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Carcamo-Orive I, Henrion MYR, Zhu K, Beckmann ND, Cundiff P, Moein S, Zhang Z, Alamprese M, D’Souza SL, Wabitsch M, Schadt EE, Quertermous T, Knowles JW, Chang R. Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PLoS Comput Biol 2020; 16:e1008491. [PMID: 33362275 PMCID: PMC7790417 DOI: 10.1371/journal.pcbi.1008491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/07/2021] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. Thus, new approaches are necessary to explore the genetic architecture of insulin resistance. To that end, we generated an iPSC library across the spectrum of insulin sensitivity in humans. RNA-seq based analysis of 310 induced pluripotent stem cell (iPSC) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive iPSC lines. Analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. Functional validation in human adipocytes and skeletal muscle cells (SKMCs) confirmed the relevance of the key driver candidate genes for insulin responsiveness. Insulin resistance is characterized by a defective response (“resistance”) to normal insulin concentrations to uptake the glucose present in the blood, and is the underlying condition that leads to type 2 diabetes (T2D) and increases the risk of cardiovascular disease. It is estimated that 25–33% of the US population are insulin resistant enough to be at risk of serious clinical consequences. For more than a decade, large population studies have tried to discover the genes that participate in the development of insulin resistance, but without much success. It is now increasingly clear that the complex genetic nature of insulin resistance requires novel approaches centered in patient specific cellular models. To fill this gap, we have generated an induced pluripotent stem cell (iPSC) library from individuals with accurate measurements of insulin sensitivity, and performed gene expression and key driver analyses. Our work demonstrates that iPSCs can be used as a revolutionary technology to model insulin resistance and to discover key genetic drivers. Moreover, they can develop our basic knowledge of the disease, and are ultimately expected to increase the therapeutic targets to treat insulin resistance and type 2 diabetes.
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Affiliation(s)
- Ivan Carcamo-Orive
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Marc Y. R. Henrion
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
- Malawi—Liverpool—Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kuixi Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Paige Cundiff
- Vertex Pharmaceuticals, Boston, Massachusetts, United States of America
| | - Sara Moein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Zenan Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Melissa Alamprese
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Sunita L. D’Souza
- Department of Cellular, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology, Ulm University, Ulm, Germany
| | - Eric E. Schadt
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Thomas Quertermous
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
| | - Joshua W. Knowles
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Rui Chang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
- INTelico Therapeutics LLC, Tucson, Arizona, United States of America
- * E-mail: (ICO); (JWK); (RC)
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