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Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW. Erratum to: Modeling precision treatment of breast cancer. Genome Biol 2015; 16:95. [PMID: 25962591 PMCID: PMC4426644 DOI: 10.1186/s13059-015-0658-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 12/01/2022] Open
Abstract
During the type-setting of the final version of the article [1] some of the additional files were swapped. The correct files are republished in this Erratum.
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Affiliation(s)
- Anneleen Daemen
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA. .,Present address: Department of Bioinformatics & Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Obi L Griffith
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA. .,The Genome Institute, Washington University School of Medicine, St Louis, MO, 63105, USA.
| | - Laura M Heiser
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Nicholas J Wang
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Oana M Enache
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | | | - Francois Pepin
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Present address: Sequenta Inc, South San Francisco, CA, 94080, USA.
| | - Steffen Durinck
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - James E Korkola
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Malachi Griffith
- The Genome Institute, Washington University School of Medicine, St Louis, MO, 63105, USA.
| | - Joe S Hur
- Samsung Electronics Headquarters, Seocho-gu, Seoul, 137-857, Korea.
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do, 446-712, Korea.
| | - Jongsuk Chung
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Kyunggi-do, 446-712, Korea.
| | - Leslie Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Christopher Umbricht
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Pankaj Seth
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Vikas P Sukhatme
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Lakshmi R Jakkula
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Yiling Lu
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, CA, 94115, USA.
| | - Eric A Collisson
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA.
| | - Laura J Van't Veer
- Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94115, USA.
| | - Paul T Spellman
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Joe W Gray
- Department of Cancer & DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA.
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Ordinario E, Han HJ, Furuta S, Heiser LM, Jakkula LR, Rodier F, Spellman PT, Campisi J, Gray JW, Bissell MJ, Kohwi Y, Kohwi-Shigematsu T. ATM suppresses SATB1-induced malignant progression in breast epithelial cells. PLoS One 2012; 7:e51786. [PMID: 23251624 PMCID: PMC3519734 DOI: 10.1371/journal.pone.0051786] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/12/2012] [Indexed: 11/24/2022] Open
Abstract
SATB1 drives metastasis when expressed in breast tumor cells by radically reprogramming gene expression. Here, we show that SATB1 also has an oncogenic activity to transform certain non-malignant breast epithelial cell lines. We studied the non-malignant MCF10A cell line, which is used widely in the literature. We obtained aliquots from two different sources (here we refer to them as MCF10A-1 and MCF10A-2), but found them to be surprisingly dissimilar in their responses to oncogenic activity of SATB1. Ectopic expression of SATB1 in MCF10A-1 induced tumor-like morphology in three-dimensional cultures, led to tumor formation in immunocompromised mice, and when injected into tail veins, led to lung metastasis. The number of metastases correlated positively with the level of SATB1 expression. In contrast, SATB1 expression in MCF10A-2 did not lead to any of these outcomes. Yet DNA copy-number analysis revealed that MCF10A-1 is indistinguishable genetically from MCF10A-2. However, gene expression profiling analysis revealed that these cell lines have significantly divergent signatures for the expression of genes involved in oncogenesis, including cell cycle regulation and signal transduction. Above all, the early DNA damage-response kinase, ATM, was greatly reduced in MCF10A-1 cells compared to MCF10A-2 cells. We found the reason for reduction to be phenotypic drift due to long-term cultivation of MCF10A. ATM knockdown in MCF10A-2 and two other non-malignant breast epithelial cell lines, 184A1 and 184B4, enabled SATB1 to induce malignant phenotypes similar to that observed for MCF10A-1. These data indicate a novel role for ATM as a suppressor of SATB1-induced malignancy in breast epithelial cells, but also raise a cautionary note that phenotypic drift could lead to dramatically different functional outcomes.
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Affiliation(s)
- Ellen Ordinario
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Hye-Jung Han
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Saori Furuta
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Laura M. Heiser
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Lakshmi R. Jakkula
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Francis Rodier
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Paul T. Spellman
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Judith Campisi
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Joe W. Gray
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Mina J. Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Yoshinori Kohwi
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
| | - Terumi Kohwi-Shigematsu
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, United States of America
- * E-mail:
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Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, Pons J, Chan SW, Lam ET, Chu C, Park K, Hong SW, Hur JS, Huh N, Neuhaus IM, Yu SS, Grekin RT, Mauro TM, Cleaver JE, Kwok PY, LeBoit PE, Getz G, Cibulskis K, Aster JC, Huang H, Purdom E, Li J, Bolund L, Arron ST, Gray JW, Spellman PT, Cho RJ. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov 2011; 1:137-43. [PMID: 21984974 PMCID: PMC3187561 DOI: 10.1158/2159-8290.cd-11-0028] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Timely intervention for cancer requires knowledge of its earliest genetic aberrations. Sequencing of tumors and their metastases reveals numerous abnormalities occurring late in progression. A means to temporally order aberrations in a single cancer, rather than inferring them from serially acquired samples, would define changes preceding even clinically evident disease. We integrate DNA sequence and copy number information to reconstruct the order of abnormalities as individual tumors evolve for 2 separate cancer types. We detect vast, unreported expansion of simple mutations sharply demarcated by recombinative loss of the second copy of TP53 in cutaneous squamous cell carcinomas (cSCC) and serous ovarian adenocarcinomas, in the former surpassing 50 mutations per megabase. In cSCCs, we also report diverse secondary mutations in known and novel oncogenic pathways, illustrating how such expanded mutagenesis directly promotes malignant progression. These results reframe paradigms in which TP53 mutation is required later, to bypass senescence induced by driver oncogenes.
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Affiliation(s)
- Steffen Durinck
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Christine Ho
- Department of Statistics, University of California, Berkeley, CA
| | - Nicholas J. Wang
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA
| | | | | | - Jennifer Pons
- Department of Dermatology, University of California, San Francisco, CA
| | - Sai-Wing Chan
- Department of Dermatology, University of California, San Francisco, CA
| | - Ernest T. Lam
- Department of Dermatology, University of California, San Francisco, CA
| | - Catherine Chu
- Department of Dermatology, University of California, San Francisco, CA
| | - Kyunghee Park
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Sung-woo Hong
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Joe S. Hur
- Samsung Electronics Headquarters Seoul, Korea
| | - Nam Huh
- Emerging Technology Research Center, Samsung Advanced Institute of Technology, Seoul, Korea
| | - Isaac M. Neuhaus
- Department of Dermatology, University of California, San Francisco, CA
| | - Siegrid S. Yu
- Department of Dermatology, University of California, San Francisco, CA
| | - Roy T. Grekin
- Department of Dermatology, University of California, San Francisco, CA
| | - Theodora M. Mauro
- Department of Dermatology, University of California, San Francisco, CA
| | - James E. Cleaver
- Department of Dermatology, University of California, San Francisco, CA
| | - Pui-Yan Kwok
- Department of Dermatology, University of California, San Francisco, CA
| | | | - Gad Getz
- The Broad Institute of MIT and Harvard, MA
| | | | - Jon C. Aster
- Department of Pathology, Brigham and Women’s Hospital, MA
| | - Haiyan Huang
- Department of Statistics, University of California, Berkeley, CA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA
| | - Jian Li
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- Institute of Human Genetics, Aarhus University, Denmark
| | - Lars Bolund
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
- Institute of Human Genetics, Aarhus University, Denmark
| | - Sarah T. Arron
- Department of Dermatology, University of California, San Francisco, CA
| | - Joe W. Gray
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
- Biomedical Engineering Department, Oregon Health Sciences University, Oregon
| | - Paul T. Spellman
- Life Sciences Division, Lawrence Berkeley National Laboratories, CA
| | - Raymond J. Cho
- Department of Dermatology, University of California, San Francisco, CA
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