Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies

Charli E Harlow; Josan Gandawijaya; Rosemary A Bamford; Emily-Rose Martin; Andrew R Wood; Peter J van der Most; Toshiko Tanaka; Hampton L Leonard; Amy S Etheridge; Federico Innocenti; Robin N Beaumont; Jessica Tyrrell; Mike A Nalls; Eleanor M Simonsick; Pranav S Garimella; Eric J Shiroma; Niek Verweij; Peter van der Meer; Ron T Gansevoort; Harold Snieder; Paul J Gallins; Dereje D Jima; Fred Wright; Yi-Hui Zhou; Luigi Ferrucci; Stefania Bandinelli; Dena G Hernandez; Pim van der Harst; Vickas V Patel; Dawn M Waterworth; Audrey Y Chu; Asami Oguro-Ando; Timothy M Frayling

doi:10.1016/j.ajhg.2022.08.004

Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies

Am J Hum Genet. 2022 Sep 1;109(9):1638-1652. doi: 10.1016/j.ajhg.2022.08.004.

Authors

Charli E Harlow¹, Josan Gandawijaya¹, Rosemary A Bamford¹, Emily-Rose Martin¹, Andrew R Wood¹, Peter J van der Most², Toshiko Tanaka³, Hampton L Leonard⁴, Amy S Etheridge⁵, Federico Innocenti⁶, Robin N Beaumont¹, Jessica Tyrrell¹, Mike A Nalls⁴, Eleanor M Simonsick³, Pranav S Garimella⁷, Eric J Shiroma⁸, Niek Verweij⁹, Peter van der Meer⁹, Ron T Gansevoort¹⁰, Harold Snieder², Paul J Gallins¹¹, Dereje D Jima¹², Fred Wright¹¹, Yi-Hui Zhou¹¹, Luigi Ferrucci³, Stefania Bandinelli¹³, Dena G Hernandez¹⁴, Pim van der Harst¹⁵, Vickas V Patel¹⁶, Dawn M Waterworth¹⁶, Audrey Y Chu¹⁷, Asami Oguro-Ando¹⁸, Timothy M Frayling¹⁹

Affiliations

¹ University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK.
² University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen 9713, the Netherlands.
³ Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA.
⁴ Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA.
⁵ Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
⁶ AbbVie Inc., 1000 Gateway Boulevard, South San Francisco, CA 94080, USA.
⁷ Division of Nephrology-Hypertension, University of California San Diego, San Diego, CA, USA.
⁸ Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD 20892, USA.
⁹ University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713, the Netherlands.
¹⁰ University of Groningen, University Medical Center Groningen, Department of Nephrology, Groningen 9713, the Netherlands.
¹¹ Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA.
¹² Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA.
¹³ Geriatric Unit, Azienda Sanitaria Firenze, Florence 50134, Italy.
¹⁴ Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA.
¹⁵ Department of Cardiology, University Medical Center Utrecht, Utrecht 3584, the Netherlands.
¹⁶ GlaxoSmithKline, Collegeville, PA 19426, USA.
¹⁷ GlaxoSmithKline, Boston, MA 02140, USA.
¹⁸ University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK. Electronic address: a.oguro-ando@exeter.ac.uk.
¹⁹ University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK. Electronic address: t.m.frayling@exeter.ac.uk.

Abstract

Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) are currently under clinical development for treating anemia in chronic kidney disease (CKD), but it is important to monitor their cardiovascular safety. Genetic variants can be used as predictors to help inform the potential risk of adverse effects associated with drug treatments. We therefore aimed to use human genetics to help assess the risk of adverse cardiovascular events associated with therapeutically altered EPO levels to help inform clinical trials studying the safety of HIF-PHIs. By performing a genome-wide association meta-analysis of EPO (n = 6,127), we identified a cis-EPO variant (rs1617640) lying in the EPO promoter region. We validated this variant as most likely causal in controlling EPO levels by using genetic and functional approaches, including single-base gene editing. Using this variant as a partial predictor for therapeutic modulation of EPO and large genome-wide association data in Mendelian randomization tests, we found no evidence (at p < 0.05) that genetically predicted long-term rises in endogenous EPO, equivalent to a 2.2-unit increase, increased risk of coronary artery disease (CAD, OR [95% CI] = 1.01 [0.93, 1.07]), myocardial infarction (MI, OR [95% CI] = 0.99 [0.87, 1.15]), or stroke (OR [95% CI] = 0.97 [0.87, 1.07]). We could exclude increased odds of 1.15 for cardiovascular disease for a 2.2-unit EPO increase. A combination of genetic and functional studies provides a powerful approach to investigate the potential therapeutic profile of EPO-increasing therapies for treating anemia in CKD.

Keywords: CRISPR-Cas9; anaemia in chronic kidney disease; cardiovascular disease risk; drug-target mendelian randomization; functional genomics; functional validation; gene editing; genome-wide association study; mendelian randomization; population studies; statistical genetics.

Publication types

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

MeSH terms

Anemia* / drug therapy
Anemia* / genetics
Coronary Artery Disease* / genetics
Genome-Wide Association Study
Humans
Mendelian Randomization Analysis
Myocardial Infarction* / genetics
Renal Insufficiency, Chronic* / genetics

Abstract

Publication types

MeSH terms

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