HIF-1 regulates heritable variation and allele expression phenotypes of the macrophage immune response gene SLC11A1 from a Z-DNA–forming microsatellite

Abstract

The Ity/Lsh/Bcg locus encodes the macrophage protein Slc11a1/Nramp1, which protects inbred mice against infection by diverse intracellular pathogens including Leishmania, Mycobacterium, and Salmonella. Human susceptibility to infectious and inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and tuberculosis, shows allelic association with a highly polymorphic regulatory, Z-DNA-forming microsatellite of (GT/AC) n dinucleotides within the proximal SLC11A1 promoter. We surmised that cis-acting allelic polymorphisms may underlie heritable differences in SLC11A1 expression and phenotypic variation in disease risk. However, it is unclear what may underlie such variation in SLC11A1 allele expression. Here we show that hypoxia-inducible Factor 1 (HIF-1) regulates allelic variation in SLC11A1 expression by binding directly to the microsatellite during macrophage activation by infection or inflammation. Targeted Hif-1␣ ablation in murine macrophages attenuated Slc11a11 expression and responsiveness to S typhimurium infection. Our data also showed that HIF-1 may be functionally linked to complex prototypical inflammatory diseases associated with certain SLC11A1 alleles. As these alleles are highly polymorphic, our finding suggests that HIF-1 may influence heritable variation in SLC11A1-dependent innate resistance to infection and inflammation within and between populations. This report also suggests that microsatellites may play critical roles in the directional evolution of complex heritable traits by regulating gene expression phenotypes. IntroductionA genetic basis for resistance to infection by intracellular pathogens was proposed several years ago. [1][2][3][4][5][6] This concept was confirmed upon the positional cloning of the dominant autosomal gene Ity/Lsh/Bcg based on its ability to confer on inbred mice an innate resistance to infection by diverse intracellular pathogens. 7 These include Salmonella typhimurium, 2 Leishmania donovani, 3 and some species of Mycobacterium such as M bovis 5 and M intracellulare. 8 Targeted ablation of Ity/Lsh/ Bcg 9 or allelic exchange in susceptible mice 10 confirmed its requirement for resistance to infection. Ity/Lsh/Bcg encodes the phagocyte-specific solute carrier 11a1 protein Slc11a1 (formerly Nramp1), 11-13 which restricts pathogen replication by inducing the expression of major histocompatibility complex (MHC) class II molecules, cytokines (eg, TNF␣), and chemokines. 14 SLC11A1/Slc11a1 belongs to a family of polytopic membrane proteins whose functions include divalent cation acquisition in mammals (DCT1/DMT1/NRAMP2), 15 taste perception in the fruit fly (malvolio), 16 and stress signal transduction in plants (EIN2). 17 In mice, a single nonsynonymous mutation in Slc11a1 codon 169 determines resistance (Gly169) or susceptibility (Asp169) to intracellular bacterial and leishmanial infections. 7 Compared with susceptible mice, macrophages from mice that are resistant to infection also show increased oxidative burst and expression of the MHC class...

Innate Immune Gene Polymorphisms in Tuberculosis

“…(v) We note that many of the polymorphisms associated with TB represent regulatory variants rather than nonsynonymous SNPs that alter the amino acid sequence (e.g., TNF, NRAMP1, and TLR2) (1,18,265). It is perhaps intuitively obvious that regulation of gene expression could be a primary target of evolutionary pressure, since such changes are gradual and account for the balance that needs to be struck between, for example, immunity against TB and autoimmune disorders (1).…”

“…Nevertheless, clear signatures of evolutionary selection pressure can be found in multiple human gene families involved in TB pathogenesis, as well as associated processes, such as autophagy (60,61). Strong evidence for selection of genetic variants modulating infectivity and resistance exists for genes encoding major histocompatibility complex/ human leukocyte antigen (MHC/HLA) (31,235), tumor necrosis factors (TNFs) and their receptors (259), immune-related GTP-ases (IRGs) (20), NRAMP1 (solute carrier protein 11A1 [SLC11A1]) (18,38), Toll-like receptors (TLRs) (16,265), vitamin D nuclear receptor (VDR) (38,260), and cell surface proteins, such as lectins (159). As yet, however, an integrative understanding is still lacking of how these factors act in concert to mitigate the effects of TB or render resistance, versus the ability of M. tuberculosis to evade such mechanisms.…”

Hypoxia inducible factor (HIF) function in innate immunity and infection

“…Finally, it has recently been discovered that HIF-1α transcriptional regulation mediates allelle expression phenotypes for the innate defense factor SLC11A1 (aka NRAMP1) through differential binding and activation of Z-DNA forming microsatellite polymorphisms in the SLC11A1 promotor [22]. Since these polymorphisms influence human susceptibility to tuberculosis, rheumatoid arthritis, Crohn's disease and other disorders, HIF-1α may influence heritable variation in innate resistance to infection and inflammation within and between populations [22].…”

“…Since these polymorphisms influence human susceptibility to tuberculosis, rheumatoid arthritis, Crohn's disease and other disorders, HIF-1α may influence heritable variation in innate resistance to infection and inflammation within and between populations [22].…”

“…Increased VEGF production and elaboration of proinflammatory cytokines facilitate recruitment and activation of additional immune effector cells. Activation of inducible nitric oxide (NO) synthetase generates a molecule (NO) with not only direct antimicrobial properties, but also the ability to further stabilize HIF-1α and rapidly amplify the innate defense pathway in the phagocyte (modified and updated from [11]) to a variety of bacterial species including Streptococcus pyogenes, Streptococcus agalactiae, Staphylococcus aureus, Salmonella typhimurium and Pseudomonas aeruginosa [7,12,22,23], suggesting it subserves a general role in bacterial/host interactions. Loss of myeloid cell HIF-1α renders mice more susceptible to invasive S. pyogenes infection [12], and decreases phagocyte killing of Gramnegative and Gram-positive bacteria in vitro [7,12,23], suggesting that the HIF-1α response pathway is broadly adaptive in host defense.…”