Functional Studies: Ionomics and zinc transport


Multidimensional ionomic analysis: A number of zinc-related genes are known to be transcriptionally regulated by dietary components and others possess an expression QTL. Therefore, to test for functional diversity, mRNA expression analyses of the candidate genes were carried out in a collection of human kidney and liver tissue samples in which we had previously quantified the zinc concentrations. As an outcome we expect both a better functional characterization of particular variants and a better understanding of mRNA and protein expression related to trace element homeostasis in human liver and kidney samples. SNP genotyping of the samples could confirm and newly identify eQTLs as well as genes with mRNA expression levels that are correlated with tissue zinc concentration. In order to link the known and newly identified functional variants back to our evolutionary hypothesis, we are currently exploring their overlap with the genomic footprints of natural selection in diverse populations.

Figure: Currently I am analyzing multidimensional genomic data (mRNA expression, protein expression, genotypes and trace element concentrations) across 150 samples from liver. As a proof of concept, we confirmed with statistical signifance the known iron overload locus in the HFE gene (left side) and identify the genes MT2A  (red) and MT1H (blue) which show a correlation between mRNA expression and tissue zinc concentrations, including the expected plateau phase.


In a complementary approach, we have described the evolutionary history of a human zinc transporter (ZIP4, SLC39A4) using population genomic as well as functional approaches, e.g. cell transfection assays of putative functional variants (Engelken, Carnero et al., 2014 PLOS genetics in press) in collaboration with other research groups. Drawing from population genomics, ancient DNA research and in vitro cellular zinc uptake experiments, this exciting study related to the micronutrient zinc in Sub-Saharan African populations has emerged. Here, we characterized one of the strongest signals of positive selection worldwide (comparable in population differences to the Duffy Malaria resistance allele), mainly through coalescent simulations as well as extensive sampling of allele frequencies in worldwide populations . This genomic signal of positive selection had been overlooked so far as it was hidden by the effects of a recombination hotspot. Experimentally, an amino acid replacement (L372V) in a human intestinal zinc uptake transporter ZIP4 (SLC39A4) was shown to lead to reduced zinc uptake in the African isoform. Curiously, the same amino acid position harbors rare mutations for a heritable disease of extreme zinc deficiency (Acrodermatitis enteropathica). Now the jury is out for the next step, namely confirming the likely selective force and phenotypes in this adaptive event: Could this be resistance to malaria or some other pathogen? And in today´s worldwide populations, may this variant have an effect on organismal zinc levels?  Johannes Engelken, Elena Carnero and Elena Bosch from the Institute of Evolutionary Biology (CSIC-UPF) together with Ruben Vicente and Miguel A Valverde from the Molecular Physiology and Channelopathies Group (Universitat Pompeu Fabra) were the main participants in this interdisciplinary project.