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Zhakula-Kostadinova N, Taylor AM. Patterns of Aneuploidy and Signaling Consequences in Cancer. Cancer Res 2024; 84:2575-2587. [PMID: 38924459 PMCID: PMC11325152 DOI: 10.1158/0008-5472.can-24-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Aneuploidy, or a change in the number of whole chromosomes or chromosome arms, is a near-universal feature of cancer. Chromosomes affected by aneuploidy are not random, with observed cancer-specific and tissue-specific patterns. Recent advances in genome engineering methods have allowed the creation of models with targeted aneuploidy events. These models can be used to uncover the downstream effects of individual aneuploidies on cancer phenotypes including proliferation, apoptosis, metabolism, and immune signaling. Here, we review the current state of research into the patterns of aneuploidy in cancer and their impact on signaling pathways and biological processes.
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Affiliation(s)
- Nadja Zhakula-Kostadinova
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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2
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Li J, Huang K, McBride F, Sadagopan A, Gallant DS, Thakur M, Khanna P, Li B, Ge M, Weiss CN, Achom M, Xu Q, Huang K, Ryback BA, Gui M, Bar-Peled L, Viswanathan SR. TFE3 fusions direct an oncogenic transcriptional program that drives OXPHOS and unveils vulnerabilities in translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607311. [PMID: 39149323 PMCID: PMC11326252 DOI: 10.1101/2024.08.09.607311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic metabolism of most other renal cancers. This TFE3 fusion-driven OXPHOS program, together with heightened glutathione levels found in renal cancers, renders tRCCs sensitive to reductive stress - a metabolic stress state induced by an imbalance of reducing equivalents. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to this metabolic state, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1 compromises tRCC cell growth by stabilizing HIF-1a and promoting metabolic reprogramming away from OXPHOS, thus representing a vulnerability to OXPHOS-dependent tRCC cells. Our study defines a distinctive tRCC-essential metabolic program driven by TFE3 fusions and nominates EGLN1 inhibition as a therapeutic strategy to counteract fusion-induced metabolic rewiring.
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Affiliation(s)
- Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Kaimeng Huang
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fiona McBride
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel. S Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Meha Thakur
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prateek Khanna
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Bingchen Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Cary N. Weiss
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Kun Huang
- Molecular Imaging Core and Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Birgitta A. Ryback
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Miao Gui
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, Zhejiang, China; Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Liron Bar-Peled
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
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3
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Krieg S, Rohde T, Rausch T, Butthof L, Wendler-Link L, Eckert C, Breuhahn K, Galy B, Korbel J, Billmann M, Breinig M, Tschaharganeh DF. Mitoferrin2 is a synthetic lethal target for chromosome 8p deleted cancers. Genome Med 2024; 16:83. [PMID: 38886830 PMCID: PMC11181659 DOI: 10.1186/s13073-024-01357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Somatic copy number alterations are a hallmark of cancer that offer unique opportunities for therapeutic exploitation. Here, we focused on the identification of specific vulnerabilities for tumors harboring chromosome 8p deletions. METHODS We developed and applied an integrative analysis of The Cancer Genome Atlas (TCGA), the Cancer Dependency Map (DepMap), and the Cancer Cell Line Encyclopedia to identify chromosome 8p-specific vulnerabilities. We employ orthogonal gene targeting strategies, both in vitro and in vivo, including short hairpin RNA-mediated gene knockdown and CRISPR/Cas9-mediated gene knockout to validate vulnerabilities. RESULTS We identified SLC25A28 (also known as MFRN2), as a specific vulnerability for tumors harboring chromosome 8p deletions. We demonstrate that vulnerability towards MFRN2 loss is dictated by the expression of its paralog, SLC25A37 (also known as MFRN1), which resides on chromosome 8p. In line with their function as mitochondrial iron transporters, MFRN1/2 paralog protein deficiency profoundly impaired mitochondrial respiration, induced global depletion of iron-sulfur cluster proteins, and resulted in DNA-damage and cell death. MFRN2 depletion in MFRN1-deficient tumors led to impaired growth and even tumor eradication in preclinical mouse xenograft experiments, highlighting its therapeutic potential. CONCLUSIONS Our data reveal MFRN2 as a therapeutic target of chromosome 8p deleted cancers and nominate MFNR1 as the complimentary biomarker for MFRN2-directed therapies.
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Affiliation(s)
- Stephan Krieg
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Rohde
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Luise Butthof
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lena Wendler-Link
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Eckert
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno Galy
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Maximilian Billmann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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Yu S, Chen C, Chen M, Liang J, Jiang K, Lou B, Lu J, Zhu X, Zhou D. MAGOH promotes gastric cancer progression via hnRNPA1 expression inhibition-mediated RONΔ160/PI3K/AKT signaling pathway activation. J Exp Clin Cancer Res 2024; 43:32. [PMID: 38268030 PMCID: PMC10809607 DOI: 10.1186/s13046-024-02946-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is associated with high mortality and heterogeneity and poses a great threat to humans. Gene therapies for the receptor tyrosine kinase RON and its spliceosomes are attracting increasing amounts of attention due to their unique characteristics. However, little is known about the mechanism involved in the formation of the RON mRNA alternative spliceosome RONΔ160. METHODS Fourteen human GC tissue samples and six normal gastric tissue samples were subjected to label-free relative quantitative proteomics analysis, and MAGOH was identified as a candidate protein for subsequent studies. The expression of MAGOH in clinical specimens was verified by quantitative real-time PCR and western blotting. We then determined the biological function of MAGOH in GC through in vitro and in vivo experiments. RNA pulldown, RNA sequencing and RNA immunoprecipitation (RIP) were subsequently conducted to uncover the underlying mechanism by which MAGOH regulated the formation of RONΔ160. RESULTS Proteomic analysis revealed that MAGOH, which is located at key nodes and participates in RNA processing and mRNA splicing, was upregulated in GC tissue and GC cell lines and was associated with poor prognosis. Functional analysis showed that MAGOH promoted the proliferation, migration and invasion of GC cells in vitro and in vivo. Mechanistically, MAGOH inhibited the expression of hnRNPA1 and reduced the binding of hnRNPA1 to RON mRNA, thereby promoting the formation of RONΔ160 to activate the PI3K/AKT signaling pathway and consequently facilitating GC progression. CONCLUSIONS Our study revealed that MAGOH could promote the formation of RONΔ160 and activate the PI3K/AKT signaling pathway through the inhibition of hnRNPA1 expression. We elucidate a novel mechanism and potential therapeutic targets for the growth and metastasis of GC based on the MAGOH-RONΔ160 axis, and these findings have important guiding significance and clinical value for the future development of effective therapeutic strategies for GC.
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Affiliation(s)
- Shanshan Yu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Cheng Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ming Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinxiao Liang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kecheng Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Lou
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohua Zhu
- Department of Oncology, Shaoxing People's Hospital, Shaoxing, China
| | - Donghui Zhou
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Wuchty S, White AK, Olthof AM, Drake K, Hume AJ, Olejnik J, Aguiar-Pulido V, Mühlberger E, Kanadia RN. Minor intron-containing genes as an ancient backbone for viral infection? PNAS NEXUS 2024; 3:pgad479. [PMID: 38274120 PMCID: PMC10810330 DOI: 10.1093/pnasnexus/pgad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.
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Affiliation(s)
- Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Institute of Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33134, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, MA 02118, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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6
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Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
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Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
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7
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Xiao F, Long Z, Guo Y, Zhu H, Zhang Z, Xiao Y, Hu G, Yang Q, Huang K, Guo H. MAGOH is correlated with poor prognosis and is essential for cell proliferation in lower-grade glioma. Aging (Albany NY) 2023; 15:5713-5733. [PMID: 37390121 PMCID: PMC10333088 DOI: 10.18632/aging.204823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
OBJECTIVE Mago-nashi homolog (MAGOH) has been shown to play a pivotal part in various tumors. However, its specific contribution in lower-grade glioma (LGG) is still unknown. METHODS Pan-cancer analysis was implemented to inspect the expression characteristics and prognostic significance of MAGOH in multiple tumors. The associations between MAGOH expression patterns and the pathological features of LGG were analyzed, as were the connections between MAGOH expression and the clinical traits, prognosis, biological activities, immune features, genomic variations, and responses to treatment in LGG. Additionally, in vitro studies were performed to detect the expression levels and biomedical functions of MAGOH in LGG. RESULTS Abnormally increased levels of MAGOH expression were connected with adverse prognosis in patients with several types of tumors, including LGG. Importantly, we found that levels of MAGOH expression were independent prognostic biomarker of patients with LGG. Increased MAGOH expression was also highly associated with several immune-related markers, immune cell infiltration, immune checkpoint genes (ICPGs), gene mutations, and responses to chemotherapy in patients with LGG. In vitro studies ascertained that abnormally increased MAGOH was essential for cell proliferation in LGG. CONCLUSION MAGOH is a valid predictive biomarker in LGG and may become a novel therapeutic target in these patients.
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Affiliation(s)
- Feng Xiao
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Zhenli Long
- Queen Marry College, School of Medicine, Nanchang University, Nanchang, China
| | - Yun Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Hong Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Yao Xiao
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Guowen Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qing Yang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
| | - Hua Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, China
- Jiangxi Health Commission Key Laboratory of Neurological Medicine, Nanchang, China
- Institute of Neuroscience, Nanchang University, Nanchang, China
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8
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Xin Y, Zhang Y. Paralog-based synthetic lethality: rationales and applications. Front Oncol 2023; 13:1168143. [PMID: 37350942 PMCID: PMC10282757 DOI: 10.3389/fonc.2023.1168143] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023] Open
Abstract
Tumor cells can result from gene mutations and over-expression. Synthetic lethality (SL) offers a desirable setting where cancer cells bearing one mutated gene of an SL gene pair can be specifically targeted by disrupting the function of the other genes, while leaving wide-type normal cells unharmed. Paralogs, a set of homologous genes that have diverged from each other as a consequence of gene duplication, make the concept of SL feasible as the loss of one gene does not affect the cell's survival. Furthermore, homozygous loss of paralogs in tumor cells is more frequent than singletons, making them ideal SL targets. Although high-throughput CRISPR-Cas9 screenings have uncovered numerous paralog-based SL pairs, the unclear mechanisms of targeting these gene pairs and the difficulty in finding specific inhibitors that exclusively target a single but not both paralogs hinder further clinical development. Here, we review the potential mechanisms of paralog-based SL given their function and genetic combination, and discuss the challenge and application prospects of paralog-based SL in cancer therapeutic discovery.
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Ryan CJ, Mehta I, Kebabci N, Adams DJ. Targeting synthetic lethal paralogs in cancer. Trends Cancer 2023; 9:397-409. [PMID: 36890003 DOI: 10.1016/j.trecan.2023.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Synthetic lethal interactions, where mutation of one gene renders cells sensitive to inhibition of another gene, can be exploited for the development of targeted therapeutics in cancer. Pairs of duplicate genes (paralogs) often share common functionality and hence are a potentially rich source of synthetic lethal interactions. Because the majority of human genes have paralogs, exploiting such interactions could be a widely applicable approach for targeting gene loss in cancer. Moreover, existing small-molecule drugs may exploit synthetic lethal interactions by inhibiting multiple paralogs simultaneously. Consequently, the identification of synthetic lethal interactions between paralogs could be extremely informative for drug development. Here we review approaches to identify such interactions and discuss some of the challenges of exploiting them.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Systems Biology Ireland, University College Dublin, Dublin, Ireland.
| | - Ishan Mehta
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Narod Kebabci
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland; Science Foundation Ireland (SFI) Centre for Research Training in Genomics Data Science, University College Dublin, Dublin, Ireland
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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10
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Mitra R, Rehman A, Singh KK, Jaganathan BG. Multifaceted roles of MAGOH Proteins. Mol Biol Rep 2023; 50:1931-1941. [PMID: 36396768 DOI: 10.1007/s11033-022-07904-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 07/14/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022]
Abstract
MAGOH and MAGOHB are paralog proteins that can substitute each other in the exon junction complex (EJC). The EJC is formed of core components EIF4A3, RBM8A, and MAGOH/MAGOHB. As a part of the EJC, MAGOH proteins are required for mRNA splicing, export, translation and nonsense-mediated mRNA decay (NMD). MAGOH is also essential for embryonic development and normal cellular functioning. The haploinsufficiency of MAGOH results in disorders such as microcephaly and cancer. The present review discusses the discovery of MAGOH, its paralog MAGOHB, their roles in cellular function as part of the EJC, and other cellular roles that are not directly associated with mRNA processing. We also discuss how MAGOH haploinsufficiency in cancer cells can be exploited to develop a novel targeted cancer treatment.
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Affiliation(s)
- Rumela Mitra
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India
| | - Ayushi Rehman
- RNA-Binding Proteins (RBPs) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India
| | - Kusum Kumari Singh
- RNA-Binding Proteins (RBPs) Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
| | - Bithiah Grace Jaganathan
- Stem Cells and Cancer Biology Research Group, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
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11
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Soederberg A, Meißgeier T, Bosserhoff AK, Linck-Paulus L. MAGOH and MAGOHB Knockdown in Melanoma Cells Decreases Nonsense-Mediated Decay Activity and Promotes Apoptosis via Upregulation of GADD45A. Cells 2022; 11:cells11233859. [PMID: 36497117 PMCID: PMC9738831 DOI: 10.3390/cells11233859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Cutaneous malignant melanoma is a highly proliferative and aggressive skin cancer with a steadily increasing incidence and a low long-term survival rate after metastatic progression. The protein MAGOH and its highly identical homologue MAGOHB are core components of the exon junction complex (EJC), which regulates splicing, stability and translation of mRNAs. The EJC, and especially MAGOH, has been shown to be involved in the development and progression of several cancers. In melanoma, the expression and function of both homologues remain essentially unexplored. This study identifies high MAGOH and MAGOHB protein expression in cutaneous melanoma cell lines and patient derived tissue samples. An siRNA-mediated knockdown of MAGOH significantly inhibits melanoma cell proliferation. The loss of MAGOH does not affect cell cycle progression, but induces apoptosis, an effect that is enhanced by a simultaneous knockdown of MAGOH and MAGOHB. MAGOH and MAGOHB do not influence the expression of the pro-apoptotic protein Bcl-XS or exon skipping. However, the knockdown of MAGOH and MAGOHB strongly decreases nonsense-mediated decay (NMD) activity, leading to an upregulation of the pro-apoptotic protein GADD45A. In conclusion, simultaneous inhibition of MAGOH and MAGOHB expression substantially affects cell survival, indicating both MAGOH homologues as promising new targets for the treatment of melanoma.
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Affiliation(s)
- Agnes Soederberg
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
| | - Tina Meißgeier
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
| | - Anja Katrin Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany
| | - Lisa Linck-Paulus
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
- Correspondence:
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12
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Achreja A, Yu T, Mittal A, Choppara S, Animasahun O, Nenwani M, Wuchu F, Meurs N, Mohan A, Jeon JH, Sarangi I, Jayaraman A, Owen S, Kulkarni R, Cusato M, Weinberg F, Kweon HK, Subramanian C, Wicha MS, Merajver SD, Nagrath S, Cho KR, DiFeo A, Lu X, Nagrath D. Metabolic collateral lethal target identification reveals MTHFD2 paralogue dependency in ovarian cancer. Nat Metab 2022; 4:1119-1137. [PMID: 36131208 DOI: 10.1038/s42255-022-00636-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022]
Abstract
Recurrent loss-of-function deletions cause frequent inactivation of tumour suppressor genes but often also involve the collateral deletion of essential genes in chromosomal proximity, engendering dependence on paralogues that maintain similar function. Although these paralogues are attractive anticancer targets, no methodology exists to uncover such collateral lethal genes. Here we report a framework for collateral lethal gene identification via metabolic fluxes, CLIM, and use it to reveal MTHFD2 as a collateral lethal gene in UQCR11-deleted ovarian tumours. We show that MTHFD2 has a non-canonical oxidative function to provide mitochondrial NAD+, and demonstrate the regulation of systemic metabolic activity by the paralogue metabolic pathway maintaining metabolic flux compensation. This UQCR11-MTHFD2 collateral lethality is confirmed in vivo, with MTHFD2 inhibition leading to complete remission of UQCR11-deleted ovarian tumours. Using CLIM's machine learning and genome-scale metabolic flux analysis, we elucidate the broad efficacy of targeting MTHFD2 despite distinct cancer genetic profiles co-occurring with UQCR11 deletion and irrespective of stromal compositions of tumours.
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Affiliation(s)
- Abhinav Achreja
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Tao Yu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anjali Mittal
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Srinadh Choppara
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Olamide Animasahun
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Minal Nenwani
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fulei Wuchu
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Noah Meurs
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Aradhana Mohan
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jin Heon Jeon
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Itisam Sarangi
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Anusha Jayaraman
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Owen
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Reva Kulkarni
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michele Cusato
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Frank Weinberg
- Hematology and Oncology, University of Illinois, Chicago, IL, USA
| | - Hye Kyong Kweon
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Chitra Subramanian
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sofia D Merajver
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sunitha Nagrath
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen R Cho
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Analisa DiFeo
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Melvin & Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Deepak Nagrath
- Laboratory for Systems Biology of Human Diseases, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
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13
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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14
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Tang S, Sethunath V, Metaferia NY, Nogueira MF, Gallant DS, Garner ER, Lairson LA, Penney CM, Li J, Gelbard MK, Alaiwi SA, Seo JH, Hwang JH, Strathdee CA, Baca SC, AbuHammad S, Zhang X, Doench JG, Hahn WC, Takeda DY, Freedman ML, Choi PS, Viswanathan SR. A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer. Cell Rep 2022; 38:110417. [PMID: 35196489 PMCID: PMC9036938 DOI: 10.1016/j.celrep.2022.110417] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/10/2021] [Accepted: 01/31/2022] [Indexed: 02/08/2023] Open
Abstract
Androgen receptor (AR) signaling is the central driver of prostate cancer across disease states. While androgen deprivation therapy (ADT) is effective in the initial treatment of prostate cancer, resistance to ADT or to next-generation androgen pathway inhibitors invariably arises, most commonly through the re-activation of the AR axis. Thus, orthogonal approaches to inhibit AR signaling in advanced prostate cancer are essential. Here, via genome-scale CRISPR-Cas9 screening, we identify protein arginine methyltransferase 1 (PRMT1) as a critical mediator of AR expression and signaling. PRMT1 regulates the recruitment of AR to genomic target sites and the inhibition of PRMT1 impairs AR binding at lineage-specific enhancers, leading to decreased expression of key oncogenes, including AR itself. In addition, AR-driven prostate cancer cells are uniquely susceptible to combined AR and PRMT1 inhibition. Our findings implicate PRMT1 as a key regulator of AR output and provide a preclinical framework for co-targeting of AR and PRMT1 in advanced prostate cancer.
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Affiliation(s)
- Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Nebiyou Y Metaferia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marina F Nogueira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Daniel S Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emma R Garner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lauren A Lairson
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher M Penney
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maya K Gelbard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shatha AbuHammad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Peter S Choi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA.
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15
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A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments. Nat Commun 2022; 13:625. [PMID: 35110534 PMCID: PMC8810922 DOI: 10.1038/s41467-022-28045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
A genetic knockout can be lethal to one human cell type while increasing growth rate in another. This context specificity confounds genetic analysis and prevents reproducible genome engineering. Genome-wide CRISPR compendia across most common human cell lines offer the largest opportunity to understand the biology of cell specificity. The prevailing viewpoint, synthetic lethality, occurs when a genetic alteration creates a unique CRISPR dependency. Here, we use machine learning for an unbiased investigation of cell type specificity. Quantifying model accuracy, we find that most cell type specific phenotypes are predicted by the function of related genes of wild-type sequence, not synthetic lethal relationships. These models then identify unexpected sets of 100-300 genes where reduced CRISPR measurements can produce genome-scale loss-of-function predictions across >18,000 genes. Thus, it is possible to reduce in vitro CRISPR libraries by orders of magnitude—with some information loss—when we remove redundant genes and not redundant sgRNAs. Context specificity confounds genetic analysis and prevents reproducible genome engineering. Here, the authors report a pan-CRISPR analysis of specificity in mammalian cells and identify ultra-compact sgRNA subsets for genome-scale screens.
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16
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Pawar A, Chowdhury OR, Chauhan R, Talole S, Bhattacharjee A. Identification of key gene signatures for the overall survival of ovarian cancer. J Ovarian Res 2022; 15:12. [PMID: 35057823 PMCID: PMC8780391 DOI: 10.1186/s13048-022-00942-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The five-year overall survival (OS) of advanced-stage ovarian cancer remains nearly 25-35%, although several treatment strategies have evolved to get better outcomes. A considerable amount of heterogeneity and complexity has been seen in ovarian cancer. This study aimed to establish gene signatures that can be used in better prognosis through risk prediction outcome for the survival of ovarian cancer patients. Different studies' heterogeneity into a single platform is presented to explore the penetrating genes for poor or better survival. The integrative analysis of multiple data sets was done to determine the genes that influence poor or better survival. A total of 6 independent data sets was considered. The Cox Proportional Hazard model was used to obtain significant genes that had an impact on ovarian cancer patients. The gene signatures were prepared by splitting the over-expressed and under-expressed genes parallelly by the variable selection technique. The data visualisation techniques were prepared to predict the overall survival, and it could support the therapeutic regime. RESULTS We preferred to select 20 genes in each data set as upregulated and downregulated. Irrespective of the selection of multiple genes, not even a single gene was found common among data sets for the survival of ovarian cancer patients. However, the same analytical approach adopted. The chord plot was presented to make a comprehensive understanding of the outcome. CONCLUSIONS This study helps us to understand the results obtained from different studies. It shows the impact of the heterogeneity from one study to another. It shows the requirement of integrated studies to make a holistic view of the gene signature for ovarian cancer survival.
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Affiliation(s)
- Akash Pawar
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Oindrila Roy Chowdhury
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Ruby Chauhan
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
| | - Sanjay Talole
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Atanu Bhattacharjee
- Section of Biostatistics, Center for Cancer Epidemiology, Tata Memorial Centre, Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
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17
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Bakouny Z, Sadagopan A, Ravi P, Metaferia NY, Li J, AbuHammad S, Tang S, Denize T, Garner ER, Gao X, Braun DA, Hirsch L, Steinharter JA, Bouchard G, Walton E, West D, Labaki C, Dudani S, Gan CL, Sethunath V, Carvalho FLF, Imamovic A, Ricker C, Vokes NI, Nyman J, Berchuck JE, Park J, Hirsch MS, Haq R, Mary Lee GS, McGregor BA, Chang SL, Feldman AS, Wu CJ, McDermott DF, Heng DYC, Signoretti S, Van Allen EM, Choueiri TK, Viswanathan SR. Integrative clinical and molecular characterization of translocation renal cell carcinoma. Cell Rep 2022; 38:110190. [PMID: 34986355 PMCID: PMC9127595 DOI: 10.1016/j.celrep.2021.110190] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/01/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Translocation renal cell carcinoma (tRCC) is a poorly characterized subtype of kidney cancer driven by MiT/TFE gene fusions. Here, we define the landmarks of tRCC through an integrative analysis of 152 patients with tRCC identified across genomic, clinical trial, and retrospective cohorts. Most tRCCs harbor few somatic alterations apart from MiT/TFE fusions and homozygous deletions at chromosome 9p21.3 (19.2% of cases). Transcriptionally, tRCCs display a heightened NRF2-driven antioxidant response that is associated with resistance to targeted therapies. Consistently, we find that outcomes for patients with tRCC treated with vascular endothelial growth factor receptor inhibitors (VEGFR-TKIs) are worse than those treated with immune checkpoint inhibitors (ICI). Using multiparametric immunofluorescence, we find that the tumors are infiltrated with CD8+ T cells, though the T cells harbor an exhaustion immunophenotype distinct from that of clear cell RCC. Our findings comprehensively define the clinical and molecular features of tRCC and may inspire new therapeutic hypotheses.
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Affiliation(s)
- Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Praful Ravi
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Nebiyou Y Metaferia
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Shatha AbuHammad
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas Denize
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Emma R Garner
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Xin Gao
- Harvard Medical School, Boston, MA, USA; Department of Internal Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Yale Cancer Center / Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Laure Hirsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - John A Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Destiny West
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Shaan Dudani
- Division of Medical Oncology/Hematology, William Osler Health System, Brampton, ON, Canada
| | - Chun-Loo Gan
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Vidyalakshmi Sethunath
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | | | - Alma Imamovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Cora Ricker
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Natalie I Vokes
- Department of Thoracic/Head and Neck Medical Oncology, Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle S Hirsch
- Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Bradley A McGregor
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Steven L Chang
- Harvard Medical School, Boston, MA, USA; Division of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Adam S Feldman
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Daniel Y C Heng
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Srinivas R Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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18
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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19
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Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nat Genet 2021; 53:1664-1672. [PMID: 34857952 DOI: 10.1038/s41588-021-00967-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/14/2021] [Indexed: 12/26/2022]
Abstract
Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensatory relationship between functionally redundant genes masks potential therapeutic targets in single-gene perturbation studies. To identify digenic dependencies, we developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families. We identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells through the hyperactivation of MAPK signaling. Furthermore, cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations such that the mechanisms of resistance to the inhibitors reinforce this mechanism of vulnerability. Together, multigene perturbation technologies unveil previously unrecognized digenic vulnerabilities that may be leveraged as new therapeutic targets in cancer.
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20
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Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Cell Syst 2021; 12:1144-1159.e6. [PMID: 34529928 DOI: 10.1016/j.cels.2021.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have an identifiable paralog, exploiting synthetic lethality between paralogs may be a broadly applicable approach for targeting gene loss in cancer. However, only a biased subset of human paralog pairs has been tested for synthetic lethality to date. Here, by analyzing genome-wide CRISPR screens and molecular profiles of over 700 cancer cell lines, we identify features predictive of synthetic lethality between paralogs, including shared protein-protein interactions and evolutionary conservation. We develop a machine-learning classifier based on these features to predict which paralog pairs are most likely to be synthetic lethal and to explain why. We show that our classifier accurately predicts the results of combinatorial CRISPR screens in cancer cell lines and furthermore can distinguish pairs that are synthetic lethal in multiple cell lines from those that are cell-line specific. A record of this paper's transparent peer review process is included in the supplemental information.
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21
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The MAGOH paralogs - MAGOH, MAGOHB and their multiple isoforms. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Parrish PCR, Thomas JD, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH. Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome. Cell Rep 2021; 36:109597. [PMID: 34469736 PMCID: PMC8534300 DOI: 10.1016/j.celrep.2021.109597] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/26/2023] Open
Abstract
CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single-gene knockout phenotypes can be masked by redundancy among related genes. Paralogs constitute two-thirds of the human protein-coding genome, so existing methods are likely inadequate for assaying a large portion of gene function. Here, we develop paired guide RNAs for paralog genetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single- and double-knockout approach targeting more than 2,000 human paralogs. We apply pgPEN to two cell types and discover that 12% of human paralogs exhibit synthetic lethality in at least one context. We recover known synthetic lethal paralogs MEK1/MEK2, important drug targets CDK4/CDK6, and other synthetic lethal pairs including CCNL1/CCNL2. Additionally, we identify ten tumor suppressor paralog pairs whose compound loss promotes cell proliferation. These findings nominate drug targets and suggest that paralog genetic interactions could shape the landscape of positive and negative selection in cancer.
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Affiliation(s)
- Phoebe C R Parrish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - James D Thomas
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Austin M Gabel
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Shriya Kamlapurkar
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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23
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Pintacuda G, Lassen FH, Hsu YHH, Kim A, Martín JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K. Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. Nat Commun 2021; 12:2580. [PMID: 33972534 PMCID: PMC8110583 DOI: 10.1038/s41467-021-22648-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/18/2021] [Indexed: 01/03/2023] Open
Abstract
Combining genetic and cell-type-specific proteomic datasets can generate biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present an open-source computational tool called Genoppi (lagelab.org/genoppi) that enables robust, standardized, and intuitive integration of quantitative proteomic results with genetic data. We use Genoppi to analyze 16 cell-type-specific protein interaction datasets of four proteins (BCL2, TDP-43, MDM2, PTEN) involved in cancer and neurological disease. Through systematic quality control of the data and integration with published protein interactions, we show a general pattern of both cell-type-independent and cell-type-specific interactions across three cancer cell types and one human iPSC-derived neuronal cell type. Furthermore, through the integration of proteomic and genetic datasets in Genoppi, our results suggest that the neuron-specific interactions of these proteins are mediating their genetic involvement in neurodegenerative diseases. Importantly, our analyses suggest that human iPSC-derived neurons are a relevant model system for studying the involvement of BCL2 and TDP-43 in amyotrophic lateral sclerosis.
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Affiliation(s)
- Greta Pintacuda
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Frederik H Lassen
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yu-Han H Hsu
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - April Kim
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline M Martín
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Edyta Malolepsza
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Justin K Lim
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nadine Fornelos
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin C Eggan
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Kasper Lage
- Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
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24
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Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: Challenges and opportunities. Cancer Cell 2021; 39:466-479. [PMID: 33450197 PMCID: PMC8157671 DOI: 10.1016/j.ccell.2020.12.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.
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Affiliation(s)
- Liang Chang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Ruiz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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25
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Castells-Roca L, Tejero E, Rodríguez-Santiago B, Surrallés J. CRISPR Screens in Synthetic Lethality and Combinatorial Therapies for Cancer. Cancers (Basel) 2021; 13:1591. [PMID: 33808217 PMCID: PMC8037779 DOI: 10.3390/cancers13071591] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
Cancer is a complex disease resulting from the accumulation of genetic dysfunctions. Tumor heterogeneity causes the molecular variety that divergently controls responses to chemotherapy, leading to the recurrent problem of cancer reappearance. For many decades, efforts have focused on identifying essential tumoral genes and cancer driver mutations. More recently, prompted by the clinical success of the synthetic lethality (SL)-based therapy of the PARP inhibitors in homologous recombinant deficient tumors, scientists have centered their novel research on SL interactions (SLI). The state of the art to find new genetic interactions are currently large-scale forward genetic CRISPR screens. CRISPR technology has rapidly evolved to be a common tool in the vast majority of laboratories, as tools to implement CRISPR screen protocols are available to all researchers. Taking advantage of SLI, combinatorial therapies have become the ultimate model to treat cancer with lower toxicity, and therefore better efficiency. This review explores the CRISPR screen methodology, integrates the up-to-date published findings on CRISPR screens in the cancer field and proposes future directions to uncover cancer regulation and individual responses to chemotherapy.
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Affiliation(s)
- Laia Castells-Roca
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eudald Tejero
- Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain;
| | - Benjamín Rodríguez-Santiago
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
| | - Jordi Surrallés
- Genome Instability and DNA Repair Syndromes Group, Sant Pau Biomedical Research Institute (IIB Sant Pau) and Join Unit UAB-IR Sant Pau on Genomic Medicine, 08041 Barcelona, Spain
- Genetics Department, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER) and Sant Pau Biomedical Research Institute (IIB Sant Pau), 08041 Barcelona, Spain
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26
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Zhou Y, Li Z, Wu X, Tou L, Zheng J, Zhou D. MAGOH/MAGOHB Inhibits the Tumorigenesis of Gastric Cancer via Inactivation of b-RAF/MEK/ERK Signaling. Onco Targets Ther 2020; 13:12723-12735. [PMID: 33328743 PMCID: PMC7735944 DOI: 10.2147/ott.s263913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Background Gastric cancer is one of the most malignant tumors all over the world. It has been reported that proteins play key roles during the tumorigenesis of gastric cancer. To identify novel potential targets for gastric cancer, differential expressed proteins between gastric cancer and adjacent normal tissues were analyzed with proteomics and bioinformatics tool. Methods The differentially expressed proteins between gastric cancer and adjacent normal tissues were analyzed by Omicsbean (multi-omics data analysis tool). Cell viability was tested by CCK-8 assay. Flow cytometry was used to measure cell apoptosis and cycle. Transwell assay was used to test cell migration and invasion. Gene and protein expressions were detected by RT-qPCR, immunohistochemistry and Western blot, respectively. Results MAGOH and MAGOHB were found to be notably upregulated in gastric cancer tissues compared with that in normal tissues. Knockdown of MAGOH significantly inhibited the proliferation of gastric cancer cells via inducing the cell apoptosis. In addition, MAGOH knockdown induced G2 phase arrest in gastric cancer cells. Moreover, MAGOH knockdown notably inhibited migration and invasion of gastric cancer cells. Importantly, double knockdown of MAGOH and MAGOHB exhibited much better anti-tumor effects on gastric cancer compared with alone treatment. Finally, double knockdown of MAGOH and MAGOHB mediated the tumorigenesis of gastric cancer via regulation of RAF/MEK/ERK signaling. Conclusion MAGOH knockdown inhibited the tumorigenesis of gastric cancer via mediation of b-RAF/MEK/ERK signaling, and double knockdown of MAGOH and MAGOHB exhibited much better anti-tumor effects. This finding might provide us a new strategy for the treatment of gastric cancer.
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Affiliation(s)
- Yong Zhou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Zhongqi Li
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Xuan Wu
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Laizhen Tou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
| | - Jingjing Zheng
- Department of General Surgery, Lishui Municipal Central Hospital, Lishui, Zhejiang 323000, People's Republic of China
| | - Donghui Zhou
- Department of Oncology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, People's Republic of China
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27
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Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A, Kalekar RL, Krill-Burger JM, Dharia NV, Kugener G, Kalfon J, Yuan C, Dumont N, Gonzalez A, Abdusamad M, Li YY, Spurr LF, Wu WW, Durbin AD, Wolpin BM, Piccioni F, Root DE, Boehm JS, Cherniack AD, Tsherniak A, Hong AL, Hahn WC, Stegmaier K, Golub TR, Vazquez F, Aguirre AJ. Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q. Cell Rep 2020; 33:108493. [PMID: 33326793 PMCID: PMC8374858 DOI: 10.1016/j.celrep.2020.108493] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/04/2020] [Accepted: 11/17/2020] [Indexed: 12/26/2022] Open
Abstract
Few therapies target the loss of tumor suppressor genes in cancer. We examine CRISPR-SpCas9 and RNA-interference loss-of-function screens to identify new therapeutic targets associated with genomic loss of tumor suppressor genes. The endosomal sorting complexes required for transport (ESCRT) ATPases VPS4A and VPS4B score as strong synthetic lethal dependencies. VPS4A is essential in cancers harboring loss of VPS4B adjacent to SMAD4 on chromosome 18q and VPS4B is required in tumors with co-deletion of VPS4A and CDH1 (E-cadherin) on chromosome 16q. We demonstrate that more than 30% of cancers selectively require VPS4A or VPS4B. VPS4A suppression in VPS4B-deficient cells selectively leads to ESCRT-III filament accumulation, cytokinesis defects, nuclear deformation, G2/M arrest, apoptosis, and potent tumor regression. CRISPR-SpCas9 screening and integrative genomic analysis reveal other ESCRT members, regulators of abscission, and interferon signaling as modifiers of VPS4A dependency. We describe a compendium of synthetic lethal vulnerabilities and nominate VPS4A and VPS4B as high-priority therapeutic targets for cancers with 18q or 16q loss. Neggers, Paolella, and colleagues identify the ATPases VPS4A and VPS4B as selective vulnerabilities and potential therapeutic targets in cancers harboring loss of chromosome 18q or 16q. In VPS4B-deficient cancers, VPS4A suppression leads to ESCRT-III dysfunction, nuclear deformation, and abscission defects. Moreover, ESCRT proteins and interferons can modulate dependency on VPS4A.
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Affiliation(s)
- Jasper E Neggers
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brenton R Paolella
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Adhana Asfaw
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael V Rothberg
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas A Skipper
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Radha L Kalekar
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - John M Krill-Burger
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Neekesh V Dharia
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Guillaume Kugener
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jérémie Kalfon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Nancy Dumont
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alfredo Gonzalez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mai Abdusamad
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yvonne Y Li
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Westley W Wu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Adam D Durbin
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse S Boehm
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Aviad Tsherniak
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew L Hong
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - William C Hahn
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kimberly Stegmaier
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Cancer and Blood Disorders Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Todd R Golub
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Francisca Vazquez
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Andrew J Aguirre
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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28
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Scalia P, Giordano A, Martini C, Williams SJ. Isoform- and Paralog-Switching in IR-Signaling: When Diabetes Opens the Gates to Cancer. Biomolecules 2020; 10:biom10121617. [PMID: 33266015 PMCID: PMC7761347 DOI: 10.3390/biom10121617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Insulin receptor (IR) and IR-related signaling defects have been shown to trigger insulin-resistance in insulin-dependent cells and ultimately to give rise to type 2 diabetes in mammalian organisms. IR expression is ubiquitous in mammalian tissues, and its over-expression is also a common finding in cancerous cells. This latter finding has been shown to associate with both a relative and absolute increase in IR isoform-A (IR-A) expression, missing 12 aa in its EC subunit corresponding to exon 11. Since IR-A is a high-affinity transducer of Insulin-like Growth Factor-II (IGF-II) signals, a growth factor is often secreted by cancer cells; such event offers a direct molecular link between IR-A/IR-B increased ratio in insulin resistance states (obesity and type 2 diabetes) and the malignant advantage provided by IGF-II to solid tumors. Nonetheless, recent findings on the biological role of isoforms for cellular signaling components suggest that the preferential expression of IR isoform-A may be part of a wider contextual isoform-expression switch in downstream regulatory factors, potentially enhancing IR-dependent oncogenic effects. The present review focuses on the role of isoform- and paralog-dependent variability in the IR and downstream cellular components playing a potential role in the modulation of the IR-A signaling related to the changes induced by insulin-resistance-linked conditions as well as to their relationship with the benign versus malignant transition in underlying solid tumors.
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Affiliation(s)
- Pierluigi Scalia
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
- Correspondence:
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- Department of Medical Biotechnologies, University of Siena, 52100 Siena, Italy
| | - Caroline Martini
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
| | - Stephen J. Williams
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
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29
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Wang Z, Chen K, Jia Y, Chuang JC, Sun X, Lin YH, Celen C, Li L, Huang F, Liu X, Castrillon DH, Wang T, Zhu H. Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. ACTA ACUST UNITED AC 2020; 1:909-922. [PMID: 34386776 DOI: 10.1038/s43018-020-00109-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SWI/SNF chromatin remodelers play critical roles in development and cancer. The causal links between SWI/SNF complex disassembly and carcinogenesis are obscured by redundancy between paralogous components. Canonical cBAF-specific paralogs ARID1A and ARID1B are synthetic lethal in some contexts, but simultaneous mutations in both ARID1s are prevalent in cancer. To understand if and how cBAF abrogation causes cancer, we examined the physiologic and biochemical consequences of ARID1A/ARID1B loss. In double knockout liver and skin, aggressive carcinogenesis followed de-differentiation and hyperproliferation. In double mutant endometrial cancer, add-back of either induced senescence. Biochemically, residual cBAF subcomplexes resulting from loss of ARID1 scaffolding were unexpectedly found to disrupt polybromo containing pBAF function. 37 of 69 mutations in the conserved scaffolding domains of ARID1 proteins observed in human cancer caused complex disassembly, partially explaining their mutation spectra. ARID1-less, cBAF-less states promote carcinogenesis across tissues, and suggest caution against paralog-directed therapies for ARID1-mutant cancer.
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Affiliation(s)
- Zixi Wang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yuemeng Jia
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jen-Chieh Chuang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuxu Sun
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Hsuan Lin
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cemre Celen
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Li
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fang Huang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Liu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diego H Castrillon
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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30
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Shreberk-Shaked M, Dassa B, Sinha S, Di Agostino S, Azuri I, Mukherjee S, Aylon Y, Blandino G, Ruppin E, Oren M. A Division of Labor between YAP and TAZ in Non-Small Cell Lung Cancer. Cancer Res 2020; 80:4145-4157. [PMID: 32816858 DOI: 10.1158/0008-5472.can-20-0125] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/07/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. The paralogous transcriptional cofactors Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ, also called WWTR1), the main downstream effectors of the Hippo signal transduction pathway, are emerging as pivotal determinants of malignancy in lung cancer. Traditionally, studies have tended to consider YAP and TAZ as functionally redundant transcriptional cofactors with similar biological impact. However, there is growing evidence that each of them also possesses distinct attributes. Here we sought to systematically characterize the division of labor between YAP and TAZ in non-small cell lung cancer (NSCLC), the most common histological subtype of lung cancer. Representative NSCLC cell lines as well as patient-derived data showed that the two paralogs orchestrated nonoverlapping transcriptional programs in this cancer type. YAP preferentially regulated gene sets associated with cell division and cell-cycle progression, whereas TAZ preferentially regulated genes associated with extracellular matrix organization. Depletion of YAP resulted in growth arrest, whereas its overexpression promoted cell proliferation. Likewise, depletion of TAZ compromised cell migration, whereas its overexpression enhanced migration. The differential effects of YAP and TAZ on key cellular processes were also associated with differential response to anticancer therapies. Uncovering the different activities and downstream effects of YAP and TAZ may thus facilitate better stratification of patients with lung cancer for anticancer therapies. SIGNIFICANCE: Thease findings show that oncogenic paralogs YAP and TAZ have distinct roles in NSCLC and are associated with differential response to anticancer drugs, knowledge that may assist lung cancer therapy decisions.
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Affiliation(s)
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Sanju Sinha
- Cancer Data Science Laboratory, NCI, NIH, Bethesda, Maryland.,Center for Bioinformatics and Computational Biology & Department of Computer Sciences, University of Maryland, College Park, Maryland
| | - Silvia Di Agostino
- Oncogenomic and Epigenetic Lab., IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy
| | - Ido Azuri
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Saptaparna Mukherjee
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Aylon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Lab., IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy
| | - Eytan Ruppin
- Cancer Data Science Laboratory, NCI, NIH, Bethesda, Maryland.,Center for Bioinformatics and Computational Biology & Department of Computer Sciences, University of Maryland, College Park, Maryland
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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31
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Lian S, Liu Z, Zhou Y, Guo J, Gong K, Wang T. The differential expression patterns and co-expression networks of paralogs as an indicator of the TNM stages of lung adenocarcinoma and squamous cell carcinoma. Genomics 2020; 112:4115-4124. [PMID: 32659329 DOI: 10.1016/j.ygeno.2020.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/27/2022]
Abstract
Cancers constitute a severe threat to human health. Elucidating the association between the expression patterns of the paralogous genes and transcription factors (TF) and the progression of cancers by comprehensively investigating the expression patterns and co-expression networks will contribute to the in-depth understanding of the pathogenesis of cancers. Here, we identified the paralogous gene pairs and systematically analyzed the expression patterns of these paralogs and the known TFs to elucidate the associations with Tumor, Node, Metastasis (TNM) staging information across ten cancers. We found that the expression of ~60% paralogs was cancer-dependent, and more than 50% of the differentially expressed TFs pairs showed positive expression correlations. The down-regulation patterns of paralogs and TFs were closely associated with the M and N developmental stages of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Our results will help to understand the roles of paralogs and TFs in cancer progression and to screen prognostic biomarkers for early cancer diagnosis.
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Affiliation(s)
- Shuaibin Lian
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China.
| | - Zixiao Liu
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Yongjie Zhou
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Jiantao Guo
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Ke Gong
- College of Physics and Electronic Engineering, Xinyang Normal University, Xinyang, China
| | - Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal, University, Xinyang 464000, Henan, China.
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32
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Sepe RM, Ghiron JHL, Zucchetti I, Caputi L, Tarallo R, Crocetta F, De Santis R, D'Aniello S, Sordino P. The EJC component Magoh in non-vertebrate chordates. Dev Genes Evol 2020; 230:295-304. [PMID: 32632492 DOI: 10.1007/s00427-020-00664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/01/2020] [Indexed: 11/26/2022]
Abstract
Earliest craniates possess a newly enlarged, elaborated forebrain with new cell types and neuronal networks. A key question in vertebrate evolution is when and how this cerebral expansion took place. The exon-junction complex (EJC) plays an essential role in mRNA processing of all Eukarya. Recently, it has been proposed that the EJC represses recursive RNA splicing in Deuterostomes, with implication in human brain diseases like microcephaly and depression. However, the EJC or EJC subunit contribution to brain development in non-vertebrate Deuterostomes remained unknown. Being interested in the evolution of chordate characters, we focused on the model species, Branchiostoma lanceolatum (Cephalochordata) and Ciona robusta (Tunicata), with the aim to investigate the ancestral and the derived expression state of Magoh orthologous genes. This study identifies that Magoh is part of a conserved syntenic group exclusively in vertebrates and suggests that Magoh has experienced duplication and loss events in mammals. During early development in amphioxus and ascidian, maternal contribution and zygotic expression of Magoh genes in various types of progenitor cells and tissues are consistent with the condition observed in other Bilateria. Later in development, we also show expression of Magoh in the brain of cephalochordate and ascidian larvae. Collectively, these results provide a basis to further define what functional role(s) Magoh exerted during nervous system development and evolution.
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Affiliation(s)
- Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Jung Hee Levialdi Ghiron
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Ivana Zucchetti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Luigi Caputi
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Raffaella Tarallo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Fabio Crocetta
- Department of Integrated Marine Ecology, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Rosaria De Santis
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy.
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, 80121, Naples, Italy.
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33
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Nanoparticle delivery of immunostimulatory oligonucleotides enhances response to checkpoint inhibitor therapeutics. Proc Natl Acad Sci U S A 2020; 117:13428-13436. [PMID: 32493746 PMCID: PMC7306768 DOI: 10.1073/pnas.2001569117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Checkpoint inhibitor (CPI) immunotherapies have revolutionized the treatment of a wide array of cancers, but their utility remains limited to a subset of patients with favorable disease phenotypes. We show that the generation of peptide-based nanocomplexes carrying immunostimulatory oligonucleotides dramatically increases the potency of certain of these compounds to stimulate toll-like receptor signaling. The administration of immunostimulatory nanocomplexes carrying CpG oligonucleotides generates antitumor effects and enhances the efficacy of checkpoint inhibitor antibody therapy in mouse models of cancer, and the nanocomplex formulation enables drastic reductions in the dose required to generate therapeutic effects. The recent advent of immune checkpoint inhibitor (CPI) antibodies has revolutionized many aspects of cancer therapy, but the efficacy of these breakthrough therapeutics remains limited, as many patients fail to respond for reasons that still largely evade understanding. An array of studies in human patients and animal models has demonstrated that local signaling can generate strongly immunosuppressive microenvironments within tumors, and emerging evidence suggests that delivery of immunostimulatory molecules into tumors can have therapeutic effects. Nanoparticle formulations of these cargoes offer a promising way to maximize their delivery and to enhance the efficacy of checkpoint inhibitors. We developed a modular nanoparticle system capable of encapsulating an array of immunostimulatory oligonucleotides that, in some cases, greatly increase their potency to activate inflammatory signaling within immune cells in vitro. We hypothesized that these immunostimulatory nanoparticles could suppress tumor growth by activating similar signaling in vivo, and thereby also improve responsiveness to immune checkpoint inhibitor antibody therapies. We found that our engineered nanoparticles carrying a CpG DNA ligand of TLR9 can suppress tumor growth in several animal models of various cancers, resulting in an abscopal effect on distant tumors, and improving responsiveness to anti-CTLA4 treatment with combinatorial effects after intratumoral administration. Moreover, by incorporating tumor-homing peptides, immunostimulatory nucleotide-bearing nanoparticles facilitate antitumor efficacy after systemic intravenous (i.v.) administration.
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34
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Nichols CA, Gibson WJ, Brown MS, Kosmicki JA, Busanovich JP, Wei H, Urbanski LM, Curimjee N, Berger AC, Gao GF, Cherniack AD, Dhe-Paganon S, Paolella BR, Beroukhim R. Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat Commun 2020; 11:2517. [PMID: 32433464 PMCID: PMC7239950 DOI: 10.1038/s41467-020-16399-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Alterations in non-driver genes represent an emerging class of potential therapeutic targets in cancer. Hundreds to thousands of non-driver genes undergo loss of heterozygosity (LOH) events per tumor, generating discrete differences between tumor and normal cells. Here we interrogate LOH of polymorphisms in essential genes as a novel class of therapeutic targets. We hypothesized that monoallelic inactivation of the allele retained in tumors can selectively kill cancer cells but not somatic cells, which retain both alleles. We identified 5664 variants in 1278 essential genes that undergo LOH in cancer and evaluated the potential for each to be targeted using allele-specific gene-editing, RNAi, or small-molecule approaches. We further show that allele-specific inactivation of either of two essential genes (PRIM1 and EXOSC8) reduces growth of cells harboring that allele, while cells harboring the non-targeted allele remain intact. We conclude that LOH of essential genes represents a rich class of non-driver cancer vulnerabilities. In tumors, hundreds of genes can undergo loss of heterozygosity (LOH). Here, the authors investigate the potential for this LOH as a class of non-driver cancer vulnerabilities.
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Affiliation(s)
- Caitlin A Nichols
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - William J Gibson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Meredith S Brown
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Jack A Kosmicki
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, 02138, USA
| | - John P Busanovich
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Hope Wei
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Laura M Urbanski
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Naomi Curimjee
- Departments of Cancer Biology, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Ashton C Berger
- Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Galen F Gao
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew D Cherniack
- Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sirano Dhe-Paganon
- Departments of Cancer Biology, Boston, MA, USA.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brenton R Paolella
- Departments of Cancer Biology, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Rameen Beroukhim
- Departments of Cancer Biology, Boston, MA, USA. .,Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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35
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Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation. Nat Genet 2020; 52:615-625. [PMID: 32393859 DOI: 10.1038/s41588-020-0618-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/26/2020] [Indexed: 12/20/2022]
Abstract
The COMPASS protein family catalyzes histone H3 Lys 4 (H3K4) methylation and its members are essential for regulating gene expression. MLL2/COMPASS methylates H3K4 on many developmental genes and bivalent clusters. To understand MLL2-dependent transcriptional regulation, we performed a CRISPR-based screen with an MLL2-dependent gene as a reporter in mouse embryonic stem cells. We found that MLL2 functions in gene expression by protecting developmental genes from repression via repelling PRC2 and DNA methylation machineries. Accordingly, repression in the absence of MLL2 is relieved by inhibition of PRC2 and DNA methyltransferases. Furthermore, DNA demethylation on such loci leads to reactivation of MLL2-dependent genes not only by removing DNA methylation but also by opening up previously CpG methylated regions for PRC2 recruitment, diluting PRC2 at Polycomb-repressed genes. These findings reveal how the context and function of these three epigenetic modifiers of chromatin can orchestrate transcriptional decisions and demonstrate that prevention of active repression by the context of the enzyme and not H3K4 trimethylation underlies transcriptional regulation on MLL2/COMPASS targets.
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36
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Li M, Nopparat J, Aguilar BJ, Chen YH, Zhang J, Du J, Ai X, Luo Y, Jiang Y, Boykin C, Lu Q. Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression. Oncogene 2020; 39:4358-4374. [PMID: 32313227 PMCID: PMC10493073 DOI: 10.1038/s41388-020-1281-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022]
Abstract
Only a small number of genes are bona fide oncogenes and tumor suppressors such as Ras, Myc, β-catenin, p53, and APC. However, targeting these cancer drivers frequently fail to demonstrate sustained cancer remission. Tumor heterogeneity and evolution contribute to cancer resistance and pose challenges for cancer therapy due to differential genomic rearrangement and expression driving distinct tumor responses to treatments. Here we report that intratumor heterogeneity of Wnt/β-catenin modulator δ-catenin controls individual cell behavior to promote cancer. The differential intratumor subcellular localization of δ-catenin mirrors its compartmentalization in prostate cancer xenograft cultures as result of mutation-rendered δ-catenin truncations. Wild-type and δ-catenin mutants displayed distinct protein interactomes that highlight rewiring of signal networks. Localization specific δ-catenin mutants influenced p120ctn-dependent Rho GTPase phosphorylation and shifted cells towards differential bFGF-responsive growth and motility, a known signal to bypass androgen receptor dependence. Mutant δ-catenin promoted Myc-induced prostate tumorigenesis while increasing bFGF-p38 MAP kinase signaling, β-catenin-HIF-1α expression, and the nuclear size. Therefore, intratumor δ-catenin heterogeneity originated from genetic remodeling promotes prostate cancer expansion towards androgen independent signaling, supporting a neomorphism model paradigm for targeting tumor progression.
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Affiliation(s)
- Mingchuan Li
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Jongdee Nopparat
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Anatomy, Prince of Songkla University, Songkhla, Thailand
| | - Byron J. Aguilar
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Yan-hua Chen
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jiao Zhang
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Jie Du
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Xin Ai
- Dept. of Urology, PLA Army General Hospital, Beijing, China
| | - Yong Luo
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Yongguang Jiang
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - Christi Boykin
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
| | - Qun Lu
- Department of Anatomy and Cell Biology, The Brody school of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
- Department of Urological Surgery, Beijing An Zhen Hospital, Capital Medical University, Beijing, China
- The Harriet and John Wooten Laboratory for Alzheimer’s and Neurodegenerative Diseases Research, The Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA 27834
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37
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Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol 2020; 38:638-648. [PMID: 32249828 DOI: 10.1038/s41587-020-0437-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Systematic mapping of genetic interactions (GIs) and interrogation of the functions of sizable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR (clustered regularly interspaced short palindromic repeats)-based screening system for combinatorial genetic manipulation that employs coexpression of CRISPR-associated nucleases 9 and 12a (Cas9 and Cas12a) and machine-learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named Cas Hybrid for Multiplexed Editing and screening Applications (CHyMErA), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive GIs and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemogenetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for GI mapping and the functional analysis of sizable genomic regions, such as alternative exons.
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Affiliation(s)
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Tanja Durbic
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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38
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Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy. Nat Commun 2020; 11:1308. [PMID: 32161261 PMCID: PMC7066191 DOI: 10.1038/s41467-020-15111-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.
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39
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van Harten AM, de Boer DV, Martens-de Kemp SR, Buijze M, Ganzevles SH, Hunter KD, Leemans CR, van Beusechem VW, Wolthuis RMF, de Menezes RX, Brakenhoff RH. Chemopreventive targeted treatment of head and neck precancer by Wee1 inhibition. Sci Rep 2020; 10:2330. [PMID: 32047167 PMCID: PMC7012863 DOI: 10.1038/s41598-020-58509-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/25/2019] [Indexed: 01/17/2023] Open
Abstract
HPV-negative head and neck squamous cell carcinomas (HNSCCs) develop in precancerous changes in the mucosal lining of the upper-aerodigestive tract. These precancerous cells contain cancer-associated genomic changes and cause primary tumors and local relapses. Therapeutic strategies to eradicate these precancerous cells are very limited. Using functional genomic screens, we identified the therapeutic vulnerabilities of premalignant mucosal cells, which are shared with fully malignant HNSCC cells. We screened 319 previously identified tumor-lethal siRNAs on a panel of cancer and precancerous cell lines as well as primary fibroblasts. In total we identified 147 tumor-essential genes including 34 druggable candidates. Of these 34, 13 were also essential in premalignant cells. We investigated the variable molecular basis of the vulnerabilities in tumor and premalignant cell lines and found indications of collateral lethality. Wee1-like kinase (WEE1) was amongst the most promising targets for both tumor and precancerous cells. All four precancerous cell lines were highly sensitive to Wee1 inhibition by Adavosertib (AZD1775), while primary keratinocytes tolerated this inhibitor. Wee1 inhibition caused induction of DNA damage during S-phase followed by mitotic failure in (pre)cancer cells. In conclusion, we uncovered Wee1 inhibition as a promising chemopreventive strategy for precancerous cells, with comparable responses as fully transformed HNSCC cells.
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Affiliation(s)
- Anne M van Harten
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - D Vicky de Boer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sanne R Martens-de Kemp
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Marijke Buijze
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Sonja H Ganzevles
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Keith D Hunter
- Academic Unit of Oral and Maxillofacial Medicine, Surgery and Pathology, University of Sheffield, South Yorkshire, England
| | - C René Leemans
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Victor W van Beusechem
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Clinical Genetics, section Oncogenetics, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Renée X de Menezes
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Biostatistics, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands.
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40
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Obeng EA, Stewart C, Abdel-Wahab O. Altered RNA Processing in Cancer Pathogenesis and Therapy. Cancer Discov 2019; 9:1493-1510. [PMID: 31611195 PMCID: PMC6825565 DOI: 10.1158/2159-8290.cd-19-0399] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/21/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022]
Abstract
Major advances in our understanding of cancer pathogenesis and therapy have come from efforts to catalog genomic alterations in cancer. A growing number of large-scale genomic studies have uncovered mutations that drive cancer by perturbing cotranscriptional and post-transcriptional regulation of gene expression. These include alterations that affect each phase of RNA processing, including splicing, transport, editing, and decay of messenger RNA. The discovery of these events illuminates a number of novel therapeutic vulnerabilities generated by aberrant RNA processing in cancer, several of which have progressed to clinical development. SIGNIFICANCE: There is increased recognition that genetic alterations affecting RNA splicing and polyadenylation are common in cancer and may generate novel therapeutic opportunities. Such mutations may occur within an individual gene or in RNA processing factors themselves, thereby influencing splicing of many downstream target genes. This review discusses the biological impact of these mutations on tumorigenesis and the therapeutic approaches targeting cells bearing these mutations.
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Affiliation(s)
- Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Connor Stewart
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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41
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De Kegel B, Ryan CJ. Paralog buffering contributes to the variable essentiality of genes in cancer cell lines. PLoS Genet 2019; 15:e1008466. [PMID: 31652272 PMCID: PMC6834290 DOI: 10.1371/journal.pgen.1008466] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/06/2019] [Accepted: 10/08/2019] [Indexed: 12/26/2022] Open
Abstract
What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other's loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background. Here, using gene essentiality profiles of 558 genetically heterogeneous tumor cell lines, we analyze the contribution of paralogy to variable essentiality. We find that, compared to singleton genes, paralogs are less frequently essential and that this is more evident when considering genes with multiple paralogs or with highly sequence-similar paralogs. In addition, we find that paralogs derived from whole genome duplication exhibit more variable essentiality than those derived from small-scale duplications. We provide evidence that in 13–17% of cases the variable essentiality of paralogs can be attributed to buffering relationships between paralog pairs, as evidenced by synthetic lethality. Paralog pairs derived from whole genome duplication and pairs that function in protein complexes are significantly more likely to display such synthetic lethal relationships. Overall we find that many of the observations made using a single strain of budding yeast can be extended to understand patterns of essentiality in genetically heterogeneous cancer cell lines. Somewhat surprisingly, the majority of human genes can be mutated or deleted in individual cell lines without killing the cells. This observation raises a number of questions—which genes can be lost and why? Here we address these questions by analyzing data on which genes are essential for the growth of over 500 cancer cell lines. In general we find that paralog genes are essential in fewer cell lines than genes that are not paralogs. Paralogs are genes that have been duplicated at some point in evolutionary history, resulting in our genome having two copies of the same gene—a paralog pair. These paralog pairs are a potential source of redundancy, similar to a car having a spare tire. If this is the case, one might expect that losing one gene from a paralog pair could be tolerated by cells, due to the existence of a 'backup gene', but losing both members would cause cells to die. By analyzing the cancer cell lines we estimate this to be the case for 13–17% of paralog pairs, and that this provides an explanation for why some genes are essential in some cell lines but not others.
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Affiliation(s)
- Barbara De Kegel
- School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Colm J. Ryan
- School of Computer Science and Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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