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Amici DR, Alhayek S, Klein AT, Wang YZ, Wilen AP, Song W, Zhu P, Thakkar A, King MA, Steffeck AW, Alasady MJ, Peek C, Savas JN, Mendillo ML. Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life. Life Sci Alliance 2024; 7:e202302370. [PMID: 38453366 PMCID: PMC10921065 DOI: 10.26508/lsa.202302370] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 09/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The recently discovered HAPSTR1 protein broadly oversees cellular stress responses. This function requires HUWE1, a ubiquitin ligase that paradoxically marks HAPSTR1 for degradation, but much about this pathway remains unclear. Here, leveraging multiplexed proteomics, we find that HAPSTR1 enables nuclear localization of HUWE1 with implications for nuclear protein quality control. We show that HAPSTR1 is tightly regulated and identify ubiquitin ligase TRIP12 and deubiquitinase USP7 as upstream regulators titrating HAPSTR1 stability. Finally, we generate conditional Hapstr1 knockout mice, finding that Hapstr1-null mice are perinatal lethal, adult mice depleted of Hapstr1 have reduced fitness, and primary cells explanted from Hapstr1-null animals falter in culture coincident with HUWE1 mislocalization and broadly remodeled signaling. Notably, although HAPSTR1 potently suppresses p53, we find that Hapstr1 is essential for life even in mice lacking p53. Altogether, we identify novel components and functional insights into the conserved HAPSTR1-HUWE1 pathway and demonstrate its requirement for mammalian life.
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Affiliation(s)
- David R Amici
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sammy Alhayek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Austin T Klein
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yi-Zhi Wang
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anika P Wilen
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Weimin Song
- https://ror.org/000e0be47 Comprehensive Metabolic Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pei Zhu
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abhishek Thakkar
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - McKenzi A King
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Wt Steffeck
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milad J Alasady
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Clara Peek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey N Savas
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Mayer MP, Blair L, Blatch GL, Borges TJ, Chadli A, Chiosis G, de Thonel A, Dinkova-Kostova A, Ecroyd H, Edkins AL, Eguchi T, Fleshner M, Foley KP, Fragkostefanakis S, Gestwicki J, Goloubinoff P, Heritz JA, Heske CM, Hibshman JD, Joutsen J, Li W, Lynes M, Mendillo ML, Mivechi N, Mokoena F, Okusha Y, Prahlad V, Repasky E, Sannino S, Scalia F, Shalgi R, Sistonen L, Sontag E, van Oosten-Hawle P, Vihervaara A, Wickramaratne A, Wang SXY, Zininga T. Stress biology: Complexity and multifariousness in health and disease. Cell Stress Chaperones 2024; 29:143-157. [PMID: 38311120 PMCID: PMC10939078 DOI: 10.1016/j.cstres.2024.01.006] [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] [Indexed: 02/06/2024] Open
Abstract
Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. Sixty-one years after the discovery of the heat shock response by Ferruccio Ritossa, many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.
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Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Laura Blair
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Gregory L Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates; Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Thiago J Borges
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Ahmed Chadli
- Georgia Cancer Center, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA
| | - Gabriela Chiosis
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aurélie de Thonel
- CNRS, UMR 7216, 75250 Paris Cedex 13, Paris, France; Univeristy of Paris Diderot, Sorbonne Paris Cité, Paris, France; Département Hospitalo-Universitaire DHU PROTECT, Paris, France
| | - Albena Dinkova-Kostova
- Division of Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan
| | - Monika Fleshner
- Department of Integrative Physiology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | | | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Jason Gestwicki
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jennifer A Heritz
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Christine M Heske
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jenny Joutsen
- Department of Pathology, Lapland Central Hospital, Lapland Wellbeing Services County, Rovaniemi, Finland
| | - Wei Li
- Department of Dermatology and the Norris Comprehensive Cancer Center, University of Southern California Keck Medical Center, Los Angeles, CA 90033, USA
| | - Michael Lynes
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nahid Mivechi
- Molecular Chaperone Biology, Medical College of Georgia, Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Fortunate Mokoena
- Department of Biochemistry, North-West University, Mmabatho 2735, South Africa
| | - Yuka Okusha
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Elizabeth Repasky
- Department of Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sara Sannino
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Federica Scalia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, Palermo, Italy; Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Emily Sontag
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | | | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Anushka Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn Xiang Yang Wang
- Developmental Therapeutics Program, VCU Comprehensive Massey Cancer Center, VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
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3
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Li Y, Dobrolecki LE, Sallas C, Zhang X, Kerr TD, Bisht D, Wang Y, Awasthi S, Kaundal B, Wu S, Peng W, Mendillo ML, Lu Y, Jeter CR, Peng G, Liu J, Westin SN, Sood AK, Lewis MT, Das J, Yi SS, Bedford MT, McGrail DJ, Sahni N. PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition. Cell Rep Med 2023; 4:101326. [PMID: 38118413 PMCID: PMC10772459 DOI: 10.1016/j.xcrm.2023.101326] [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: 04/16/2023] [Revised: 09/07/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Multiple cancers exhibit aberrant protein arginine methylation by both type I arginine methyltransferases, predominately protein arginine methyltransferase 1 (PRMT1) and to a lesser extent PRMT4, and by type II PRMTs, predominately PRMT5. Here, we perform targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across 12 cancer cell lines. We find that inhibition of type I and II PRMTs suppresses phosphorylated and total ATR in cancer cells. Loss of ATR from PRMT inhibition results in defective DNA replication stress response activation, including from PARP inhibitors. Inhibition of type I and II PRMTs is synergistic with PARP inhibition regardless of homologous recombination function, but type I PRMT inhibition is more toxic to non-malignant cells. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves survival in both BRCA-mutant and wild-type patient-derived xenografts without toxicity. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to sensitize tumors to PARP inhibition.
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Affiliation(s)
- Yang Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Christina Sallas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Xudong Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis D Kerr
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqi Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yiling Lu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Collene R Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, and Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA; Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA.
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4
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McGrail DJ, Li Y, Smith RS, Feng B, Dai H, Hu L, Dennehey B, Awasthi S, Mendillo ML, Sood AK, Mills GB, Lin SY, Yi SS, Sahni N. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins. Cell Rep Med 2023; 4:101255. [PMID: 37909041 PMCID: PMC10694618 DOI: 10.1016/j.xcrm.2023.101255] [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: 06/29/2020] [Revised: 10/02/2022] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10%-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA-binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated genome-wide association study loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification.
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Affiliation(s)
- Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44106, USA; Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA.
| | - Yang Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roger S Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bin Feng
- GSK Oncology Experimental Medicine Unit, Waltham, MA 02451, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Briana Dennehey
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR 97201, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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5
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Klein AT, Mendillo ML. Addicted to proteostasis: How KRAS-driven cancers acquire resistance to clinical KRAS inhibitors. Cell Chem Biol 2023; 30:1334-1336. [PMID: 37977128 DOI: 10.1016/j.chembiol.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 10/11/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
The development of KRAS inhibitors was a remarkable feat, yet their efficacy is limited by inevitable resistance. In the September issue of Science, Lv et al.1 demonstrate how KRAS-driven cancers rewire signaling to restore protein homeostasis and acquire resistance to KRAS inhibitors with implications for novel combination therapeutic strategies.
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Affiliation(s)
- Austin T Klein
- Deptartment of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- Deptartment of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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6
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Amici DR, Cingoz H, Alasady MJ, Alhayek S, Phoumyvong CM, Sahni N, Yi SS, Mendillo ML. The HAPSTR2 retrogene buffers stress signaling and resilience in mammals. Nat Commun 2023; 14:152. [PMID: 36631436 PMCID: PMC9834230 DOI: 10.1038/s41467-022-35697-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
We recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian evolution, via genomic integration of a reverse transcribed HAPSTR1 transcript, and has since been preserved under purifying selection. HAPSTR2, expressed primarily in neural and germline tissues and a subset of cancers, retains established biochemical features of HAPSTR1 to achieve two functions. In normal physiology, HAPSTR2 directly interacts with HAPSTR1, markedly augmenting HAPSTR1 protein stability in a manner independent from HAPSTR1's canonical E3 ligase, HUWE1. Alternatively, in the context of HAPSTR1 loss, HAPSTR2 expression is sufficient to buffer stress signaling and resilience. Thus, we discover a mammalian retrogene which safeguards fitness.
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Affiliation(s)
- David R Amici
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Harun Cingoz
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Milad J Alasady
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Sammy Alhayek
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Claire M Phoumyvong
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
| | - Marc L Mendillo
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
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7
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Hua X, Li Y, Pentaparthi SR, McGrail DJ, Zou R, Guo L, Shrawat A, Cirillo KM, Li Q, Bhat A, Xu M, Qi D, Singh A, McGrath F, Andrews S, Aung KL, Das J, Zhou Y, Lodi A, Mills GB, Eckhardt SG, Mendillo ML, Tiziani S, Wu E, Huang JH, Sahni N, Yi SS. Landscape of MicroRNA Regulatory Network Architecture and Functional Rerouting in Cancer. Cancer Res 2023; 83:59-73. [PMID: 36265133 PMCID: PMC9811166 DOI: 10.1158/0008-5472.can-20-0371] [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] [Received: 02/03/2020] [Revised: 12/15/2020] [Accepted: 10/14/2022] [Indexed: 02/05/2023]
Abstract
Somatic mutations are a major source of cancer development, and many driver mutations have been identified in protein coding regions. However, the function of mutations located in miRNA and their target binding sites throughout the human genome remains largely unknown. Here, we built detailed cancer-specific miRNA regulatory networks across 30 cancer types to systematically analyze the effect of mutations in miRNAs and their target sites in 3' untranslated region (3' UTR), coding sequence (CDS), and 5' UTR regions. A total of 3,518,261 mutations from 9,819 samples were mapped to miRNA-gene interactions (mGI). Mutations in miRNAs showed a mutually exclusive pattern with mutations in their target genes in almost all cancer types. A linear regression method identified 148 candidate driver mutations that can significantly perturb miRNA regulatory networks. Driver mutations in 3'UTRs played their roles by altering RNA binding energy and the expression of target genes. Finally, mutated driver gene targets in 3' UTRs were significantly downregulated in cancer and functioned as tumor suppressors during cancer progression, suggesting potential miRNA candidates with significant clinical implications. A user-friendly, open-access web portal (mGI-map) was developed to facilitate further use of this data resource. Together, these results will facilitate novel noncoding biomarker identification and therapeutic drug design targeting the miRNA regulatory networks. SIGNIFICANCE A detailed miRNA-gene interaction map reveals extensive miRNA-mediated gene regulatory networks with mutation-induced perturbations across multiple cancers, serving as a resource for noncoding biomarker discovery and drug development.
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Affiliation(s)
- Xu Hua
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sairahul R. Pentaparthi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel J. McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Raymond Zou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Li Guo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aditya Shrawat
- College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kara M. Cirillo
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Qing Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Akshay Bhat
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Min Xu
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Dan Qi
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Ashok Singh
- Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Francis McGrath
- Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven Andrews
- Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kyaw Lwin Aung
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jishnu Das
- Center for Systems Immunology, Department of Immunology, and Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Gordon B. Mills
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97201, USA,Precision Oncology, Knight Cancer Institute, Portland, OR 97201, USA
| | - S. Gail Eckhardt
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA,Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, TX 78712, USA
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stefano Tiziani
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA,Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA,Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA,Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, TX 78712, USA
| | - Erxi Wu
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA,Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA,Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA,Department of Pharmaceutical Sciences, Texas A & M University Health Science Center, College of Pharmacy, College Station, TX 77843, USA,Corresponding Authors: S. Stephen Yi, The University of Texas at Austin, 1601 Trinity St, Austin, TX 78712. Phone: 512-495-5245; , Nidhi Sahni, The University of Texas MD Anderson Cancer Center, 1881 East Rd, Houston, TX 77054. Phone: 512-237-9506; , Jason H. Huang, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-2475; , Erxi Wu, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-3785;
| | - Jason H. Huang
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA,Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA,Corresponding Authors: S. Stephen Yi, The University of Texas at Austin, 1601 Trinity St, Austin, TX 78712. Phone: 512-495-5245; , Nidhi Sahni, The University of Texas MD Anderson Cancer Center, 1881 East Rd, Houston, TX 77054. Phone: 512-237-9506; , Jason H. Huang, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-2475; , Erxi Wu, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-3785;
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA,Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding Authors: S. Stephen Yi, The University of Texas at Austin, 1601 Trinity St, Austin, TX 78712. Phone: 512-495-5245; , Nidhi Sahni, The University of Texas MD Anderson Cancer Center, 1881 East Rd, Houston, TX 77054. Phone: 512-237-9506; , Jason H. Huang, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-2475; , Erxi Wu, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-3785;
| | - S. Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA,Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, TX 78712, USA,Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA,Corresponding Authors: S. Stephen Yi, The University of Texas at Austin, 1601 Trinity St, Austin, TX 78712. Phone: 512-495-5245; , Nidhi Sahni, The University of Texas MD Anderson Cancer Center, 1881 East Rd, Houston, TX 77054. Phone: 512-237-9506; , Jason H. Huang, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-2475; , Erxi Wu, Baylor Research Institute, 5701 Airport Road, Temple, TX 76502. Phone: 254-724-3785;
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8
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Ali ES, Lipońska A, O'Hara BP, Amici DR, Torno MD, Gao P, Asara JM, Yap MNF, Mendillo ML, Ben-Sahra I. The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis. Mol Cell 2022; 82:3284-3298.e7. [PMID: 35772404 PMCID: PMC9444906 DOI: 10.1016/j.molcel.2022.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 03/13/2022] [Revised: 05/15/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022]
Abstract
Bicarbonate (HCO3-) ions maintain pH homeostasis in eukaryotic cells and serve as a carbonyl donor to support cellular metabolism. However, whether the abundance of HCO3- is regulated or harnessed to promote cell growth is unknown. The mechanistic target of rapamycin complex 1 (mTORC1) adjusts cellular metabolism to support biomass production and cell growth. We find that mTORC1 stimulates the intracellular transport of HCO3- to promote nucleotide synthesis through the selective translational regulation of the sodium bicarbonate cotransporter SLC4A7. Downstream of mTORC1, SLC4A7 mRNA translation required the S6K-dependent phosphorylation of the translation factor eIF4B. In mTORC1-driven cells, loss of SLC4A7 resulted in reduced cell and tumor growth and decreased flux through de novo purine and pyrimidine synthesis in human cells and tumors without altering the intracellular pH. Thus, mTORC1 signaling, through the control of SLC4A7 expression, harnesses environmental bicarbonate to promote anabolic metabolism, cell biomass, and growth.
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Affiliation(s)
- Eunus S Ali
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael D Torno
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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9
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Amici DR, Ansel DJ, Metz KA, Smith RS, Phoumyvong CM, Gayatri S, Chamera T, Edwards SL, O’Hara BP, Srivastava S, Brockway S, Takagishi SR, Cho BK, Goo YA, Kelleher NL, Ben-Sahra I, Foltz DR, Li J, Mendillo ML. C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways. Proc Natl Acad Sci U S A 2022; 119:e2111262119. [PMID: 35776542 PMCID: PMC9271168 DOI: 10.1073/pnas.2111262119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/05/2022] [Indexed: 12/21/2022] Open
Abstract
All cells contain specialized signaling pathways that enable adaptation to specific molecular stressors. Yet, whether these pathways are centrally regulated in complex physiological stress states remains unclear. Using genome-scale fitness screening data, we quantified the stress phenotype of 739 cancer cell lines, each representing a unique combination of intrinsic tumor stresses. Integrating dependency and stress perturbation transcriptomic data, we illuminated a network of genes with vital functions spanning diverse stress contexts. Analyses for central regulators of this network nominated C16orf72/HAPSTR1, an evolutionarily ancient gene critical for the fitness of cells reliant on multiple stress response pathways. We found that HAPSTR1 plays a pleiotropic role in cellular stress signaling, functioning to titrate various specialized cell-autonomous and paracrine stress response programs. This function, while dispensable to unstressed cells and nematodes, is essential for resilience in the presence of stressors ranging from DNA damage to starvation and proteotoxicity. Mechanistically, diverse stresses induce HAPSTR1, which encodes a protein expressed as two equally abundant isoforms. Perfectly conserved residues in a domain shared between HAPSTR1 isoforms mediate oligomerization and binding to the ubiquitin ligase HUWE1. We show that HUWE1 is a required cofactor for HAPSTR1 to control stress signaling and that, in turn, HUWE1 feeds back to ubiquitinate and destabilize HAPSTR1. Altogether, we propose that HAPSTR1 is a central rheostat in a network of pathways responsible for cellular adaptability, the modulation of which may have broad utility in human disease.
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Affiliation(s)
- David R. Amici
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Daniel J. Ansel
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Kyle A. Metz
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Roger S. Smith
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Claire M. Phoumyvong
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Sitaram Gayatri
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Tomasz Chamera
- Functional and Chemical Genomics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Stacey L. Edwards
- Functional and Chemical Genomics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Brendan P. O’Hara
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Shashank Srivastava
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Sonia Brockway
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Seesha R. Takagishi
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Byoung-Kyu Cho
- Northwestern Proteomics Center of Excellence Core Facility, Northwestern University, Evanston, IL 60208
| | - Young Ah Goo
- Northwestern Proteomics Center of Excellence Core Facility, Northwestern University, Evanston, IL 60208
| | - Neil L. Kelleher
- Northwestern Proteomics Center of Excellence Core Facility, Northwestern University, Evanston, IL 60208
| | - Issam Ben-Sahra
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Daniel R. Foltz
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
| | - Jian Li
- Functional and Chemical Genomics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Marc L. Mendillo
- Simpson Querrey Center for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60610
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10
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Smith RS, Takagishi SR, Amici DR, Metz K, Gayatri S, Alasady MJ, Wu Y, Brockway S, Taiberg SL, Khalatyan N, Taipale M, Santagata S, Whitesell L, Lindquist S, Savas JN, Mendillo ML. HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state. Sci Adv 2022; 8:eabj6526. [PMID: 35294249 PMCID: PMC8926329 DOI: 10.1126/sciadv.abj6526] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/25/2022] [Indexed: 05/14/2023]
Abstract
Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no substantial role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have notably similar chromatin occupancy and regulate a common set of genes that include both HSPs and noncanonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
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Affiliation(s)
- Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA 94143, USA
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kyle Metz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sitaram Gayatri
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yaqi Wu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stephanie L. Taiberg
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Jeffrey N. Savas
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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11
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Kunder R, Velyunskiy M, Dunne SF, Cho BK, Kanojia D, Begg L, Orriols AM, Fleming-Trujillo E, Vadlamani P, Vialichka A, Bolin R, Perrino JN, Roth D, Clutter MR, Zielinski-Mozny NA, Goo YA, Cristofanilli M, Mendillo ML, Vassilopoulos A, Horiuchi D. Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer. Cell Chem Biol 2022; 29:358-372.e5. [PMID: 34525344 PMCID: PMC8901784 DOI: 10.1016/j.chembiol.2021.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest clinical outcome. The PIM family of kinases has emerged as a factor that is both overexpressed in TNBC and associated with poor outcomes. Preclinical data suggest that TNBC with an elevated MYC expression is sensitive to PIM inhibition. However, clinical observations indicate that the efficacy of PIM inhibitors as single agents may be limited, suggesting the need for combination therapies. Our screening effort identifies PIM and the 20S proteasome inhibition as the most synergistic combination. PIM inhibitors, when combined with proteasome inhibitors, induce significant antitumor effects, including abnormal accumulation of poly-ubiquitinated proteins, increased proteotoxic stress, and the inability of NRF1 to counter loss in proteasome activity. Thus, the identified combination could represent a rational combination therapy against MYC-overexpressing TNBC that is readily translatable to clinical investigations.
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Affiliation(s)
- Ratika Kunder
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Michelle Velyunskiy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Adlai E. Stevenson High School, Lincolnshire, IL 60069, USA
| | - Sara F Dunne
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Deepak Kanojia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lauren Begg
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Adrienne M Orriols
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Erica Fleming-Trujillo
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Pranathi Vadlamani
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alesia Vialichka
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jessica N Perrino
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Diane Roth
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew R Clutter
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Nicolette A Zielinski-Mozny
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Massimo Cristofanilli
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Athanassios Vassilopoulos
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Dai Horiuchi
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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12
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Amici DR, Pinal-Fernandez I, Christopher-Stine L, Mammen AL, Mendillo ML. A network of core and subtype-specific gene expression programs in myositis. Acta Neuropathol 2021; 142:887-898. [PMID: 34499219 PMCID: PMC8555743 DOI: 10.1007/s00401-021-02365-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/06/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022]
Abstract
Myositis comprises a heterogeneous group of skeletal muscle disorders which converge on chronic muscle inflammation and weakness. Our understanding of myositis pathogenesis is limited, and many myositis patients lack effective therapies. Using muscle biopsy transcriptome profiles from 119 myositis patients (spanning major clinical and serological disease subtypes) and 20 normal controls, we generated a co-expression network of 8101 dynamically regulated transcripts. This network organized the myositis transcriptome into a map of gene expression modules representing interrelated biological processes and disease signatures. Universally myositis-upregulated network modules included muscle regeneration, specific cytokine signatures, the acute phase response, and neutrophil degranulation. Universally myositis-suppressed pathways included a specific subset of myofilaments, the mitochondrial envelope, and nuclear isoforms of the anti-apoptotic humanin protein. Myositis subtype-specific modules included type 1 interferon signaling and titin (dermatomyositis), RNA processing (antisynthetase syndrome), and vasculogenesis (inclusion body myositis). Importantly, therapies exist to target influential proteins in many myositis-dysregulated modules, and nearly all modules contained understudied proteins and non-coding RNAs - many of which were extraordinarily dysregulated in myositis and may represent novel therapeutic targets. Finally, we apply our network to patient classification, finding that a deep learning algorithm trained on patient-level network "images" successfully assigned patients to clinical groups and further into molecular subclusters. Altogether, we provide a global resource to probe and contextualize differential gene expression in myositis.
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Affiliation(s)
- David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Iago Pinal-Fernandez
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Lisa Christopher-Stine
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew L Mammen
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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13
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Amici DR, Jackson JM, Truica MI, Smith RS, Abdulkadir SA, Mendillo ML. FIREWORKS: a bottom-up approach to integrative coessentiality network analysis. Life Sci Alliance 2021; 4:e202000882. [PMID: 33328249 PMCID: PMC7756899 DOI: 10.26508/lsa.202000882] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 08/17/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Genetic coessentiality analysis, a computational approach which identifies genes sharing a common effect on cell fitness across large-scale screening datasets, has emerged as a powerful tool to identify functional relationships between human genes. However, widespread implementation of coessentiality to study individual genes and pathways is limited by systematic biases in existing coessentiality approaches and accessibility barriers for investigators without computational expertise. We created FIREWORKS, a method and interactive tool for the construction and statistical analysis of coessentiality networks centered around gene(s) provided by the user. FIREWORKS incorporates a novel bias reduction approach to reduce false discoveries, enables restriction of coessentiality analyses to custom subsets of cell lines, and integrates multiomic and drug-gene interaction datasets to investigate and target contextual gene essentiality. We demonstrate the broad utility of FIREWORKS through case vignettes investigating gene function and specialization, indirect therapeutic targeting of "undruggable" proteins, and context-specific rewiring of genetic networks.
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Affiliation(s)
- David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jasen M Jackson
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mihai I Truica
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Roger S Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sarki A Abdulkadir
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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14
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Brockway S, Wang G, Jackson JM, Amici DR, Takagishi SR, Clutter MR, Bartom ET, Mendillo ML. Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq. Nat Commun 2020; 11:5722. [PMID: 33184288 PMCID: PMC7661543 DOI: 10.1038/s41467-020-19553-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/20/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
Chemical-genetic interaction profiling in model organisms has proven powerful in providing insights into compound mechanism of action and gene function. However, identifying chemical-genetic interactions in mammalian systems has been limited to low-throughput or computational methods. Here, we develop Quantitative and Multiplexed Analysis of Phenotype by Sequencing (QMAP-Seq), which leverages next-generation sequencing for pooled high-throughput chemical-genetic profiling. We apply QMAP-Seq to investigate how cellular stress response factors affect therapeutic response in cancer. Using minimal automation, we treat pools of 60 cell types—comprising 12 genetic perturbations in five cell lines—with 1440 compound-dose combinations, generating 86,400 chemical-genetic measurements. QMAP-Seq produces precise and accurate quantitative measures of acute drug response comparable to gold standard assays, but with increased throughput at lower cost. Moreover, QMAP-Seq reveals clinically actionable drug vulnerabilities and functional relationships involving these stress response factors, many of which are activated in cancer. Thus, QMAP-Seq provides a broadly accessible and scalable strategy for chemical-genetic profiling in mammalian cells. Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.
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Affiliation(s)
- Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Geng Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jasen M Jackson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Seesha R Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Matthew R Clutter
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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15
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Zhou Y, Han C, Wang E, Lorch AH, Serafin V, Cho BK, Gutierrez Diaz BT, Calvo J, Fang C, Khodadadi-Jamayran A, Tabaglio T, Marier C, Kuchmiy A, Sun L, Yacu G, Filip SK, Jin Q, Takahashi YH, Amici DR, Rendleman EJ, Rawat R, Bresolin S, Paganin M, Zhang C, Li H, Kandela I, Politanska Y, Abdala-Valencia H, Mendillo ML, Zhu P, Palhais B, Van Vlierberghe P, Taghon T, Aifantis I, Goo YA, Guccione E, Heguy A, Tsirigos A, Wee KB, Mishra RK, Pflumio F, Accordi B, Basso G, Ntziachristos P. Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia. Cancer Discov 2020; 10:1388-1409. [PMID: 32444465 DOI: 10.1158/2159-8290.cd-19-1436] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/21/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
Splicing alterations are common in diseases such as cancer, where mutations in splicing factor genes are frequently responsible for aberrant splicing. Here we present an alternative mechanism for splicing regulation in T-cell acute lymphoblastic leukemia (T-ALL) that involves posttranslational stabilization of the splicing machinery via deubiquitination. We demonstrate there are extensive exon skipping changes in disease, affecting proteasomal subunits, cell-cycle regulators, and the RNA machinery. We present that the serine/arginine-rich splicing factors (SRSF), controlling exon skipping, are critical for leukemia cell survival. The ubiquitin-specific peptidase 7 (USP7) regulates SRSF6 protein levels via active deubiquitination, and USP7 inhibition alters the exon skipping pattern and blocks T-ALL growth. The splicing inhibitor H3B-8800 affects splicing of proteasomal transcripts and proteasome activity and acts synergistically with proteasome inhibitors in inhibiting T-ALL growth. Our study provides the proof-of-principle for regulation of splicing factors via deubiquitination and suggests new therapeutic modalities in T-ALL. SIGNIFICANCE: Our study provides a new proof-of-principle for posttranslational regulation of splicing factors independently of mutations in aggressive T-cell leukemia. It further suggests a new drug combination of splicing and proteasomal inhibitors, a concept that might apply to other diseases with or without mutations affecting the splicing machinery.This article is highlighted in the In This Issue feature, p. 1241.
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Affiliation(s)
- Yalu Zhou
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Adam H Lorch
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Blanca T Gutierrez Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Julien Calvo
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Christian Marier
- Genome Technology Center, New York University School of Medicine, New York, New York
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Limin Sun
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - George Yacu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Szymon K Filip
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Radhika Rawat
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Silvia Bresolin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Maddalena Paganin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Yuliya Politanska
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hiam Abdala-Valencia
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts
| | - Bruno Palhais
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Ernesto Guccione
- Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adriana Heguy
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Genome Technology Center, New York University School of Medicine, New York, New York
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York.,Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York
| | - Keng Boon Wee
- Applied Bioinformatics Laboratories, Office of Science and Research, New York University School of Medicine, New York, New York.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Rama K Mishra
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.,Center for Molecular Innovation and Drug Discovery, Northwestern University, Chicago, Illinois
| | - Francoise Pflumio
- Team Niche and Cancer in hematopoiesis, CEA, Fontenay-aux-Roses, France.,Laboratory of Hematopoietic Stem Cells and Leukemia/Service Stem Cells and Radiation/iRCM/JACOB/DRF, CEA, Fontenay-aux-Roses, France
| | - Benedetta Accordi
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois. .,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
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16
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Abstract
Heat Shock Factor 1 (HSF1), the master transcriptional regulator of the heat shock response (HSR), was first cloned more than 30 years ago. Most early research interrogating the role that HSF1 plays in biology focused on its cytoprotective functions, as a factor that promotes the survival of organisms by protecting against the proteotoxicity associated with neurodegeneration and other pathological conditions. However, recent studies have revealed a deleterious role of HSF1, as a factor that is co-opted by cancer cells to promote their own survival to the detriment of the organism. In cancer, HSF1 operates in a multifaceted manner to promote oncogenic transformation, proliferation, metastatic dissemination, and anti-cancer drug resistance. Here we review our current understanding of HSF1 activation and function in malignant progression and discuss the potential for HSF1 inhibition as a novel anticancer strategy. Collectively, this ever-growing body of work points to a prominent role of HSF1 in nearly every aspect of carcinogenesis.
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Affiliation(s)
- Milad J Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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17
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Scherz-Shouval R, Mendillo ML, Gaglia G, Ben-Aharon I, Beck AH, Whitesell L, Lindquist S. Abstract PR07: Mechanisms of stromal reprogramming mediated by heat shock factor 1. Cancer Res 2016. [DOI: 10.1158/1538-7445.tme16-pr07] [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
For tumors to form, progress and metastasize, they must recruit and reprogram normal cells in their microenvironment into a pro-tumorigenic stroma. Yet little is known about the pathways leading to stromal reprogramming. We hypothesized that such reprogramming would not be mediated by classic oncogenes, since the stroma is relatively genetically stable. Instead we propose that cancer cells hijack normal cytoprotective stress responses, and subvert them to enable stromal reprogramming. We found that Heat-shock factor 1 (HSF1), master regulator of the heat-shock response, plays a crucial role in this process. Across a broad range of human cancers, HSF1 is activated in cancer-associated fibroblasts (CAFs). In early stage breast and lung cancer, high stromal HSF1 activation is strongly associated with poor patient outcome. In fibroblasts co-cultured with cancer cells, HSF1 drives a transcriptional program that supports cancer phenotypes. This program is profoundly different from the transcriptional program it drives in cancer cells or in heat-shocked cells. Here we characterize mechanisms leading to activation of this unique stromal program and describe the contribution of cancer cells to this process. We then explore the stromal HSF1 program in patients. We apply computational and experimental approaches to define independent cancer and stromal HSF1 signatures and highlight the prognostic value of these signatures in human breast cancer. Billions of years of evolution through changing environments led organisms to develop an arsenal of cytoprotective pathways to promote their survival under stressful conditions. Our work provides insights into the ways by which tumors co-opt these normal biological networks to support their survival in the stressful tumor microenvironment.
This abstract is also presented as Poster B40.
Citation Format: Ruth Scherz-Shouval, Marc L. Mendillo, Giorgio Gaglia, Irit Ben-Aharon, Andrew H. Beck, Luke Whitesell, Susan Lindquist. Mechanisms of stromal reprogramming mediated by heat shock factor 1. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr PR07.
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Affiliation(s)
| | - Marc L. Mendillo
- 2MIT Whitehead Institute for Biomedical Research, Cambridge, MA,
| | - Giorgio Gaglia
- 2MIT Whitehead Institute for Biomedical Research, Cambridge, MA,
| | | | | | - Luke Whitesell
- 2MIT Whitehead Institute for Biomedical Research, Cambridge, MA,
| | - Susan Lindquist
- 2MIT Whitehead Institute for Biomedical Research, Cambridge, MA,
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18
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Tsvetkov P, Mendillo ML, Zhao J, Carette JE, Merrill PH, Cikes D, Varadarajan M, van Diemen FR, Penninger JM, Goldberg AL, Brummelkamp TR, Santagata S, Lindquist S. Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome. eLife 2015; 4. [PMID: 26327695 PMCID: PMC4551903 DOI: 10.7554/elife.08467] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022] Open
Abstract
Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Marc L Mendillo
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jinghui Zhao
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Parker H Merrill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Ferdy R van Diemen
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, United States
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19
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Petrocca F, Altschuler G, Tan SM, Mendillo ML, Yan H, Jerry DJ, Kung AL, Hide W, Ince TA, Lieberman J. Abstract SY43-03: Screening for triple negative breast cancer vulnerabilities. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-sy43-03] [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
There is no targeted therapy for triple negative breast cancers (TNBC), which have the worst prognosis of human breast cancers. TNBCs are prone to relapse and metastasize after cytotoxic drug treatment. This group of cancers, defined by low or absent expression of estrogen, progesterone and Her2 receptors, are heterogeneous in genetic, epigenetic and phenotypic features, making it difficult to identify specific drug targets suitable for this group of cancers as a whole. About half or more of TNBCs have an epithelial phenotype (classified based on gene expression profiling as basal-like or basal-A) and a large minority of the remaining tumors are mesenchymal (classified as basal-B). To identify selective genetic dependencies of the basal-like subtype of TNBC that are not required for survival of normal breast epithelial cells, which might be good targets for targeted drug therapy, we first performed a genome-wide siRNA lethality screen that compared two human breast epithelial TNBC cell lines transformed with the same genes in different media - basal-like BPLER and myoepithelial HMLER. BPLER are highly malignant and enriched for tumor-initiating cells, forming tumors in nude mice after injection of just 50 cells, while the more differentiated HMLER cell line only forms tumors when more than 50,000 cells are injected. The screen identified 154 genes on which BPLER, but not HMLER, depended. Expression of the 154 BPLER dependency genes correlated with poor prognosis in breast, but not lung or colon, cancer. Of note, no oncogenic kinases, which are often chosen as cancer drug targets, were identified in the screen. Proteasome genes were overrepresented hits. Basal-like TNBC lines as a group were selectively sensitive to proteasome inhibitor drugs relative to normal epithelial, luminal breast cancer and mesenchymal TNBC lines. Proteasome inhibition reduced growth of established basal-like TNBC tumors in mice and blocked tumor-initiation and metastasis. Tumor-initiating cells (T-ICs) within basal-like cancers did not survive proteasome inhibition. Developing ways to target T-ICs is a priority of cancer drug development. Proteasome addiction in basal-like TNBCs was mediated by NOXA and linked to MCL-1 dependence, which was also a common dependency gene of basal-like TNBCs. Because of the heterogeneity of TNBCs, we next assessed how many of the BPLER dependencies were shared with other breast cancers. A targeted screen was performed comparing the viability of 10 breast cancer cell lines (3 luminal A, 5 basal-A and 2 basal-B TNBCs) and telomerase-immortalized normal breast epithelial cells after knockdown of the 154 BPLER dependency genes. This screen confirmed the selective dependence of basal-A TNBCs on the proteasome and MCL-1. This screen identified 17 additional hits that were shared dependencies in at least 4 of 5 basal-like TNBC cell lines. A novel hit, required for survival of 4 of 5 basal-A TNBC cell lines, but not normal breast epithelial cells, was the spindle checkpoint regulator NDC80.
This work was supported by Department of Defense grants to FP and JL and by a grant from the Harvard Stem Cell Institute. The authors have no financial conflicts of interest to disclose.
Citation Format: Fabio Petrocca, Gabriel Altschuler, Shen Mynn Tan, Marc L. Mendillo, Haoheng Yan, D. Joseph Jerry, Andrew L. Kung, Winston Hide, Tan A. Ince, Judy Lieberman. Screening for triple negative breast cancer vulnerabilities. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY43-03. doi:10.1158/1538-7445.AM2014-SY43-03
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Affiliation(s)
| | | | | | | | | | | | - Andrew L. Kung
- 5Dana-Farber Cancer Institute and Children's Hospital, Boston, MA
| | | | - Tan A. Ince
- 6University of Miami Miller School of Medicine, Miami, FL
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20
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Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J. The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection. PLoS Pathog 2014; 10:e1003904. [PMID: 24516381 PMCID: PMC3916389 DOI: 10.1371/journal.ppat.1003904] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 06/14/2013] [Accepted: 12/12/2013] [Indexed: 12/17/2022] Open
Abstract
The genus Orthopoxviridae contains a diverse group of human pathogens including monkeypox, smallpox and vaccinia. These viruses are presumed to be less dependent on host functions than other DNA viruses because they have large genomes and replicate in the cytoplasm, but a detailed understanding of the host factors required by orthopoxviruses is lacking. To address this topic, we performed an unbiased, genome-wide pooled RNAi screen targeting over 17,000 human genes to identify the host factors that support orthopoxvirus infection. We used secondary and tertiary assays to validate our screen results. One of the strongest hits was heat shock factor 1 (HSF1), the ancient master regulator of the cytoprotective heat-shock response. In investigating the behavior of HSF1 during vaccinia infection, we found that HSF1 was phosphorylated, translocated to the nucleus, and increased transcription of HSF1 target genes. Activation of HSF1 was supportive for virus replication, as RNAi knockdown and HSF1 small molecule inhibition prevented orthopoxvirus infection. Consistent with its role as a transcriptional activator, inhibition of several HSF1 targets also blocked vaccinia virus replication. These data show that orthopoxviruses co-opt host transcriptional responses for their own benefit, thereby effectively extending their functional genome to include genes residing within the host DNA. The dependence on HSF1 and its chaperone network offers multiple opportunities for antiviral drug development.
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Affiliation(s)
- Claire Marie Filone
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
- * E-mail:
| | - Ignacio S. Caballero
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ken Dower
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Marc L. Mendillo
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Glenn S. Cowley
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Daniel K. Rozelle
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Judy Yen
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kathleen H. Rubins
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nir Hacohen
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - David E. Root
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Lisa E. Hensley
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
| | - John Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
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21
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Smith CE, Mendillo ML, Bowen N, Hombauer H, Campbell CS, Desai A, Putnam CD, Kolodner RD. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway. PLoS Genet 2013; 9:e1003869. [PMID: 24204293 PMCID: PMC3814310 DOI: 10.1371/journal.pgen.1003869] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [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: 07/01/2013] [Accepted: 08/25/2013] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway. Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. In addition to these genes, various DNA replication factors and the excision factor EXO1 function in the repair of damaged DNA by the MMR pathway. Although EXO1 is considered to be the major repair nuclease functioning in mismatch repair, the relatively low mutation rates caused by an exo1 deletion suggest otherwise. Here we used genetics, microscopy and protein biochemistry to analyze the model organism Saccharomyces cerevisiae to further characterize a poorly understood mismatch repair pathway that functions in the absence of EXO1 that is highly dependent on the Mlh1-Pms1 complex. Surprisingly, we found that the highly conserved metal binding site that is critical for the endonuclease activity of the Mlh1-Pms1 heterodimer is required for MMR in the absence of Exo1 to a much greater extent than in the presence of Exo1. Thus, this work establishes that there are at least two different polynucleotide excision pathways that function in MMR.
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Affiliation(s)
- Catherine E Smith
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, California, United States of America
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22
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Petrocca F, Altschuler G, Tan SM, Mendillo ML, Yan H, Jerry DJ, Kung AL, Hide W, Ince TA, Lieberman J. A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. Cancer Cell 2013; 24:182-96. [PMID: 23948298 PMCID: PMC3773329 DOI: 10.1016/j.ccr.2013.07.008] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [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] [Received: 03/01/2013] [Revised: 06/12/2013] [Accepted: 07/15/2013] [Indexed: 01/16/2023]
Abstract
Basal-like triple-negative breast cancers (TNBCs) have poor prognosis. To identify basal-like TNBC dependencies, a genome-wide siRNA lethality screen compared two human breast epithelial cell lines transformed with the same genes: basal-like BPLER and myoepithelial HMLER. Expression of the screen's 154 BPLER dependency genes correlated with poor prognosis in breast, but not lung or colon, cancer. Proteasome genes were overrepresented hits. Basal-like TNBC lines were selectively sensitive to proteasome inhibitor drugs relative to normal epithelial, luminal, and mesenchymal TNBC lines. Proteasome inhibition reduced growth of established basal-like TNBC tumors in mice and blocked tumor-initiating cell function and macrometastasis. Proteasome addiction in basal-like TNBCs was mediated by NOXA and linked to MCL-1 dependence.
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Affiliation(s)
- Fabio Petrocca
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: or
| | - Gabriel Altschuler
- Department of Biostatistics, Harvard School of Public Health, Boston MA 02115, USA
| | - Shen Mynn Tan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Marc L. Mendillo
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Haoheng Yan
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - D. Joseph Jerry
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Andrew L. Kung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital, Boston, MA 02115, USA
| | - Winston Hide
- Department of Biostatistics, Harvard School of Public Health, Boston MA 02115, USA
| | - Tan A. Ince
- Department of Pathology, Braman Family Breast Cancer Institute and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: or
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23
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Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA, Whitesell L, Lindquist S. Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science 2013; 341:1238303. [PMID: 23869022 PMCID: PMC3959726 DOI: 10.1126/science.1238303] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [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: 12/11/2022]
Abstract
The ribosome is centrally situated to sense metabolic states, but whether its activity, in turn, coherently rewires transcriptional responses is unknown. Here, through integrated chemical-genetic analyses, we found that a dominant transcriptional effect of blocking protein translation in cancer cells was inactivation of heat shock factor 1 (HSF1), a multifaceted transcriptional regulator of the heat-shock response and many other cellular processes essential for anabolic metabolism, cellular proliferation, and tumorigenesis. These analyses linked translational flux to the regulation of HSF1 transcriptional activity and to the modulation of energy metabolism. Targeting this link with translation initiation inhibitors such as rocaglates deprived cancer cells of their energy and chaperone armamentarium and selectively impaired the proliferation of both malignant and premalignant cells with early-stage oncogenic lesions.
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Affiliation(s)
- Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Marc L. Mendillo
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yun-chi Tang
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Casey C. Perley
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stéphane P. Roche
- Department of Chemistry, Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, Boston MA, USA
| | - Bang Wong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajiv Narayan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hyoungtae Kwon
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martina Koeva
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angelika Amon
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Todd R. Golub
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - John A. Porco
- Department of Chemistry, Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, Boston MA, USA
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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24
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Mendillo ML, Santagata S, Koeva M, Bell GW, Hu R, Tamimi RM, Fraenkel E, Ince TA, Whitesell L, Lindquist S. HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. Cell 2012; 150:549-62. [PMID: 22863008 PMCID: PMC3438889 DOI: 10.1016/j.cell.2012.06.031] [Citation(s) in RCA: 512] [Impact Index Per Article: 42.7] [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: 10/13/2011] [Revised: 04/10/2012] [Accepted: 06/04/2012] [Indexed: 01/25/2023]
Abstract
Heat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival, and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their nontransformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, many are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death. Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications.
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Affiliation(s)
- Marc L. Mendillo
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sandro Santagata
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Martina Koeva
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - George W. Bell
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rong Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rulla M. Tamimi
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Tan A. Ince
- Department of Pathology, Braman Family Breast Cancer Institute and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Luke Whitesell
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Susan Lindquist
- The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, MIT Cambridge, MA 02139, USA
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25
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Santagata S, Hu R, Lin NU, Mendillo ML, Collins LC, Hankinson SE, Schnitt SJ, Whitesell L, Lindquist S, Tamimi RM, Ince TA. P5-01-13: High Levels of Nuclear Heat Shock Factor 1 (HSF1) Are Associated with Poor Prognosis in Breast Cancer: Results from the Nurses' Health Study. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p5-01-13] [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
Purpose: Heat shock factor 1 (HSF1) is the master transcriptional regulator of the cellular response to heat and a wide variety of other stressors. We previously reported that HSF1 promotes the survival and proliferation of malignant cells. At this time, however, the clinical and prognostic significance of HSF1 in cancer is unknown.
Patients and methods: Breast cancer samples from 1,841 participants in the Nurses’ Health Study (NHS) were scored for levels of nuclear HSF1. Associations of HSF1 status with clinical parameters and survival outcomes were investigated by Kaplan-Meier analysis and Cox proportional hazard models. The associations were further delineated by Kaplan-Meier analysis using publicly available mRNA expression data.
Results: Nuclear HSF1 levels were elevated in ∼80% of in situ and invasive breast carcinomas. In invasive carcinomas, HSF1 expression was associated with high histologic grade, larger tumor size, and nodal involvement at diagnosis (P<0.0001). Overall, in multivariate analysis, high-HSF1 levels were associated with increased breast cancer-specific mortality (HR, 1.62; 95% CI, 1.21−2.17). This association was seen in the ER-positive population (HR, 2.10; 95% CI, 1.25−2.47), even in early-stage lymph node negative cases (HR, 1.98; 95% CI, 1.17−3.33). In public expression profiling data, high-HSF1 mRNA levels were also associated with an increase in ER-positive breast cancer-specific mortality.
Conclusions: Increased HSF1 is associated with reduced survival in breast cancer. The findings indicate that HSF1 should be evaluated prospectively as an independent prognostic indicator in ER-positive breast cancer and that HSF1 may provide a useful therapeutic target.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-01-13.
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Affiliation(s)
- S Santagata
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - R Hu
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - NU Lin
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - ML Mendillo
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - LC Collins
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - SE Hankinson
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - SJ Schnitt
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - L Whitesell
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - S Lindquist
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - RM Tamimi
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
| | - TA Ince
- 1Brigham and Women's Hospital, Boston, MA; Harvard School of Public Health, Boston, MA; Dana Farber Cancer Center, Boston, MA; Whitehead Institute for Biomedical Sciences, Cambridge, MA; Beth Israel Deaconess Medical Center, Boston, MA; University of Miami Miller School of Medicine, Miami, FL
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26
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Mendillo ML, Santagata S, Koeva M, Fraenkel E, Ince TA, Whitesell L, Lindquist S. P3-01-09: Oncogenic Activation of HSF1 Enables the Malignant Progression of Breast Carcinoma. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p3-01-09] [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
HSF1 is best known for its role as the master transcriptional regulator of the evolutionarily conserved heat-shock response. In mice, Hsf1 knock-outs dramatically reduce susceptibility to malignant transformation and tumor formation, and markedly increased survival in cancers driven by both oncogenic and tumor suppressor mutations. Likewise, RNAi-mediated knockdown markedly reduces the growth and survival of human cell lines established from cancers driven by a diversity of genetic lesions. The transcriptional network that HSF1 coordinates during heat-shock is known, but is unknown in malignancy. We compare HSF1 function in isogenic breast cancer cells of high and low malignant potential. HSF1 orchestrates a far-reaching transcriptional program that is dependent on transformation and the degree of malignancy. The oncogenic HSF1 program differs markedly from the classical heat-shock response. It is enriched for genes involved in a myriad of cellular processes known to be important in malignancy, including transcription, translation, glucose metabolism and cellular adhesion. It includes only a particular subset of heat-shock protein genes, and many of these are regulated in a manner that differs from their regulation by heat-shock. We also find that HSF1 is overexpressed and activated in a large subset of all conventionally defined classes of breast cancer. Moreover, tumors with high expression of the oncogenic HSF1 transcriptional network are strongly associated with poor outcome as monitored by metastasis and death. Our findings suggest that the oncogenic HSF1 activation program is rooted in fundamental aspects of tumor biology and will prove a powerful new tool in the clinical management of patients with breast cancer and, likely, other malignancies as well.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-01-09.
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Affiliation(s)
- ML Mendillo
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - S Santagata
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - M Koeva
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - E Fraenkel
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - TA Ince
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - L Whitesell
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
| | - S Lindquist
- 1Whitehead Institute for Biomedical Research, Cambridge, MA; Brigham and Women's Hospital, Boston, Boston, MA; Massachusetts Institute of Technology, Cambridge, MA; University of Miami Miller School of Medicine, Miami, FL; Howard Hughes Medical Institute, Cambridge, MA
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27
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Mendillo ML, Putnam CD, Mo AO, Jamison JW, Li S, Woods VL, Kolodner RD. Probing DNA- and ATP-mediated conformational changes in the MutS family of mispair recognition proteins using deuterium exchange mass spectrometry. J Biol Chem 2010; 285:13170-82. [PMID: 20181951 PMCID: PMC2857143 DOI: 10.1074/jbc.m110.108894] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [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: 01/28/2010] [Revised: 02/23/2010] [Indexed: 11/06/2022] Open
Abstract
We have performed deuterium exchange mass spectrometry (DXMS) to probe the conformational changes that the bacterial MutS homodimer and the homologous eukaryotic heterodimer Msh2-Msh6 undergo when binding to ATP or DNA. The DXMS data support the view that high affinity binding to mispair-containing DNA and low affinity binding to fully base-paired DNA both involve forming rings by MutS protein family dimers around the DNA; however, mispair binding protects additional regions from deuterium exchange. DXMS also reveals two distinct conformations upon binding one or two ATP molecules and that binding of two ATP molecules propagates conformational changes to other regions of the protein complexes. The regions showing major changes in deuterium exchange upon ATP binding tend to occur in regions distinct from those involved in DNA binding, suggesting that although communication occurs between DNA and nucleotide binding, sliding clamps formed by binding both ATP and mispairs could result from the simultaneous action of two independent conformational changes.
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Affiliation(s)
- Marc L. Mendillo
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
| | - Christopher D. Putnam
- From the Departments of
Medicine and
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
| | | | | | - Sheng Li
- From the Departments of
Medicine and
| | | | - Richard D. Kolodner
- From the Departments of
Medicine and
- Cellular and Molecular Medicine
- Cancer Center, and
- Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, La Jolla, California 92093-0669
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28
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Affiliation(s)
- Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Medicine, University of California at San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA.
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29
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Mendillo ML, Putnam CD, Kolodner RD. Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo. J Biol Chem 2007; 282:16345-54. [PMID: 17426027 DOI: 10.1074/jbc.m700858200] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [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: 11/06/2022] Open
Abstract
The Escherichia coli mispair-binding protein MutS forms dimers and tetramers in vitro, although the functional form in vivo is under debate. Here we demonstrate that the MutS tetramer is extended in solution using small angle x-ray scattering and the crystal structure of the C-terminal 34 amino acids of MutS containing the tetramer-forming domain fused to maltose-binding protein (MBP). Wild-type C-terminal MBP fusions formed tetramers and could bind MutS and MutS-MutL-DNA complexes. In contrast, D835R and R840E mutations predicted to disrupt tetrameric interactions only allowed dimerization of MBP. A chromosomal MutS truncation mutation eliminating the dimerization/tetramerization domain eliminated mismatch repair, whereas the tetramer-disrupting MutS D835R and R840E mutations only modestly affected MutS function. These results demonstrate that dimerization but not tetramerization of the MutS C terminus is essential for mismatch repair.
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MESH Headings
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Amino Acid Substitution
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/genetics
- Chromosomes, Bacterial/metabolism
- Crystallography, X-Ray
- DNA Repair
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Dimerization
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- MutL Proteins
- MutS DNA Mismatch-Binding Protein/chemistry
- MutS DNA Mismatch-Binding Protein/genetics
- MutS DNA Mismatch-Binding Protein/metabolism
- Mutation, Missense
- Protein Binding/genetics
- Protein Structure, Quaternary
- Protein Structure, Tertiary
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Affiliation(s)
- Marc L Mendillo
- Ludwig Institute for Cancer Research, Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0669, USA
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30
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Mazur DJ, Mendillo ML, Kolodner RD. Inhibition of Msh6 ATPase activity by mispaired DNA induces a Msh2(ATP)-Msh6(ATP) state capable of hydrolysis-independent movement along DNA. Mol Cell 2006; 22:39-49. [PMID: 16600868 DOI: 10.1016/j.molcel.2006.02.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [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] [Received: 12/02/2005] [Revised: 01/25/2006] [Accepted: 02/08/2006] [Indexed: 10/24/2022]
Abstract
The Msh2-Msh6 heterodimer plays a key role in the repair of mispaired bases in DNA. Critical to its role in mismatch repair is the ATPase activity that resides within each subunit. Here we show that both subunits can simultaneously bind ATP and identify the Msh6 subunit as containing the high-affinity ATP binding site and Msh2 as containing a high-affinity ADP binding site. Stable binding of ATP to Msh6 causes decreased affinity of Msh2 for ADP, and binding to mispaired DNA stabilized the binding of ATP to Msh6. Our results support a model in which mispair binding encourages a dual-occupancy state with ATP bound to Msh6 and Msh2; this state supports hydrolysis-independent sliding along DNA.
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Affiliation(s)
- Dan J Mazur
- Ludwig Institute for Cancer Research, CMME 3058, 9500 Gilman Drive, La Jolla, California 92093, USA
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Mendillo ML, Hess MT, Mazur DJ, Kolodner RD. Biochemical basis for dominant mutations in the
Saccaromyces cerevisiae Msh6
gene. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.lb56-b] [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)
- Marc L Mendillo
- Ludwig Institute for Cancer ResearchUniversity of California, San Diego9500 Gilman Drive, CMME, Room 3019La JollaCa92093
| | - Martin T Hess
- Ludwig Institute for Cancer ResearchUniversity of California, San Diego9500 Gilman Drive, CMME, Room 3019La JollaCa92093
| | - Dan J Mazur
- Ludwig Institute for Cancer ResearchUniversity of California, San Diego9500 Gilman Drive, CMME, Room 3019La JollaCa92093
| | - Richard D Kolodner
- Ludwig Institute for Cancer ResearchUniversity of California, San Diego9500 Gilman Drive, CMME, Room 3019La JollaCa92093
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32
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Abstract
Here, the ATP-binding, ATP hydrolysis, mispair-binding, sliding clamp formation, and Mlh1-Pms1 complex interaction properties of dominant mutant Msh2-Msh6 complexes have been characterized. The results demonstrate two mechanisms for dominance. In one, seen with the Msh6-S1036P and Msh6-G1067D mutant complexes, the mutant complex binds mispaired bases, is defective for ATP-induced sliding clamp formation and assembly of ternary complexes with Mlh1-Pms1, and occludes mispaired bases from other mismatch repair pathways. In the second, seen with the Msh6-G1142D complex, the mutant complex binds mispaired bases and is defective for ATP-induced sliding clamp formation but assembles ternary complexes with Mlh1-Pms1 that either occlude the mispaired base or prevent Mlh1-Pms1 from acting in alternate mismatch repair pathways.
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Affiliation(s)
- Martin T Hess
- Department of Medicine, Cancer Center, Ludwig Institute for Cancer Research, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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33
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Mendillo ML, Mazur DJ, Kolodner RD. Analysis of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 complexes with DNA using a reversible DNA end-blocking system. J Biol Chem 2005; 280:22245-57. [PMID: 15811858 DOI: 10.1074/jbc.m407545200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Lac repressor-operator interaction was used as a reversible DNA end-blocking system in conjunction with an IAsys biosensor instrument (Thermo Affinity Sensors), which detects total internal reflectance and allows monitoring of binding and dissociation in real time, in order to develop a system for studying the ability of mismatch repair proteins to move along the DNA. The MSH2-MSH6 complex bound to a mispaired base was found to be converted by ATP binding to a form that showed rapid sliding along the DNA and dissociation via the DNA ends and also showed slow, direct dissociation from the DNA. In contrast, the MSH2-MSH6 complex bound to a base pair containing DNA only showed direct dissociation from the DNA. The MLH1-PMS1 complex formed both mispair-dependent and mispair-independent ternary complexes with the MSH2-MSH6 complex on DNA. The mispair-independent ternary complexes were formed most efficiently on DNA molecules with free ends under conditions where ATP hydrolysis did not occur, and only exhibited direct dissociation from the DNA. The mispair-dependent ternary complexes were formed in the highest yield on DNA molecules with blocked ends, required ATP and magnesium for formation, and showed both dissociation via the DNA ends and direct dissociation from the DNA.
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Affiliation(s)
- Marc L Mendillo
- Ludwig Institute for Cancer Research, Department of Medicine and Cancer Center, School of Medicine, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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