Signatures of evolutionary adaptation in quantitative trait loci influencing trace element homeostasis in liver
Open accessAbstract
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.
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Three SNPs in the 3' flanking region of SLC30A9 (rs2880666, rs6447133, rs7659700) have been previously identified as QTLs influencing zinc content in the liver and are in moderate linkage disequilibrium (0.66 < r2 < 0.76) with rs1047626.
“three SNPs in the 3’ flanking region of the SLC30A9 gene (rs2880666, rs6447133, rs7659700) have been previously identified as QTLs influencing zinc content in the liver [23] and they are found in moderate linkage disequilibrium (0.66 < r2 < 0.76) with rs1047626”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [23]
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Sabidó, E., Wu, Y., Borrego, L. B., Porstmann, T., Chang, C.-Y., Vitek, O., Stoffel, M., & Aebersold, R. H. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.36 · Cited by 36 · see citing works
Self-citationNatural selection on HFE in Asian populations contributes to enhanced non-heme iron absorption
Ye, K., Cao, C. Q., Lin, X., O'Brien, K. O., & Gu, Z. (2015) · BMC Genetics · doi:10.1186/s12863-015-0223-y · Cited by 31 · see citing works
Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis
Benyamin, B., Esko, T., Ried, J. S., Radhakrishnan, A., Vermeulen, S. H., Traglia, M., Gögele, M., Anderson, D., Broer, L., Podmore, C., et al. (2014) · Nature Communications · doi:10.1038/ncomms5926 · Cited by 30 · see citing works
Gautrey, H., Nicol, F., Sneddon, A. A., et al. (2011) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2011.03.016 · Cited by 29 · see citing works
Zhang, C., Li, J., Tian, L., Lu, D., Yuan, K., Yuan, Y., & Xu, S. (2015) · Scientific Reports · doi:10.1038/srep09658 · Cited by 27 · see citing works
Savas, S., Briollais, L., Ibrahim-zada, I., Jarjanazi, H., Choi, Y., Musquera, M., Fleshner, N. E., Venkateswaran, V., & Özçelik, H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012601 · Cited by 21 · see citing works
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Rye, M. S., Wiertsema, S. P., Scaman, E. S. H., Thornton, R. B., Francis, R. W., Vijayasekaran, S., Coates, H. L. C., Jamieson, S. E., & Blackwell, J. M. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.03.023 · Cited by 9 · see citing works
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Costas, J. (2018) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32545 · Cited by 58 · see citing works
Human genetic adaptation related to cellular zinc homeostasis
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., et al. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010950 · Cited by 8 · see citing works
Self-citation
- Authors
- Engelken, J., Espadas, G., Mancuso, F. M., Bonet, N., Scherr, A.-L., Jímenez-Álvarez, V., Codina-Solà, M., Medina-Stacey, D., Spataro, N., Stoneking, M., Calafell, F., Sabidó, E., & Bosch, E.
- Affiliations
- Universitat Pompeu Fabra (ES)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Sabidó, Eduard
- Bosch, Elena
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-17
- Volume
- 33
- Issue
- 3
- Pages
- 738-754
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC4760079
- OpenAlex
- W2248694846
- Cited by
- 31
- References
- 92
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 2 · 2023: 6 · 2022: 3 · 2021: 3 · 2020: 3 · 2019: 3 · 2018: 1 · 2017: 2 · 2016: 3
- FWCI
- 1.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by-nc)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc)
- Funders
- Volkswagen Foundation
- Generalitat de Catalunya (2009SGR, 2014SGR)
- Instituto de Salud Carlos III (PT13/0001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Nursing › Nutrition and Dietetics › Trace Elements in Health
- Health Sciences › Medicine › Hematology › Iron Metabolism and Disorders
- Keywords
- trace element homeostasis, liver, quantitative trait loci, expression QTL, single nucleotide polymorphisms, HFE gene, C282Y mutation, iron metabolism, selenium, metallothionein, GPX2, glutathione peroxidase 1, SELENBP1, SLC39A8, selective sweeps, genetic differentiation, human adaptation, regulatory variants
- MeSH terms
- Adaptation, Biological, Adult, Alleles, Biological Evolution, Female, Gene Frequency, Genotype, Homeostasis, Humans, Liver, Male, Metals, Middle Aged, Phenotype, Selection, Genetic, Trace Elements, Genetic Variation, Cluster Analysis, Evolution, Molecular, Proteome, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Proteomics, Genetic Association Studies, Transcriptome
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