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Roca-Umbert A, Garcia-Calleja J, Vogel-González M, Fierro-Villegas A, Ill-Raga G, Herrera-Fernández V, Bosnjak A, Muntané G, Gutiérrez E, Campelo F, Vicente R, Bosch E. Human genetic adaptation related to cellular zinc homeostasis. PLoS Genet 2023; 19:e1010950. [PMID: 37747921 PMCID: PMC10553801 DOI: 10.1371/journal.pgen.1010950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/05/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023] Open
Abstract
SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans.
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Affiliation(s)
- Ana Roca-Umbert
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jorge Garcia-Calleja
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Marina Vogel-González
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandro Fierro-Villegas
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Ill-Raga
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Víctor Herrera-Fernández
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Anja Bosnjak
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Muntané
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Gutiérrez
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
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