1
|
Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024; 56:900-912. [PMID: 38388848 PMCID: PMC11096114 DOI: 10.1038/s41588-024-01665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
Collapse
Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
2
|
Patel RS, Romero R, Watson EV, Liang AC, Burger M, Westcott PMK, Mercer KL, Bronson RT, Wooten EC, Bhutkar A, Jacks T, Elledge SJ. A GATA4-regulated secretory program suppresses tumors through recruitment of cytotoxic CD8 T cells. Nat Commun 2022; 13:256. [PMID: 35017504 PMCID: PMC8752777 DOI: 10.1038/s41467-021-27731-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
The GATA4 transcription factor acts as a master regulator of development of multiple tissues. GATA4 also acts in a distinct capacity to control a stress-inducible pro-inflammatory secretory program that is associated with senescence, a potent tumor suppression mechanism, but also operates in non-senescent contexts such as tumorigenesis. This secretory pathway is composed of chemokines, cytokines, growth factors, and proteases. Since GATA4 is deleted or epigenetically silenced in cancer, here we examine the role of GATA4 in tumorigenesis in mouse models through both loss-of-function and overexpression experiments. We find that GATA4 promotes non-cell autonomous tumor suppression in multiple model systems. Mechanistically, we show that Gata4-dependent tumor suppression requires cytotoxic CD8 T cells and partially requires the secreted chemokine CCL2. Analysis of transcriptome data in human tumors reveals reduced lymphocyte infiltration in GATA4-deficient tumors, consistent with our murine data. Notably, activation of the GATA4-dependent secretory program combined with an anti-PD-1 antibody robustly abrogates tumor growth in vivo.
Collapse
Affiliation(s)
- Rupesh S Patel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Scripps Green Hospital, San Diego, CA, USA
| | - Rodrigo Romero
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emma V Watson
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Anthony C Liang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Megan Burger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kim L Mercer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Eric C Wooten
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
3
|
Naxerova K, Di Stefano B, Makofske JL, Watson EV, de Kort MA, Martin TD, Dezfulian M, Ricken D, Wooten EC, Kuroda MI, Hochedlinger K, Elledge SJ. Integrated loss- and gain-of-function screens define a core network governing human embryonic stem cell behavior. Genes Dev 2021; 35:1527-1547. [PMID: 34711655 PMCID: PMC8559676 DOI: 10.1101/gad.349048.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
In this Resource/Methodology, Naxerova et al. describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. They identify a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance, and their results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks. Understanding the genetic control of human embryonic stem cell function is foundational for developmental biology and regenerative medicine. Here we describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. We identified a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance. We discovered that the chromatin-modifying complex SAGA and in particular its subunit TADA2B are central regulators of pluripotency, survival, growth, and lineage specification. Joint analysis of all screens revealed that genetic alterations that broadly inhibit differentiation across multiple germ layers drive proliferation and survival under pluripotency-maintaining conditions and coincide with known cancer drivers. Our results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks.
Collapse
Affiliation(s)
- Kamila Naxerova
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jessica L Makofske
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Emma V Watson
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marit A de Kort
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Timothy D Martin
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mohammed Dezfulian
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dominik Ricken
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Eric C Wooten
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
4
|
Patel RS, Romero R, Liang AC, Watson EV, Burger M, Westcott PM, Mercer KL, Bronson RT, Wooten EC, Bhutkar A, Jacks T, Elledge SJ. Abstract IA17: The role of the senescence-associated secretory phenotype in cancer. Cancer Immunol Res 2021. [DOI: 10.1158/2326-6074.tumimm20-ia17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cellular senescence is a stress-activated differentiation pathway that causes proliferation arrest governed by two powerful tumor suppressor pathways, USP28-TP53-CDKN1A and CDKN2A-RB. Senescent cells exhibit a pro-inflammatory secretory program termed the senescence-associated secretory phenotype (SASP) that is composed of chemokines, cytokines, growth factors, and proteases. SASP induction is independent of TP53 and RB function and its role in cancer has not been fully elucidated. We genetically targeted the master regulator of SASP, GATA4, and found that SASP functions as a non-cell autonomous tumor suppressor mechanism. We show that SASP is tumor suppressive in mouse models of cancer using both deletion and overexpression contexts. SASP-dependent tumor suppression requires the immune system, specifically CD8 cytotoxic T cells, to suppress tumor growth. Human tumors deficient in GATA4 have reduced lymphocyte infiltrates, indicating that human cancers may avoid immune infiltration by limiting SASP.
Citation Format: Rupesh S. Patel, Rodrigo Romero, Anthony C. Liang, Emma V. Watson, Megan Burger, Peter M.K. Westcott, Kim L. Mercer, Roderick T. Bronson, Eric C. Wooten, Arjun Bhutkar, Tyler Jacks, Stephen J. Elledge. The role of the senescence-associated secretory phenotype in cancer [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr IA17.
Collapse
Affiliation(s)
| | - Rodrigo Romero
- 2Massachusetts Institute of Technology, Cambridge, MA, USA,
| | | | | | - Megan Burger
- 2Massachusetts Institute of Technology, Cambridge, MA, USA,
| | | | - Kim L. Mercer
- 2Massachusetts Institute of Technology, Cambridge, MA, USA,
| | | | | | - Arjun Bhutkar
- 2Massachusetts Institute of Technology, Cambridge, MA, USA,
| | - Tyler Jacks
- 4Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | |
Collapse
|
5
|
Sack LM, Davoli T, Li MZ, Li Y, Xu Q, Naxerova K, Wooten EC, Bernardi RJ, Martin TD, Chen T, Leng Y, Liang AC, Scorsone KA, Westbrook TF, Wong KK, Elledge SJ. Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. Cell 2018; 173:499-514.e23. [PMID: 29576454 PMCID: PMC6643283 DOI: 10.1016/j.cell.2018.02.037] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [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] [Received: 06/06/2017] [Revised: 11/10/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
Abstract
Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors.
Collapse
Affiliation(s)
- Laura Magill Sack
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Teresa Davoli
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Mamie Z Li
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yuyang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Shandong Provincial Hospital affiliated to Shandong University, Jinan 250021, China
| | - Qikai Xu
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kamila Naxerova
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Eric C Wooten
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ronald J Bernardi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy D Martin
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ting Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Yumei Leng
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Anthony C Liang
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kathleen A Scorsone
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas F Westbrook
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| |
Collapse
|
6
|
Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science 2017; 355:355/6322/eaaf8399. [PMID: 28104840 DOI: 10.1126/science.aaf8399] [Citation(s) in RCA: 820] [Impact Index Per Article: 117.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 12/16/2016] [Indexed: 12/18/2022]
Abstract
Immunotherapies based on immune checkpoint blockade are highly effective in a subset of patients. An ongoing challenge is the identification of biomarkers that predict which patients will benefit from these therapies. Aneuploidy, also known as somatic copy number alterations (SCNAs), is widespread in cancer and is posited to drive tumorigenesis. Analyzing 12 human cancer types, we find that, for most, highly aneuploid tumors show reduced expression of markers of cytotoxic infiltrating immune cells, especially CD8+ T cells, and increased expression of cell proliferation markers. Different types of SCNAs predict the proliferation and immune signatures, implying distinct underlying mechanisms. Using published data from two clinical trials of immune checkpoint blockade therapy for metastatic melanoma, we found that tumor aneuploidy inversely correlates with patient survival. Together with other tumor characteristics such as tumor mutational load, aneuploidy may thus help identify patients most likely to respond to immunotherapy.
Collapse
Affiliation(s)
- Teresa Davoli
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hajime Uno
- Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
| | - Eric C Wooten
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
7
|
Davoli T, Mengwasser KE, Duan J, Chen T, Christensen C, Wooten EC, Anselmo AN, Li MZ, Wong KK, Kahle KT, Elledge SJ. Functional genomics reveals that tumors with activating phosphoinositide 3-kinase mutations are dependent on accelerated protein turnover. Genes Dev 2017; 30:2684-2695. [PMID: 28087713 PMCID: PMC5238728 DOI: 10.1101/gad.290122.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/12/2016] [Indexed: 12/17/2022]
Abstract
Davoli et al. identified ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors. Their results suggest that disruption of protein turnover homeostasis via ribosome or proteasome inhibition may be a novel treatment strategy for PI3K mutant human tumors. Activating mutations in the phosphoinositide 3-kinase (PI3K) signaling pathway are frequently identified in cancer. To identify pathways that support PI3K oncogenesis, we performed a genome-wide RNAi screen in isogenic cell lines harboring wild-type or mutant PIK3CA to search for PI3K synthetic-lethal (SL) genes. A combined analysis of these results with a meta-analysis of two other large-scale RNAi screening data sets in PI3K mutant cancer cell lines converged on ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors. Genetic or pharmacologic inhibition of either pathway alone, but not together, selectively killed PI3K mutant tumor cells in an mTOR-dependent manner. The expression of ribosomal and proteasomal components was significantly up-regulated in primary human colorectal tumors harboring PI3K pathway activation. Importantly, a PI3K SL gene signature containing the top hits of the SL genes identified in our meta-analysis robustly predicted overall patient survival in colorectal cancer, especially among patients with tumors with an activated PI3K pathway. These results suggest that disruption of protein turnover homeostasis via ribosome or proteasome inhibition may be a novel treatment strategy for PI3K mutant human tumors.
Collapse
Affiliation(s)
- Teresa Davoli
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Kristen E Mengwasser
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Jingjing Duan
- Department of Neurobiology, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cellular and Molecular Physiology, Centers for Mendelian Genomics, Yale School of Medicine, New Haven, Connecticut 06511, USA
| | - Ting Chen
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Camilla Christensen
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Eric C Wooten
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Anthony N Anselmo
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Mamie Z Li
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Kwok-Kin Wong
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kristopher T Kahle
- Department of Neurobiology, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cellular and Molecular Physiology, Centers for Mendelian Genomics, Yale School of Medicine, New Haven, Connecticut 06511, USA
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| |
Collapse
|
8
|
Wooten EC, Hebl VB, Wolf MJ, Greytak SR, Orr NM, Draper I, Calvino JE, Kapur NK, Maron MS, Kullo IJ, Ommen SR, Bos JM, Ackerman MJ, Huggins GS. Formin homology 2 domain containing 3 variants associated with hypertrophic cardiomyopathy. ACTA ACUST UNITED AC 2012; 6:10-8. [PMID: 23255317 DOI: 10.1161/circgenetics.112.965277] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Incomplete penetrance and variable expression of hypertrophic cardiomyopathy (HCM) is well appreciated. Common genetic polymorphisms variants that may affect HCM penetrance and expression have been predicted but are not well established. METHODS AND RESULTS We performed a case-control genomewide association study to identify common HCM-associated genetic polymorphisms and then asked whether such common variants were more represented in HCM or could explain the heterogeneity of HCM phenotypes. We identified an intronic FHOD3 variant (rs516514) associated with HCM (odds ratio, 2.45; 95% confidence interval, 1.76-3.41; P=1.25×10(-7)) and validated this finding in an independent cohort. Next, we tested FHOD3-V1151I (rs2303510), a nonsynonymous variant in partial linkage disequilibrium with rs516514, and we detected an even stronger association with HCM (P=1.76×10(-9)). Although HCM patients were more likely to carry these, FHOD3 allele subjects homozygous for FHOD3-1151I had similar HCM phenotypes as carriers of the V1151 allele. FHOD3 expression is increased in the setting of HCM, and both alleles of FHOD3-V1151I were detected in HCM myectomy tissue. Previously, FHOD3 was found to be required for formation of the sarcomere, and here we demonstrate that its fly homolog fhos is required for normal adult heart systolic contraction. CONCLUSIONS Here we demonstrate the association of a common nonsynonymous FHOD3 genetic variant with HCM. This discovery further strengthens the potential role of gene mutations and polymorphisms that alter the amino acid sequence of sarcomere proteins and HCM.
Collapse
Affiliation(s)
- Eric C Wooten
- Molecular Cardiology Research Institute Center for Translational Genomics, Department of Medicine, Cardiology Division, Tufts Medical Center, Boston, MA 02111, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Affiliation(s)
- Eric C Wooten
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Tufts University School of Medicine, Tufts Medical Center, Boston, MA, USA.
| | | |
Collapse
|
10
|
Tangri N, Alam A, Wooten EC, Huggins GS. Lack of association of Klotho gene variants with valvular and vascular calcification in Caucasians: a candidate gene study of the Framingham Offspring Cohort. Nephrol Dial Transplant 2011; 26:3998-4002. [PMID: 21565945 DOI: 10.1093/ndt/gfr188] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Valvular and vascular calcification are important early aging phenotypes and represent risk factors for cardiovascular morbidity and mortality. Klotho is a gene primarily expressed in the kidney that has an important role in calcium-phosphate homeostasis. The functional KL-VS variant of Klotho has been associated with aging and cardiovascular disease in human studies, but its role in valvular and vascular calcification remains unknown. We performed a candidate gene study in the Framingham Offspring Cohort to evaluate the effect of KL-VS variant of the Klotho gene on valvular calcification. METHODS We analyzed the Klotho KL-VS genotype (rs9536314) from the Affymetrix 550K genome-wide dataset, distributed by dbGAP, on 1389 cases and 2139 controls from the Framingham Heart Study Offspring Cohort. Allele and genotype frequencies were compared between cases and controls. Valvular calcification was defined as presence of calcification on the mitral annulus or the aortic valve as determined by echocardiography. A sensitivity analysis of coronary artery calcification by electron beam computed tomography was performed on 1363 patients. RESULTS The frequency of the TT versus the TG allele was not different between the cases and the controls (39 versus 41%). The KL-VS variant of Klotho was not associated with valvular or vascular calcification, despite adequate power to detect association (86% for odds ratios ≥1.2). In sensitivity analyses, no association (P > 0.001) between other common variants of Klotho, β-Klotho or fibroblast growth factor-23 and the end points of valvular or vascular calcification was observed. CONCLUSIONS In our adequately powered candidate gene study, we did not observe an association with the functional KL-VS variant of Klotho and presence of valvular or vascular calcification. Future studies aimed at combining cohorts with echocardiographic phenotypes need to be conducted to identify genetic variants associated with valvular calcification.
Collapse
Affiliation(s)
- Navdeep Tangri
- Department of Medicine, Tufts Medical Center, Boston, MA, USA.
| | | | | | | |
Collapse
|
11
|
Wooten EC, Iyer LK, Montefusco MC, Hedgepeth AK, Payne DD, Kapur NK, Housman DE, Mendelsohn ME, Huggins GS. Application of gene network analysis techniques identifies AXIN1/PDIA2 and endoglin haplotypes associated with bicuspid aortic valve. PLoS One 2010; 5:e8830. [PMID: 20098615 PMCID: PMC2809109 DOI: 10.1371/journal.pone.0008830] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [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: 10/27/2009] [Accepted: 12/30/2009] [Indexed: 01/19/2023] Open
Abstract
Bicuspid Aortic Valve (BAV) is a highly heritable congenital heart defect. The low frequency of BAV (1% of general population) limits our ability to perform genome-wide association studies. We present the application of four a priori SNP selection techniques, reducing the multiple-testing penalty by restricting analysis to SNPs relevant to BAV in a genome-wide SNP dataset from a cohort of 68 BAV probands and 830 control subjects. Two knowledge-based approaches, CANDID and STRING, were used to systematically identify BAV genes, and their SNPs, from the published literature, microarray expression studies and a genome scan. We additionally tested Functionally Interpolating SNPs (fitSNPs) present on the array; the fourth consisted of SNPs selected by Random Forests, a machine learning approach. These approaches reduced the multiple testing penalty by lowering the fraction of the genome probed to 0.19% of the total, while increasing the likelihood of studying SNPs within relevant BAV genes and pathways. Three loci were identified by CANDID, STRING, and fitSNPS. A haplotype within the AXIN1-PDIA2 locus (p-value of 2.926x10(-06)) and a haplotype within the Endoglin gene (p-value of 5.881x10(-04)) were found to be strongly associated with BAV. The Random Forests approach identified a SNP on chromosome 3 in association with BAV (p-value 5.061x10(-06)). The results presented here support an important role for genetic variants in BAV and provide support for additional studies in well-powered cohorts. Further, these studies demonstrate that leveraging existing expression and genomic data in the context of GWAS studies can identify biologically relevant genes and pathways associated with a congenital heart defect.
Collapse
Affiliation(s)
- Eric C. Wooten
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - Lakshmanan K. Iyer
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - Maria Claudia Montefusco
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - Alyson Kelley Hedgepeth
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - Douglas D. Payne
- Cardiothoracic Surgery Division, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Navin K. Kapur
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - David E. Housman
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Michael E. Mendelsohn
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
| | - Gordon S. Huggins
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
12
|
Georgescu S, Naggar JC, Welzig MC, Zhang Y, Park H, Wooten EC, Aronovitz MJ, Karas RH, Huggins GS, Galper JB. Increased TGFb signaling in type I diabetic mice is associated with parasympathetic dysfunction of the heart. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.524.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Serban Georgescu
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Jack C Naggar
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | | | - Yali Zhang
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Ho‐Jin Park
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Eric C Wooten
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Mark J Aronovitz
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Richard H Karas
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Gordon S Huggins
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| | - Jonas B Galper
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMA
| |
Collapse
|
13
|
Rouf R, Greytak S, Wooten EC, Wu J, Boltax J, Picard M, Svensson EC, Dillmann WH, Patten RD, Huggins GS. Increased FOG-2 in failing myocardium disrupts thyroid hormone-dependent SERCA2 gene transcription. Circ Res 2008; 103:493-501. [PMID: 18658259 DOI: 10.1161/circresaha.108.181487] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reduced expression of sarcoplasmic reticulum calcium ATPase (SERCA)2 and other genes in the adult cardiac gene program has raised consideration of an impaired responsiveness to thyroid hormone (T3) that develops in the advanced failing heart. Here, we show that human and murine cardiomyopathy hearts have increased expression of friend of GATA (FOG)-2, a cardiac nuclear hormone receptor corepressor protein. Cardiac-specific overexpression of FOG-2 in transgenic mice led to depressed cardiac function, activation of the fetal gene program, congestive heart failure, and early death. SERCA2 transcript and protein levels were reduced in FOG-2 transgenic hearts, and FOG-2 overexpression impaired T3-mediated SERCA2 expression in cultured cardiomyocytes. FOG-2 physically interacts with thyroid hormone receptor-alpha1 and abrogated even high levels of T3-mediated SERCA2 promoter activity. These results demonstrate that SERCA2 is an important target of FOG-2 and that increased FOG-2 expression may contribute to a decline in cardiac function in end-stage heart failure by impaired T3 signaling.
Collapse
Affiliation(s)
- Rosanne Rouf
- MCRI Center for Translational Genomics, Molecular Cardiology Research Institute, Tufts University School of Medicine, 750 Washington St, Box 8486, Boston, MA 02111, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck SG, Gutierrez MC, Tham YL, Kalidas M, Elledge R, Mohsin S, Osborne CK, Chamness GC, Allred DC, Lewis MT, Wong H, O'Connell P. Patterns of resistance and incomplete response to docetaxel by gene expression profiling in breast cancer patients. J Clin Oncol 2005; 23:1169-77. [PMID: 15718313 DOI: 10.1200/jco.2005.03.156] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Chemotherapy for operable breast cancer decreases the risk of death. Docetaxel is one of the most active agents in breast cancer, but resistance or incomplete response is frequent. PATIENTS AND METHODS Core biopsies from 24 patients were obtained before treatment with neoadjuvant docetaxel (four cycles, 100 mg/m(2) every 3 weeks), and response was assessed after chemotherapy. After 3 months of neoadjuvant chemotherapy, surgical specimens (n = 13) were obtained, and laser capture microdissection (LCM; n = 8) was performed to enrich for tumor cells. From each core, surgical, and LCM specimen, sufficient total RNA (3 to 6 microg) was extracted for cDNA array analysis using the Affymetrix HgU95-Av2 GeneChip (Affymetrix, Santa Clara, CA). RESULTS From the initial core biopsies, differential patterns of expression of 92 genes correlated with docetaxel response (P = .001). However, the molecular patterns of the residual cancers after 3 months of docetaxel treatment were strikingly similar, independent of initial sensitivity or resistance. This relative genetic homogeneity after treatment was observed in both LCM and non-LCM surgical specimens. The residual tumor after treatment in tumors that were initially sensitive indicates selection of a residual and resistant subpopulation of cells. The gene expression pattern was populated by genes involved in cell cycle arrest at G(2)M (eg, mitotic cyclins and cdc2) and survival pathways involving the mammalian target of rapamycin. CONCLUSION A specific and consistent gene expression pattern was found in residual tumors after docetaxel treatment. These profiles provide therapeutic targets that could lead to improved treatment.
Collapse
Affiliation(s)
- Jenny C Chang
- Breast Center, Department of Medicine, Baylor College of Medicine, 1 Baylor Plaza, MS 600, Houston, TX 77030, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Castro-Chavez F, Yechoor VK, Saha PK, Martinez-Botas J, Wooten EC, Sharma S, O'Connell P, Taegtmeyer H, Chan L. Coordinated upregulation of oxidative pathways and downregulation of lipid biosynthesis underlie obesity resistance in perilipin knockout mice: a microarray gene expression profile. Diabetes 2003; 52:2666-74. [PMID: 14578284 DOI: 10.2337/diabetes.52.11.2666] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Obesity is a major risk factor for diabetes and heart disease. We previously reported that the inactivation of the gene for perilipin (plin), an adipocyte lipid droplet surface protein, produced lean and obesity-resistant mice. To dissect the underlying mechanisms involved, we used oligonucleotide microarrays to analyze the gene-expression profile of white adipose tissue (WAT), liver, heart, skeletal muscle, and kidney of plin(-/-) and plin(+/+) mice. As compared with wild-type littermates, the WAT of plin(-/-) mice had 270 and 543 transcripts that were significantly up- or downregulated. There was a coordinated upregulation of genes involved in beta-oxidation, the Krebs cycle, and the electron transport chain concomitant with a downregulation of genes involved in lipid biosynthesis. There was also a significant downregulation of the stearoyl CoA desaturase-1 gene, which has been associated with obesity resistance. Thus, in response to the constitutive activation of lipolysis associated with absence of perilipin, WAT activated pathways to rid itself of the products of lipolysis and activated pathways of energy expenditure that contribute to the observed obesity resistance. The biochemical pathways involved in obesity resistance in plin(-/-) mice identified in this study may represent potential targets for the treatment of obesity.
Collapse
Affiliation(s)
- Fernando Castro-Chavez
- Section of Diabetes, Endocrinology and Metabolism, Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Wooten EC, Fults D, Duggirala R, Williams K, Kyritsis AP, Bondy ML, Levin VA, O'Connell P. A study of loss of heterozygosity at 70 loci in anaplastic astrocytoma and glioblastoma multiforme with implications for tumor evolution. Neuro Oncol 1999; 1:169-76. [PMID: 11550311 PMCID: PMC1920743 DOI: 10.1093/neuonc/1.3.169] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cancers that arise from astrocytes in the adult CNS present as either anaplastic astrocytomas (AAs) or as more aggressive glioblastomas multiforme (GBMs). GBMs either form de novo or progress from AAs. We proposed to examine the molecular genetic relationship between these CNS tumors by conducting a genome-wide allelic imbalance analysis that included 70 loci on examples of AA and GBM. We found significant loss of heterozygosity (LOH) at 13 discrete chromosomal loci in both AAs and GBMs. Loss was significant in both AAs and GBMs at 9 of these loci. AAs show the highest rates of LOH at chromosomes 1p, 4q, 6p, 9p, 11p, 11q, 13q, 14q, 15p, 17p, 17q, and 19q. GBMs showed the greatest losses at 1p, 6q, 8p, 9p, 10p, 10q, 11p, 13q, 17p, 17q, 18p, 18q, and 19q. GBMs also demonstrated significant amplification at the epidermal growth factor receptor locus (7p12). These data suggest that there are three classes of loci involved in glioma evolution. First are loci that are likely involved in early events in the evolution of both AAs and GBMs. The second class consists of AA-specific loci, typified by higher LOH frequency than observed in GBMs (4q, 6p, 17p, 17q, 19q). The third class consists of GBM-specific loci (6q, 8p, 10, 18q). Damage at these loci may either lead to de novo GBMs or permit existing AAs to progress to GBMs. Glioma-related LOH profiles may have prognostic implications that could lead to better diagnosis and treatment of brain cancer patients.
Collapse
Affiliation(s)
- E C Wooten
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78284-7750, USA
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Wooten EC, Friauf WS. An electronic reticle generator for use with CT scanners. J Comput Assist Tomogr 1980; 4:130-1. [PMID: 7354169 DOI: 10.1097/00004728-198002000-00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A simple electronic device for superimposing a dot grid of known spacing on a TV monitor used for the display of computed tomography images is described. The device connects directly to the cable leading to the TV monitor and requires no other system interconnection.
Collapse
|