title: Allelic mRNA expression imbalance in C-type lectins reveals a frequent regulatory SNP in the human surfactant protein A (SP-A) gene.
abstract: Genetic variation in C-type lectins influences infectious disease susceptibility but remains poorly understood. We used allelic mRNA expression imbalance (AEI) technology for surfactant protein (SP)-A1, SP-A2, SP-D, dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN), macrophage mannose receptor (MRC1) and Dectin-1, expressed in human macrophages and/or lung tissues. Frequent AEI, an indicator of regulatory polymorphisms, was observed in SP-A2, SP-D and DC-SIGN. AEI was measured for SP-A2 in 38 lung tissues using four marker single-nucleotide polymorphisms (SNPs) and was confirmed by next-generation sequencing of one lung RNA sample. Genomic DNA at the SP-A2 DNA locus was sequenced by Ion Torrent technology in 16 samples. Correlation analysis of genotypes with AEI identified a haplotype block, and, specifically, the intronic SNP rs1650232 (30% minor allele frequency); the only variant consistently associated with an approximately twofold change in mRNA allelic expression. Previously shown to alter a NAGNAG splice acceptor site with likely effects on SP-A2 expression, rs1650232 generates an alternative splice variant with three additional bases at the start of exon 3. Validated as a regulatory variant, rs1650232 is in partial linkage disequilibrium with known SP-A2 marker SNPs previously associated with risk for respiratory diseases including tuberculosis. Applying functional DNA variants in clinical association studies, rather than marker SNPs, will advance our understanding of genetic susceptibility to infectious diseases.
authors: Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, College of Medicine, Columbus, OH 43210, USA.
authors: A K
authors: AK
authors: Azad
authors: A
authors: A
authors: Curtis
authors: A
authors: A
authors: Papp
authors: A
authors: A
authors: Webb
authors: D
authors: D
authors: Knoell
authors: W
authors: W
authors: Sadee
authors: L S
authors: LS
authors: Schlesinger
mesh_terms: D022981:Allelic Imbalance; D001483:Base Sequence; D015815:Cell Adhesion Molecules / Q000235:genetics; D002478:Cells, Cultured; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D037181:Lectins, C-Type / Q000235:genetics*; D015810:Linkage Disequilibrium; D008168:Lung / Q000378:metabolism*; D008264:Macrophages / Q000378:metabolism*; D008562:Membrane Glycoproteins; D020641:Polymorphism, Single Nucleotide; D037662:Pulmonary Surfactant-Associated Protein A / Q000235:genetics*; D037663:Pulmonary Surfactant-Associated Protein D / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics*; D011956:Receptors, Cell Surface / Q000235:genetics; D011971:Receptors, Immunologic / Q000235:genetics; D017423:Sequence Analysis, RNA; D014376:Tuberculosis / Q000235:genetics; D000099215:DC-Specific ICAM-3 Grabbing Nonintegrin; D000099181:Dectin-1
chemical_list: D015815:Cell Adhesion Molecules; D037181:Lectins, C-Type; D008562:Membrane Glycoproteins; D037662:Pulmonary Surfactant-Associated Protein A; D037663:Pulmonary Surfactant-Associated Protein D; D012333:RNA, Messenger; D011956:Receptors, Cell Surface; D011971:Receptors, Immunologic; D000099215:DC-Specific ICAM-3 Grabbing Nonintegrin; C546929:CLEC7A protein, human; D000099181:Dectin-1; C573543:MRC1 protein, human