Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans

• Published in: Genome Biology Vol. 17; no. 1; p. 246
• Main Authors: Sams, Aaron J, Dumaine, Anne, Nédélec, Yohann, Yotova, Vania, Alfieri, Carolina, Tanner, Jerome E, Messer, Philipp W, Barreiro, Luis B
• Format: Journal Article
• Language: English
• Published: England BioMed Central 29.11.2016
• Subjects: 2',5'-Oligoadenylate Synthetase - genetics; Alternative splicing; Animals; Deoxyribonucleic acid; DNA; Evolution; Evolution, Molecular; Gene Expression Regulation, Enzymologic; Gene regulation; Genealogy; Genes; Genome, Human; Genomes; Haplotypes; Haplotypes - genetics; Hepatitis; Homo neanderthalensis; Humans; Hypotheses; Immune response; Immunity, Innate - genetics; Infections - genetics; Infections - immunology; Infections - pathology; Innate immunity; Isoforms; Neanderthals - genetics; Neanderthals - immunology; Neutrality; Polymorphism, Single Nucleotide; Population; Positive selection; Protein Isoforms - genetics; Protein Isoforms - immunology; Selection, Genetic - genetics; Selection, Genetic - immunology; Transcription; Viral infections; Viruses; West Nile virus; Eurasia; Africa; Introgression; Innate immunity; Natural selection
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-016-1098-6

The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2. We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.