Selina Imboywa

CD33 Alzheimer's disease locus: altered monocyte function and amyloid biology

In our functional dissection of the CD33 Alzheimers disease susceptibility locus, we found that the rs3865444C risk allele was associated with greater cell surface expression of CD33 in the monocytes (t50 = 10.06, Pjoint = 1.3 × 10−13) of young and older individuals. It was also associated with diminished internalization of amyloid-β 42 peptide, accumulation of neuritic amyloid pathology and fibrillar amyloid on in vivo imaging, and increased numbers of activated human microglia.

Common genetic variants modulate pathogen-sensing responses in human dendritic cells.

Introduction Variation in an individual’s response to environmental factors is likely to influence susceptibility to complex human diseases. The genetic basis of such variation is poorly understood. Here, we identify natural genetic variants that underlie variation in the host innate immune response to infection and analyze the mechanisms by which such variants alter these responses. Identifying the genetic basis of variability in the host response to pathogens. A cohort of 534 individuals donated blood for (a) genotyping of common DNA variants and (b) isolation of immune DCs. DCs were stimulated with viral and bacterial components, and the variability in individuals’ gene expression responses was mapped to specific DNA variants, which were then shown to affect binding of particular transcription factors. Methods We derived dendritic cells (DCs) from peripheral blood monocytes of healthy individuals (295 Caucasians, 122 African Americans, 117 East Asians) and stimulated them with Escherichia coli lipopolysaccharide (LPS), influenza virus, or the cytokine interferon-β (IFN-β) to generate 1598 transcriptional profiles. We genotyped each of these individuals at sites of common genetic variation and identified the genetic variants that best explain variation in gene expression and gene induction between individuals. We then tested mechanistic predictions from these associations using synthetic promoter constructs and genome engineering. Results We identified 264 loci containing genetic variants associated with variation in absolute gene expression in human DCs, of which 121 loci were associated with variation in the induction of gene expression by one or more stimuli. Fine-mapping identified candidate causal single-nucleotide polymorphisms (SNPs) associated with expression variance, and deeper functional experiments localized three of these SNPs to the binding sites of stimulus-activated transcription factors. We also identified a cis variant in the transcription factor, IRF7, associated in trans with the induction of a module of antiviral genes in response to influenza infection. Of the identified genetic variants, 35 were also associated with autoimmune or infectious disease loci found by genome-wide association studies. Discussion The genetic variants we uncover and the molecular basis for their action provide mechanistic explanations and principles for how the innate immune response to pathogens and cytokines varies across individuals. Our results also link disease-associated variants to specific immune pathways in DCs, which provides greater insight into mechanisms underlying complex human phenotypes. Extending our approach to many immune cell types and pathways will provide a global map linking human genetic variants to specific immunological processes. Immune Variation It is difficult to determine the mechanistic consequences of context-dependent genetic variants, some of which may be related to disease (see the Perspective by Gregersen). Two studies now report on the effects of stimulating immunological monocytes and dendritic cells with proteins that can elicit a response to bacterial or viral infection and assess the functional links between genetic variants and profiles of gene expression. M. N. Lee et al. (10.1126/science.1246980) analyzed the expression of more than 400 genes, in dendritic cells from 534 healthy subjects, which revealed how expression quantitative trait loci (eQTLs) affect gene expression within the interferon-β and the Toll-like receptor 3 and 4 pathways. Fairfax et al. (10.1126/science.1246949) performed a genome-wide analysis to show that many eQTLs affected monocyte gene expression in a stimulus- or time-specific manner. Mapping of human host-pathogen gene-by-environment interactions identifies pathogen-specific loci. [Also see Perspective by Gregersen] Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-β (IFN-β). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.

Functional screening in Drosophila identifies Alzheimer's disease susceptibility genes and implicates Tau-mediated mechanisms

Using a Drosophila model of Alzheimers disease (AD), we systematically evaluated 67 candidate genes based on AD-associated genomic loci (P < 10(-4)) from published human genome-wide association studies (GWAS). Genetic manipulation of 87 homologous fly genes was tested for modulation of neurotoxicity caused by human Tau, which forms neurofibrillary tangle pathology in AD. RNA interference (RNAi) targeting 9 genes enhanced Tau neurotoxicity, and in most cases reciprocal activation of gene expression suppressed Tau toxicity. Our screen implicates cindr, the fly ortholog of the human CD2AP AD susceptibility gene, as a modulator of Tau-mediated disease mechanisms. Importantly, we also identify the fly orthologs of FERMT2 and CELF1 as Tau modifiers, and these loci have been independently validated as AD susceptibility loci in the latest GWAS meta-analysis. Both CD2AP and FERMT2 have been previously implicated with roles in cell adhesion, and our screen additionally identifies a fly homolog of the human integrin adhesion receptors, ITGAM and ITGA9, as a modifier of Tau neurotoxicity. Our results highlight cell adhesion pathways as important in Tau toxicity and AD susceptibility and demonstrate the power of model organism genetic screens for the functional follow-up of human GWAS.

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

While the impact of common genetic variants on transcript abundance in response to cellular stimuli has been analyzed in depth, less is known about how stimulation modulates the genetic control of isoform usage. Using RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to viral infection or stimulation with Type 1 interferon. We identified more than a thousand single nucleotide polymorphisms associated with isoform usage (isoQTLs), many of which are independent of expression QTLs for the same gene. Compared to eQTLs, isoQTLs are enriched for splice sites and untranslated regions, and depleted of upstream sequences. In five loci, they provide a possible mechanism of action underlying DNA variants associated with immune-related disorders. Among these five is the ERAP2 locus, where the major haplotype is under balancing selection and associated with Crohn’s disease risk. At baseline and following Type 1 interferon stimulation, the major haplotype is associated with absence of ERAP2 expression; but in response to influenza infection, the major haplotype results in the expression of two previously uncharacterized, alternatively transcribed, spliced and translated short isoforms. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in the innate immune response, and in the case of ERAP2, may confer a historical fitness advantage in response to virus, but increase risk for autoimmunity in the modern environment.