Browsing by Autor "Rasmus Nielsen"

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Erythroid and Cardiovascular High Altitude-Selected Haplotypes in Andean Aymaras and Tibetans
(Elsevier BV, 2017) Ricardo Amaru; Jihyun Song; N. Scott Reading; Victor R. Gordeuk; Teddy Quispe; Lorna G. Moore; Rasmus Nielsen; Josef T. Prchal
Abstract Humans migrating out of Africa encountered new conditions, including living at high altitude. Tibetans and Andean Aymaras have inhabited regions of 4,000 meters or more for ~44,000 and 14,000 years respectively (Hu et al, PLoS Genet 2017, Rademaker et al, Science 2014). There is a distinct difference in erythroid phenotypes: Aymaras are polycythemic at high altitude, while most Tibetans are not. Mutations providing an advantage in highlanders will improve fitness under hypoxic conditions,including modulation of erythropoiesis through the hypoxia-inducible factor (HIF) pathway. There are few shared, naturally-selected gene regions in Aymaras and Tibetans and these have different phenotypic associations (Bigham et al, Am J Hum Biol 2013). Aymara high-altitude selected haplotypes have not been published. Tibetan EPAS 1 (encoding HIF2a protein) haplotypes in part originated from ancient Denisovans and entered the Tibetan genome through introgression (Huerta-Sanchez et al, Nature 2014). Tibetan variant prolyl hydroxylase 2 (PHD2), a negative regulator of HIFs encoded by EGLN1 gene, encodes in cis both PHD2D4E and PHD2C127S which together have increased activity in hypoxia (Lorenzo et al, Nature Genetics 2014) and, together with a Tibetan EPAS 1 haplotype, protects from high altitude polycythemia (Tashi et al, JMM 2017). We and others previously identified other Tibetans haplotypes that are not unique but are enriched in Tibetans, including a “Tibetan” haplotype of PKLR encoding liver- and red cell-specific pyruvate kinase (PK) (Simonson et al, Science 2010, and Yi et al, Science 2010). We studied Tibetan-enriched haplotypes of EGLN1, EPAS1 and PKLR in 72 Bolivian Andean Aymaras, all residing at 4,000 m, and compared them with 347 Tibetans living at altitudes of 200 m and 4,300 m (Table). We genotyped PHD2D4E and PHD2C127S variants of EGLN1 and 10 Tibetan specific single nucleotide polymorphisms (SNPs) of EPAS1, 5 Denisovan and 5 non-Denisovan, each under different linkage disequilibrium (Hu et all, PLoS Genet 2017), 7 Tibetan enriched PKLR SNPs, and searched for Aymara selected variants by whole genome sequencing. The prevalence of the Tibetan-selected EGLN1 and EPAS1 haplotypes increased with increasing altitude of residence in Tibetans, suggesting a continuous evolutionary advantage (Tashi et al, JMM 2017). Aymaras did not have the PHD2D4E haplotype, and PHD2C127S was found at lower prevalence in heterozygote form. Aymaras shared two of five non-Denisovan EPAS1 SNPs selected in Tibetans; one, rs130005507 G allele, had a similar prevalence to Tibetans, but another, rs142764723 C allele, had a lower prevalence. We report that >90% of Tibetans and ~50% of Aymaras, but only ~10% of Europeans, have the “Tibetan ” PKLR haplotype. Aymara females with homozygous PKLR haplotypes have lower hemoglobins than heterozygotes (p=0.022). Further, the PKLR transcript in reticulocytes decreases with increasing altitude and this progressive decrease is even more pronounced in the “Tibetan” haplotype. We found Aymaras' selected haplotypes encoding BRINP3, NOS2, TBX5 ; these genes are associated with cardiovascular development and function but not hypoxia sensing. They are not enriched in Tibetans. We conclude that Aymara highlanders do not have the Tibetan PHD2D4E mutation or Denisovan-like EPAS1 variants. Furthermore, they share only two of five Tibetan non- Denisovan EPAS1 variants. The absence of these variants in Aymaras supports that Tibetan and Aymara high altitude inhabitants do not have the same ancestry, that they developed different evolutionary adaptations (Bigham et al, Am J Hum Biol 2013), and that Tibetans' EGLN1 and EPAS1 mutations are unique to that part of the world. We hypothesize that decreased PK enzyme activity would be expected to increase 2,3-diphosphoglycerate (2,3-DPG) (as is shown in people with PK enzyme deficiency) and thus be beneficial to high altitude adaptation by progressively augmenting tissue oxygen delivery with increasing altitude. Based on its association with lower hemoglobin in Aymara females, the selected “Tibetan” PKLR haplotype, present in about half of Aymaras, may contribute to their hypoxic adaptation. Additional evaluation of evolutionary selected genes including PKLR, BRINP3, NOS 2, and TBX5 and their functional consequences are in progress with Aymaras living at El Alto (4,150 m), Cochabamba (2,500 m) and Santa Cruz, (416m), Bolivia. Download : Download high-res image (320KB) Download : Download full-size image Disclosures No relevant conflicts of interest to declare.
Novel Form of Alternative Splicing of NFKB1. Its Role in Polycythemia and Adaptation to High Altitude in Andean Aymara
(Elsevier BV, 2018) Jihyun Song; Seonggyun Han; Ricardo Amaru; Teddy Quispe; Dongwook Kim; Jacob E. Crawford; Josef Stehlik; Rasmus Nielsen; Younghee Lee; Josef T. Prchal
Abstract Evolutionary adaptations to high altitude in Tibetans, Ethiopians, and Andean populations of South America have shown that Tibetans and Ethiopians have normal hemoglobin %, while most of Aymara and Quechua of the Andean highlands are polycythemic. Whole genome sequencing (WGS) in Quechua identified enriched SENP1 and ANP32D genes correlating with polycythemia (Zhou et al, Am J Hum Genet. 2013 Sep 5; 93(3): 452-462) but these genes were neither enriched nor segregated with polycythemia in Aymara. Instead, we identified that genes enriched in Aymara are related to regulation of cardiovascular development in high-altitude adapted Andeans, BRINP3, NOS2, and TBX5 (Crawford et al, Am J Hum Genet. 2017 Nov 2;101(5):752-767). To further search for Aymara propensity to polycythemia, we analyzed transcriptomes from Aymara and Europeans living in La Paz, Bolivia (3,639-4,150m) from limited amount of peripheral blood reticulocytes, platelets and granulocytes, but only granulocyte RNA was adequate for unbiased whole transcriptome analyses. In Aymaras, 2,585 genes were upregulated and 365 genes were downregulated (Adjp<0.05, fold difference <-2.0, and >2.0). Many of these modulated genes are involved in inflammatory pathways including B-cell activation (FDR=0.005) and NF-κB signaling pathway (FDR=0.011). We then analyzed differential exon usage in the transcriptome and identified 2,475 genes with alternative splicing events, comprising 1,568 exon skipping, 485 intron retention, 175 alternative 3' splice sites, 144 alternative 5' splice sites, and 902 mutually exclusive exons. These alternative spliced genes were also overrepresented in inflammatory pathways (TNF receptor, IL-1 and IL-23 mediated signaling, and NF-κB signaling). Notably we detected the previously unreported NFKB1 alternate transcripts skipping exon 4 or 5, which lead to the out-of-framed NFKB1 mRNA, generating the truncated nonfunctional NF-κB protein (Figure). Inflammation is a potent suppressor of erythropoiesis and the NF-κB is transcriptional regulator of plethora of inflammatory genes. Further, NF-κB also interacts with erythropoiesis-regulators, hypoxia-inducible factors (HIFs). By the integrative analysis of the Aymara transcriptome and WGS, we identified 46 NFKB1 splicing quantitative trait loci (sQTLs). Among these 46 sQTLs, five single nucleotide polymorphisms (SNP) were in high linkage disequilibrium, and two (rs230511 and rs230504) were more enriched in Aymara (allele frequency: 0.878) (Figure) and within a genomic region where Andeans are genetically differentiated from lowland Native Americans (peak FST = 0.37, peak PBSn1 = 0.31). These sQTLs rs230511 and rs230504 were corelated with two functionally important exon skipping (exon 4 and 5) in NFKB1 as described above. Furthermore, these two SNPs were correlated with higher hemoglobin levels and lower leukocytes; the wild-type NFKB1 transcript inversely correlated with hemoglobin%. We report Aymara have differentially expressed and alternatively spliced transcripts of genes modulating inflammation, particularly NFKB1. This Aymara enriched NFKB1 haplotype variant stands out as a major cause of Aymara adaptation to high altitude, as this truncated nonfunctional NF-κB variant peptide correlates with higher hemoglobin, lower leukocytes and suppresses inflammation. These data indicate that NFKB1 SNPs enriched in Aymara are associated with alternative spliced NFKB1 transcripts which contribute to polycythemia in Aymara. Further evaluation of NF-κB and HIFs' transcriptional activity and their correlation with inflammatory makers, hepcidin and erythroferrone in Aymara and Europeans living at the same high altitude is under way. JS and SH contributed equally to this work. YL and JTP act as equivalent co-senior authors. Figure. Figure. Disclosures No relevant conflicts of interest to declare.