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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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Branigan GL, Olsen KS, Burda I, Haemmerle MW, Ho J, Venuto A, D’Antonio ND, Briggs IE, DiBenedetto AJ. Zebrafish Paralogs brd2a and brd2b Are Needed for Proper Circulatory, Excretory and Central Nervous System Formation and Act as Genetic Antagonists during Development. J Dev Biol 2021; 9:jdb9040046. [PMID: 34842711 PMCID: PMC8629005 DOI: 10.3390/jdb9040046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Brd2 belongs to the BET family of epigenetic transcriptional co-regulators that act as adaptor-scaffolds for the assembly of chromatin-modifying complexes and other factors at target gene promoters. Brd2 is a protooncogene and candidate gene for juvenile myoclonic epilepsy in humans, a homeobox gene regulator in Drosophila, and a maternal-zygotic factor and cell death modulator that is necessary for normal development of the vertebrate central nervous system (CNS). As two copies of Brd2 exist in zebrafish, we use antisense morpholino knockdown to probe the role of paralog Brd2b, as a comparative study to Brd2a, the ortholog of human Brd2. A deficiency in either paralog results in excess cell death and dysmorphology of the CNS, whereas only Brd2b deficiency leads to loss of circulation and occlusion of the pronephric duct. Co-knockdown of both paralogs suppresses single morphant defects, while co-injection of morpholinos with paralogous RNA enhances them, suggesting novel genetic interaction with functional antagonism. Brd2 diversification includes paralog-specific RNA variants, a distinct localization of maternal factors, and shared and unique spatiotemporal expression, providing unique insight into the evolution and potential functions of this gene.
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Affiliation(s)
- Gregory L. Branigan
- Medical Scientist Training Program, Center for Innovation in Brain Science, Department of Pharmacology, University of Arizona College of Medicine-Tucson, 1501 N Campbell Ave., Tucson, AZ 85724, USA;
| | - Kelly S. Olsen
- Biological and Biomedical Sciences Program, Department of Microbiology and Immunology, University of North Carolina School of Medicine-Chapel Hill, 321 S Columbia St., Chapel Hill, NC 27516, USA;
| | - Isabella Burda
- Department of Molecular Biology and Genetics, Weill Institute for Cell & Molecular Biology, Cornell University, 239 Weill Hall, Ithaca, NY 14853, USA;
| | - Matthew W. Haemmerle
- Institute for Diabetes, Obesity, and Metabolism, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Room 12-124, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA;
| | - Jason Ho
- Robert Wood Johnson Medical School, Rutgers University, Clinical Academic Building (CAB), 125 Paterson St., New Brunswick, NJ 08901, USA;
| | - Alexandra Venuto
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Nicholas D. D’Antonio
- Sidney Kimmel Medical College, Thomas Jefferson University Hospital, 1025 Walnut St. #100, Philadelphia, PA 19107, USA;
| | - Ian E. Briggs
- Department of Biology, Villanova University, 800 Lancaster Ave., Villanova, PA 19085, USA;
| | - Angela J. DiBenedetto
- Department of Biology, Villanova University, 800 Lancaster Ave., Villanova, PA 19085, USA;
- Correspondence:
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3
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Chen N, Liu G, Guo M, Li Y, Yao Z, Hu B. Calcarine as a bridge between brain function and structure in irritable bowel syndrome: A multiplex network analysis. J Gastroenterol Hepatol 2021; 36:2408-2415. [PMID: 33354807 DOI: 10.1111/jgh.15382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/09/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIM Jointly analyzing structural and functional brain networks enables a better understanding of pathological underpinnings of irritable bowel syndrome (IBS). Multiplex network analysis provides a novel framework to study complex networks consisting of different types of connectivity patterns in multimodal data. METHODS In the present work, we integrated functional and structural networks to a multiplex network. Then, the multiplex metrics and the inner-layer/inter-layer hub nodes were investigated through 34 patients with IBS and 33 healthy controls. RESULTS Significantly differential multiplex degree in both left and right parts of calcarine was found, and meanwhile, IBS patients lost inner-layer hub properties in these regions. In addition, the left fusiform was no longer practicing as an inner-layer hub node, while the right median cingulate acted as a new inner-layer hub node in the IBS patients. Besides, the right calcarine, which lost its inner-layer hub identity, became a new inter-layer hub node, and the multiplex degree of the left hippocampus, which lost its inter-layer hub identity in IBS patients, was significantly positively correlated with the IBS Symptom Severity Score scores. CONCLUSIONS Inner-layer hub nodes of multiplex networks were preferentially vulnerable, and some inner-layer hub nodes would convert into inter-layer hub nodes in IBS patients. Besides, the inter-layer hub nodes might be influenced by IBS severity and therefore converted to general nodes.
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Affiliation(s)
- Nan Chen
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Guangyao Liu
- Department of Magnetic Resonance, Lanzhou University Second Hospital, Lanzhou, China
| | - Man Guo
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Yongchao Li
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Zhijun Yao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Bin Hu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China.,Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University and Institute of Semiconductors, Chinese Academy of Sciences, Lanzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Ministry of Education, Engineering Research Center of Open Source Software and Real-Time System (Lanzhou University), Lanzhou, China
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Li Y, McGrail DJ, Latysheva N, Yi S, Babu MM, Sahni N. Pathway perturbations in signaling networks: Linking genotype to phenotype. Semin Cell Dev Biol 2020; 99:3-11. [PMID: 29738884 PMCID: PMC6230320 DOI: 10.1016/j.semcdb.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/29/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023]
Abstract
Genes and gene products interact with each other to form signal transduction networks in the cell. The interactome networks are under intricate regulation in physiological conditions, but could go awry upon genome instability caused by genetic mutations. In the past decade with next-generation sequencing technologies, an increasing number of genomic mutations have been identified in a variety of disease patients and healthy individuals. As functional and systematic studies on these mutations leap forward, they begin to reveal insights into cellular homeostasis and disease mechanisms. In this review, we discuss recent advances in the field of network biology and signaling pathway perturbations upon genomic changes, and highlight the success of various omics datasets in unraveling genotype-to-phenotype relationships.
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Affiliation(s)
- Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natasha Latysheva
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Song Yi
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Mastroianno S, Palumbo P, Castellana S, Leone MP, Massaro R, Potenza DR, Mazza T, Russo A, Castori M, Carella M, Di Stolfo G. Double missense mutations in cardiac myosin-binding protein C and myopalladin genes: A case report with diffuse coronary disease, complete atrioventricular block, and progression to dilated cardiomyopathy. Ann Noninvasive Electrocardiol 2019; 25:e12687. [PMID: 31524317 DOI: 10.1111/anec.12687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/25/2022] Open
Abstract
Cardiomyopathies caused by double gene mutations are rare but conferred a remarkably increased risk of end-stage progression, arrhythmias, and poor outcome. Compound genetic mutations leading to complex phenotype in the setting of cardiomyopathies represent an important challenge in clinical practice, and genetic tests allow risk stratification and personalized clinical management of patients. We report a case of a 50-year-old woman with congestive heart failure characterized by dilated cardiomyopathy, diffuse coronary disease, complete atrioventricular block, and missense mutations in cardiac myosin-binding protein C (MYBPC3) and myopalladin (MYPN). We discuss the plausible role of genetic profile in phenotype determination.
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Affiliation(s)
- Sandra Mastroianno
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Pietro Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatic Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo-Istituto Mendel, Roma, Italy
| | - Maria Pia Leone
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Raimondo Massaro
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Domenico Rosario Potenza
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatic Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo-Istituto Mendel, Roma, Italy
| | - Aldo Russo
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Di Stolfo
- Cardiovascular Department, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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Korcsmaros T, Schneider MV, Superti-Furga G. Next generation of network medicine: interdisciplinary signaling approaches. Integr Biol (Camb) 2017; 9:97-108. [PMID: 28106223 DOI: 10.1039/c6ib00215c] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more. In terms of drug discovery, network medicine exploits our understanding of the network connectivity and signaling system dynamics to help identify optimal, often novel, drug targets. Contrary to initial expectations, however, network approaches have not yet delivered a revolution in molecular medicine. In this review, we propose that a key reason for the limited impact, so far, of network medicine is a lack of quantitative multi-disciplinary studies involving scientists from different backgrounds. To support this argument, we present existing approaches from structural biology, 'omics' technologies (e.g., genomics, proteomics, lipidomics) and computational modeling that point towards how multi-disciplinary efforts allow for important new insights. We also highlight some breakthrough studies as examples of the potential of these approaches, and suggest ways to make greater use of the power of interdisciplinarity. This review reflects discussions held at an interdisciplinary signaling workshop which facilitated knowledge exchange from experts from several different fields, including in silico modelers, computational biologists, biochemists, geneticists, molecular and cell biologists as well as cancer biologists and pharmacologists.
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Affiliation(s)
- Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK. and Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria and Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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