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Trpchevska N, Freidin MB, Broer L, Oosterloo BC, Yao S, Zhou Y, Vona B, Bishop C, Bizaki-Vallaskangas A, Canlon B, Castellana F, Chasman DI, Cherny S, Christensen K, Concas MP, Correa A, Elkon R, Mengel-From J, Gao Y, Giersch ABS, Girotto G, Gudjonsson A, Gudnason V, Heard-Costa NL, Hertzano R, Hjelmborg JVB, Hjerling-Leffler J, Hoffman HJ, Kaprio J, Kettunen J, Krebs K, Kähler AK, Lallemend F, Launer LJ, Lee IM, Leonard H, Li CM, Lowenheim H, Magnusson PKE, van Meurs J, Milani L, Morton CC, Mäkitie A, Nalls MA, Nardone GG, Nygaard M, Palviainen T, Pratt S, Quaranta N, Rämö J, Saarentaus E, Sardone R, Satizabal CL, Schweinfurth JM, Seshadri S, Shiroma E, Shulman E, Simonsick E, Spankovich C, Tropitzsch A, Lauschke VM, Sullivan PF, Goedegebure A, Cederroth CR, Williams FMK, Nagtegaal AP, Nelis M, Mägi R, Esko T. Genome-wide association meta-analysis identifies 48 risk variants and highlights the role of the stria vascularis in hearing loss. Am J Hum Genet 2022; 109:1077-1091. [PMID: 35580588 PMCID: PMC9247887 DOI: 10.1016/j.ajhg.2022.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/15/2022] [Indexed: 02/08/2023] Open
Abstract
Hearing loss is one of the top contributors to years lived with disability and is a risk factor for dementia. Molecular evidence on the cellular origins of hearing loss in humans is growing. Here, we performed a genome-wide association meta-analysis of clinically diagnosed and self-reported hearing impairment on 723,266 individuals and identified 48 significant loci, 10 of which are novel. A large proportion of associations comprised missense variants, half of which lie within known familial hearing loss loci. We used single-cell RNA-sequencing data from mouse cochlea and brain and mapped common-variant genomic results to spindle, root, and basal cells from the stria vascularis, a structure in the cochlea necessary for normal hearing. Our findings indicate the importance of the stria vascularis in the mechanism of hearing impairment, providing future paths for developing targets for therapeutic intervention in hearing loss.
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Affiliation(s)
- Natalia Trpchevska
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Berthe C Oosterloo
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany; Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany; Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Charles Bishop
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Argyro Bizaki-Vallaskangas
- Department of Otolaryngology, University of Tampere, 33100 Tampere, Finland; Pirkanmaan Sairaanhoitopiiri, 33520 Tampere, Finland
| | - Barbara Canlon
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Fabio Castellana
- Unit of Data Sciences and Technology Innovation for Population Health, National Institute of Gastroenterology "Saverio de Bellis", Research Hospital, Castellana Grotte, 70124 Bari, Italy
| | - Daniel I Chasman
- Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Cherny
- Department of Anatomy and Anthropology and Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Kaare Christensen
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, 34127 Trieste, Italy
| | - Adolfo Correa
- Jackson Heart Study, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
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- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jonas Mengel-From
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Yan Gao
- Jackson Heart Study, The University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anne B S Giersch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, 34127 Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, 34139 Trieste, Italy
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland Baltimore, Baltimore, MD 21201, USA; Department of Anatomy and Neurobiology, University of Maryland Baltimore, Baltimore, MD 21201, USA; Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, MD 21201, USA
| | - Jacob V B Hjelmborg
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark
| | - Jens Hjerling-Leffler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Howard J Hoffman
- Division of Scientific Programs, Epidemiology and Statistics Program, National Institute on Deafness and Other Communications Disorders (NIDCD), NIH, Bethesda, MD 20892, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Johannes Kettunen
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90220 Oulu, Finland; Biocenter Oulu, University of Oulu, 90220 Oulu, Finland; Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Francois Lallemend
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program National Institute on Aging, Bethesda, MD 20892, USA
| | - I-Min Lee
- Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hampton Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA
| | - Chuan-Ming Li
- Division of Scientific Programs, Epidemiology and Statistics Program, National Institute on Deafness and Other Communications Disorders (NIDCD), NIH, Bethesda, MD 20892, USA
| | - Hubert Lowenheim
- Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cynthia C Morton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Manchester Centre for Audiology and Deafness, University of Manchester, Manchester M13 9PL, UK
| | - Antti Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA
| | | | - Marianne Nygaard
- The Danish Twin Registry, Department of Public Health, University of Southern Denmark, 5000 Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Sheila Pratt
- Department of Communication Science & Disorders, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicola Quaranta
- Otolaryngology Unit, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland
| | - Rodolfo Sardone
- Unit of Data Sciences and Technology Innovation for Population Health, National Institute of Gastroenterology "Saverio de Bellis", Research Hospital, Castellana Grotte, 70124 Bari, Italy
| | - Claudia L Satizabal
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of Population Health Sciences, University of Texas Health Sciences Center, San Antonio, TX 78229, USA
| | - John M Schweinfurth
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study, Framingham, MA 01702, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases and Department of Population Health Sciences, University of Texas Health Sciences Center, San Antonio, TX 78229, USA
| | - Eric Shiroma
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Baltimore, MD 21224, USA
| | - Eldad Shulman
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Eleanor Simonsick
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Christopher Spankovich
- Department of Otolaryngology and Communicative Sciences, The University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Anke Tropitzsch
- Department of Otolaryngology-Head & Neck Surgery, University of Tübingen Medical Center, 72076 Tübingen, Germany
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Genetics, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Andre Goedegebure
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Christopher R Cederroth
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177 Stockholm, Sweden; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, NG1 5DU Nottingham, UK; Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, NG7 2UH Nottingham, UK.
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Andries Paul Nagtegaal
- Department of Otorhinolaryngology, Erasmus Medical Center, 3015 CE Rotterdam, the Netherlands
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Aharonov R, Dinstag G, Shulman E, Elis E, Ben-Zvi D, Tirosh O, Hoang DT, SInha S, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Rajagopal PS, Gilbert MR, Aldape KD, Beker T, Ruppin E. ENLIGHT: Pancancer response prediction to targeted and immunotherapies via tumor transcriptomics. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e13556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13556 Background: Precision oncology is gradually advancing into mainstream clinical practice. Despite the significant recent growth in the number of approved biomarkers for immune and targeted therapies, demonstrating significant survival benefits, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers. Methods: We developed ENLIGHT - a transcriptomics-based computational platform that identifies and utilizes clinically relevant genetic interactions (GIs) to predict a patient’s response to cancer treatments. ENLIGHT markedly extends and improves upon SELECT, a previous GI-based framework for obtaining transcriptomics-based response biomarkers. In this study, we focus on three key translational aspects: (i) the number of drugs for which predictions can be obtained (ii) defining a biomarker-based test for Personalized Medicine (PM) that would identify favorable treatments for an individual; and (iii) Improving clinical trial design by excluding a sub-population of patients likely not to respond to the treatment. A key translational feature of the approach is that it does not require training on treatment response data. Thus, in addition to its ability to predict patients' response to approved and well-studied therapies, it can predict the response to new, unexplored treatments. Results: We first tested Enlight in the PM scenario, analyzing 21 patient cohorts from diverse indications, treated with a variety of targeted and immunotherapies. The ENLIGHT treatment matching score is associated with better response with an aggregate Odds Ratio (OR) of 2.59 (95% confidence interval [1.85, 3.55], p= 3.41 e-8). Applied to the WINTHER trial data, encompassing multiple indications and individualized treatments, ENLIGHT recommendations achieved a highly remarkable OR of 11.15 ([2.3, 54.5], p = 8 e-04), demonstrating ENLIGHT’s strong predictive power across a broad spectrum of treatments and cancer types. Second, using ENLIGHT to exclude patients from clinical trials increases the trial response rate, achieving more than 90% of the response rate attainable under an optimal exclusion strategy. Conclusions: ENLIGHT is a powerful transcriptomics-based precision oncology pipeline developed by Pangea Biomed that broadly predicts response to both extant and novel targeted and immune therapies in translationally oriented, clinical terms, going beyond case-specific biomarkers.
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Affiliation(s)
| | | | | | | | | | | | - Danh-Tai Hoang
- The Biological Data Science Institute, College of Science, The Australian National University, Canberra, Australia
| | | | - Andrea B. Apolo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - William L. Dahut
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Raanan Berger
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | | | | | - Fatima Karzai
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Padma Sheila Rajagopal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Mark R. Gilbert
- National Cancer Institute at the National Institutes of Health, Bethesda, MD
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