trentina per la Ricerca sui Tumori (F.D.), the Swiss Science Foundation (PASMP3_134379/1 to J.-P.T.), the National Institute of General Medical Sciences ( T32GM007753 to S.C.B.), and a US NIH Director{\textquoteright}s New Innovator Award (DP2OD002750 to L.A.G.). L.A.G. is an equity holder and consultant in Foundation Medicine, a consultant to Novartis and Millenium/Takeda, and a recipient of a grant from Novartis. ",

year = "2013",

month = apr,

day = "25",

doi = "10.1016/j.cell.2013.03.021",

language = "אנגלית",

volume = "153",

pages = "666--677",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "3",

}

Baca, SC, Prandi, D, Lawrence, MS, Mosquera, JM, Romanel, A, Drier, Y, Park, K, Kitabayashi, N, MacDonald, TY, Ghandi, M, Van Allen, E, Kryukov, GV, Sboner, A, Theurillat, JP, Soong, TD, Nickerson, E, Auclair, D, Tewari, A, Beltran, H, Onofrio, RC, Boysen, G, Guiducci, C, Barbieri, CE, Cibulskis, K, Sivachenko, A, Carter, SL, Saksena, G, Voet, D, Ramos, AH, Winckler, W, Cipicchio, M, Ardlie, K, Kantoff, PW, Berger, MF, Gabriel, SB, Golub, TR, Meyerson, M, Lander, ES, Elemento, O, Getz, G, Demichelis, F, Rubin, MA & Garraway, LA 2013, 'Punctuated evolution of prostate cancer genomes', Cell, vol. 153, no. 3, pp. 666-677. https://doi.org/10.1016/j.cell.2013.03.021

TY - JOUR

T1 - Punctuated evolution of prostate cancer genomes

AU - Baca, Sylvan C.

AU - Prandi, Davide

AU - Lawrence, Michael S.

AU - Mosquera, Juan Miguel

AU - Romanel, Alessandro

AU - Drier, Yotam

AU - Park, Kyung

AU - Kitabayashi, Naoki

AU - MacDonald, Theresa Y.

AU - Ghandi, Mahmoud

AU - Van Allen, Eliezer

AU - Kryukov, Gregory V.

AU - Sboner, Andrea

AU - Theurillat, Jean Philippe

AU - Soong, T. David

AU - Nickerson, Elizabeth

AU - Auclair, Daniel

AU - Tewari, Ashutosh

AU - Beltran, Himisha

AU - Onofrio, Robert C.

AU - Boysen, Gunther

AU - Guiducci, Candace

AU - Barbieri, Christopher E.

AU - Cibulskis, Kristian

AU - Sivachenko, Andrey

AU - Carter, Scott L.

AU - Saksena, Gordon

AU - Voet, Douglas

AU - Ramos, Alex H.

AU - Winckler, Wendy

AU - Cipicchio, Michelle

AU - Ardlie, Kristin

AU - Kantoff, Philip W.

AU - Berger, Michael F.

AU - Gabriel, Stacey B.

AU - Golub, Todd R.

AU - Meyerson, Matthew

AU - Lander, Eric S.

AU - Elemento, Olivier

AU - Getz, Gad

AU - Demichelis, Francesca

AU - Rubin, Mark A.

AU - Garraway, Levi A.

N1 - Funding Information: We thank the members of the Broad Institute Genome Sequencing Platform for their part in this work. This study was supported by the US National Human Genome Research Institute (NHGRI) Large Scale Sequencing Program (U54 HG003067 to the Broad Institute, E.S.L.), the Kohlberg Foundation (L.A.G.), the Starr Cancer Consortium (M.A.R., F.D., A.T., G.G., and L.A.G.), the Prostate Cancer Foundation (M.A.R.), US Department of Defense Synergy Awards (PC101020 to F.D., L.A.G., and M.A.R.) and a New Investigator Award (PC094516 to F.D.), the Dana-Farber/Harvard Cancer Center Prostate Cancer SPORE (US National Institutes of Health [NIH] P50 CA090381), the US National Cancer Institute, Early Detection Research Network (U01CA111275 and NCI EDRN to F.D. and M.A.R.), the US National Cancer Institute (R01 CA125612 to F.D. and M.A.R.), the Fondazione Trentina per la Ricerca sui Tumori (F.D.), the Swiss Science Foundation (PASMP3_134379/1 to J.-P.T.), the National Institute of General Medical Sciences ( T32GM007753 to S.C.B.), and a US NIH Director’s New Innovator Award (DP2OD002750 to L.A.G.). L.A.G. is an equity holder and consultant in Foundation Medicine, a consultant to Novartis and Millenium/Takeda, and a recipient of a grant from Novartis.

PY - 2013/4/25

Y1 - 2013/4/25

N2 - The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.

AB - The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.

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DO - 10.1016/j.cell.2013.03.021

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AN - SCOPUS:84875757638

SN - 0092-8674

VL - 153

SP - 666

EP - 677

JO - Cell

JF - Cell

IS - 3

ER -

Punctuated evolution of prostate cancer genomes

Abstract

Bibliographical note

UN SDGs

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