Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

Benjamin S Glicksberg; Letizia Amadori; Nicholas K Akers; Katyayani Sukhavasi; Oscar Franzén; Li Li; Gillian M Belbin; Kristin L Ayers; Khader Shameer; Marcus A Badgeley; Kipp W Johnson; Ben Readhead; Bruce J Darrow; Eimear E Kenny; Christer Betsholtz; Raili Ermel; Josefin Skogsberg; Arno Ruusalepp; Eric E Schadt; Joel T Dudley; Hongxia Ren; Jason C Kovacic; Chiara Giannarelli; Shuyu D Li; Johan L M Björkegren; Rong Chen

doi:10.1186/s12920-019-0542-3

Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

BMC Med Genomics. 2019 Jul 25;12(Suppl 6):108. doi: 10.1186/s12920-019-0542-3.

Authors

Benjamin S Glicksberg^{1

2

3}, Letizia Amadori^{1

4}, Nicholas K Akers¹, Katyayani Sukhavasi⁵, Oscar Franzén^{1

6

7}, Li Li^{1

2}, Gillian M Belbin^{1

8}, Kristin L Ayers^{1

9}, Khader Shameer^{1

2}, Marcus A Badgeley^{1

2}, Kipp W Johnson^{1

2}, Ben Readhead^{1

2}, Bruce J Darrow⁴, Eimear E Kenny^{8

10}, Christer Betsholtz¹¹, Raili Ermel¹², Josefin Skogsberg¹³, Arno Ruusalepp^{6

11}, Eric E Schadt^{1

2

6

9}, Joel T Dudley^{1

2

14}, Hongxia Ren¹⁵, Jason C Kovacic⁴, Chiara Giannarelli^{1

4}, Shuyu D Li^{16

17}, Johan L M Björkegren^{18

19

20

21}, Rong Chen^{22

23}

Affiliations

¹ Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
² The Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
³ Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, 94158, CA, USA.
⁴ Cardiovascular Research Center and Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
⁵ Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia.
⁶ Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden.
⁷ Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Novum, 14157, Huddinge, Sweden.
⁸ Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
⁹ Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA.
¹⁰ Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
¹¹ Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden.
¹² Department of Cardiac Surgery, Tartu University Hospital, 1a Ludwig Puusepa Street, 50406, Tartu, Estonia.
¹³ Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden.
¹⁴ Department of Health Policy and Research, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
¹⁵ Department of Pediatrics, Herman B Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Stark Neurosciences Research Institute, Indiana University, 635 Barnhill Dr., MS2049, Indianapolis, IN, 46202, USA.
¹⁶ Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. shuyudan.li@mssm.edu.
¹⁷ Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA. shuyudan.li@mssm.edu.
¹⁸ Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. johan.bjorkegren@mssm.edu.
¹⁹ Department of Pathophysiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Biomeedikum, Ravila 19, 50411, Tartu, Estonia. johan.bjorkegren@mssm.edu.
²⁰ Clinical Gene Networks AB, Jungfrugatan 10, 114 44, Stockholm, Sweden. johan.bjorkegren@mssm.edu.
²¹ Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset Huddinge, 141 86, Stockholm, Sweden. johan.bjorkegren@mssm.edu.
²² Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. rong.chen@mssm.edu.
²³ Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA. rong.chen@mssm.edu.

Abstract

Background: Genetic loss-of-function variants (LoFs) associated with disease traits are increasingly recognized as critical evidence for the selection of therapeutic targets. We integrated the analysis of genetic and clinical data from 10,511 individuals in the Mount Sinai BioMe Biobank to identify genes with loss-of-function variants (LoFs) significantly associated with cardiovascular disease (CVD) traits, and used RNA-sequence data of seven metabolic and vascular tissues isolated from 600 CVD patients in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study for validation. We also carried out in vitro functional studies of several candidate genes, and in vivo studies of one gene.

Results: We identified LoFs in 433 genes significantly associated with at least one of 10 major CVD traits. Next, we used RNA-sequence data from the STARNET study to validate 115 of the 433 LoF harboring-genes in that their expression levels were concordantly associated with corresponding CVD traits. Together with the documented hepatic lipid-lowering gene, APOC3, the expression levels of six additional liver LoF-genes were positively associated with levels of plasma lipids in STARNET. Candidate LoF-genes were subjected to gene silencing in HepG2 cells with marked overall effects on cellular LDLR, levels of triglycerides and on secreted APOB100 and PCSK9. In addition, we identified novel LoFs in DGAT2 associated with lower plasma cholesterol and glucose levels in BioMe that were also confirmed in STARNET, and showed a selective DGAT2-inhibitor in C57BL/6 mice not only significantly lowered fasting glucose levels but also affected body weight.

Conclusion: In sum, by integrating genetic and electronic medical record data, and leveraging one of the world's largest human RNA-sequence datasets (STARNET), we identified known and novel CVD-trait related genes that may serve as targets for CVD therapeutics and as such merit further investigation.

Keywords: Cardiovascular traits; Electronic Medical Records; Genetic association; Integrative data analysis; Loss-of-function variant; Target identification and validation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cardiovascular Diseases / blood
Cardiovascular Diseases / genetics*
Cholesterol / blood
Genomics*
Genotype
Humans
Mutation*
Triglycerides / blood

Substances

Triglycerides
Cholesterol

Abstract

Publication types

MeSH terms

Substances

Grants and funding