Population-specific variations in KCNH2 predispose patients to delayed ventricular repolarization upon dihydroartemisinin-piperaquine therapy

Funding Information: The study was supported by European and Developing Countries Clinical Trial Partnership (grant number RIA2017T-2018), Medicines for Malaria Venture (Geneva, Switzerland), UK Medical Research Council, Swedish International Development Cooperation Agency, German Ministry for Education and Research, University Claude Bernard (Lyon, France), Malaria Research and Training Centre (Bamako, Mali), Centre National de Recherche et de Formation sur le Paludisme (Burkina Faso), Institut de Recherche en Sciences de la Sant. (Bobo-Dioulasso, Burkina Faso), and Centre National de Formation et de Recherche en Sant. Rurale (Republic of Guinea). In addition, the authors received support from the Swedish Research Council (grant numbers 2019-01837, 2021-02801, 2021-05666, and 2021-06048), the Grants, Innovation and Product Development Unit of the South African Medical Research Council with funds received from Novartis and GSK R&D for Project Africa GRADIENT (grant numbers GSKNVS2/202101/004), the Robert Bosch Foundation, Stuttgart, Germany, and Conselho Nacional de Desenvolvimento Cient\u00EDfico e Tecnol\u00F3gico (CNPq), Brazil (grant number 200075/2022\u20135). T.N.S. is a CNPq Research Productivity Fellow. M.D.C. performed sequencing, analyzed the data, and conducted statistical analyses. Y.Z. conducted computational variant analyses. M.M.T. was involved in the acquisition of drug concentrations. A.D. and S.S. contributed to bioinformatics analyses. N.O. was the cardiologist responsible for cardiac toxicity assessment. A.H.T, M.L.A., B.F., and I.S. oversaw clinical patient recruitment and management. A.A.D. coordinated and oversaw the WANECAM study and critically reviewed the manuscript. P.J.G. and V.M.L designed and supervised the study. M.D.C. and V.M.L. wrote the manuscript. All authors read, reviewed, and approved of the final version of the manuscript. Funding Information: The study was supported by European and Developing Countries Clinical Trial Partnership (grant number RIA2017T-2018), Medicines for Malaria Venture (Geneva, Switzerland), UK Medical Research Council, Swedish International Development Cooperation Agency, German Ministry for Education and Research, University Claude Bernard (Lyon, France), Malaria Research and Training Centre (Bamako, Mali), Centre National de Recherche et de Formation sur le Paludisme (Burkina Faso), Institut de Recherche en Sciences de la Sant. (Bobo-Dioulasso, Burkina Faso), and Centre National de Formation et de Recherche en Sant. Rurale (Republic of Guinea). In addition, the authors received support from the Swedish Research Council (grant numbers 2019-01837, 2021-02801, 2021-05666, and 2021-06048), the Grants, Innovation and Product Development Unit of the South African Medical Research Council with funds received from Novartis and GSK R&D for Project Africa GRADIENT (grant numbers GSKNVS2/202101/004), the Robert Bosch Foundation, Stuttgart, Germany, and Conselho Nacional de Desenvolvimento e Tecnol\u00F3gico (CNPq), Brazil (grant number 200075/2022\u20135). T.N.S. is a CNPq Research Productivity Fellow. Publisher Copyright: Copyright © 2024 Camara et al.Dihydroartemisinin-piperaquine is efficacious for the treatment of uncomplicated malaria and its use is increasing globally. Despite the positive results in fighting malaria, inhibition of the Kv11.1 channel (hERG; encoded by the KCNH2 gene) by piperaquine has raised concerns about cardiac safety. Whether genetic factors could modulate the risk of piperaquine-mediated QT prolongations remained unclear. Here, we first profiled the genetic landscape of KCNH2 variability using data from 141,614 individuals. Overall, we found 1,007 exonic variants distributed over the entire gene body, 555 of which were missense. By optimizing the gene-specific parametrization of 16 partly orthogonal computational algorithms, we developed a KCNH2-specific ensemble classifier that identified a total of 116 putatively deleterious missense variations. To evaluate the clinical relevance of KCNH2 variability, we then sequenced 293 Malian patients with uncomplicated malaria and identified 13 variations within the voltage sensing and pore domains of Kv11.1 that directly interact with channel blockers. Cross-referencing of genetic and electrocardiographic data before and after piperaquine exposure revealed that carriers of two common variants, rs1805121 and rs41314375, experienced significantly higher QT prolongations (ΔQTc of 41.8 ms and 61 ms, respectively, vs 14.4 ms in controls) with more than 50% of carriers having increases in QTc >30 ms. Furthermore, we identified three carriers of rare population-specific variations who experienced clinically relevant delayed ventricular repolarization. Combined, our results map population-scale genetic variability of KCNH2 and identify genetic biomarkers for piperaquine-induced QT prolongation that could help to flag at-risk patients and optimize efficacy and adherence to antimalarial therapy.publishersversionpublishe

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