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Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs

View Article: PubMed Central - PubMed

ABSTRACT

Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood samples. We were able to link 71 (39%) of the AID-SNPs to two or more nearby genes, providing evidence that for part of the AID loci multiple causal genes exist. While 54 of the AID loci are shared by one or more AID, 17% of them do not share candidate causal genes. In addition to finding novel genes such as ULK3, we also implicate novel disease mechanisms and pathways like autophagy in celiac disease pathogenesis. Furthermore, 42 of the AID SNPs specifically affected the expression of 53 non-coding RNA genes. To further understand how the non-coding genome contributes to AID, the SNPs were linked to functional regulatory elements, which suggest a model where AID genes are regulated by network of chromatin looping/non-coding RNAs interactions. The looping model also explains how a causal candidate gene is not necessarily the gene closest to the AID SNP, which was the case in nearly 50% of cases.

No MeSH data available.


Related in: MedlinePlus

Validation of the functional role of ULK3 locus in autophagy in celiac disease. (A) Genotype-dependent expression levels of autophagy genes in coeliac disease biopsies. There were 3 AA, 15 AG and 13 GG genotypes. The expression for 217 autophagy genes could be extracted from the microarray data of coeliac disease biopsies and the genotype data at the ULK3 SNP were extracted using Immunochip for 31 CeD patients. The heatmap shows the normalized expression values stratified according to the genotypes. The difference in gene expression between AA and GG was tested by t-test and P < 0.05 was considered significant. (B) Association of rs1378938 with interleukin 6 levels in response to lipopolysaccharide. The CeD-associated risk allele rs1378938*T (in red) results in lowered interleukin 6 (P = 0.019) cytokine levels upon LPS stimulation of primary mononuclear cells. The x-axis displays the three different genotypes and the number of individuals in each group. The y-axis presents the age and gender corrected cytokine levels.
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Figure 3: Validation of the functional role of ULK3 locus in autophagy in celiac disease. (A) Genotype-dependent expression levels of autophagy genes in coeliac disease biopsies. There were 3 AA, 15 AG and 13 GG genotypes. The expression for 217 autophagy genes could be extracted from the microarray data of coeliac disease biopsies and the genotype data at the ULK3 SNP were extracted using Immunochip for 31 CeD patients. The heatmap shows the normalized expression values stratified according to the genotypes. The difference in gene expression between AA and GG was tested by t-test and P < 0.05 was considered significant. (B) Association of rs1378938 with interleukin 6 levels in response to lipopolysaccharide. The CeD-associated risk allele rs1378938*T (in red) results in lowered interleukin 6 (P = 0.019) cytokine levels upon LPS stimulation of primary mononuclear cells. The x-axis displays the three different genotypes and the number of individuals in each group. The y-axis presents the age and gender corrected cytokine levels.

Mentions: To investigate the functional impact of ULK3 locus on autophagy pathway in CeD, we tested whether known autophagy genes were differentially regulated in intestinal biopsies of CeD patients [35]. We indeed observed an enrichment of autophagy genes being differentially expressed (Fig. 3A) compared to a random set of genes in CeD biopsies (P = 2.2 × 10−16). We further confirmed that the ULK3 affecting SNP genotype is correlated with the expression levels of autophagy genes in CeD biopsies (Supplemental Fig. 3). Autophagy is also involved in regulating inflammatory process in response to human pathogens by influencing cytokine production and secretion. We therefore tested whether ULK3 SNP influences the production of cytokines in PBMCs in response to lipopolysaccharide (LPS), a cell-wall component of Gram negative bacteria. We found a significant difference (P = 0.019) in the levels of IL-6 between rs1378938 CC and TT genotypes, where the risk allele T is associated with lower levels of IL-6 in response to LPS (Fig. 3B). This finding indicated that ULK3 dependent autophagy might be involved in regulation of inflammation and emphasizes the importance of studying non-gluten antigens (e.g. host–microbiome interaction) in the context of CeD pathogenesis.


Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs
Validation of the functional role of ULK3 locus in autophagy in celiac disease. (A) Genotype-dependent expression levels of autophagy genes in coeliac disease biopsies. There were 3 AA, 15 AG and 13 GG genotypes. The expression for 217 autophagy genes could be extracted from the microarray data of coeliac disease biopsies and the genotype data at the ULK3 SNP were extracted using Immunochip for 31 CeD patients. The heatmap shows the normalized expression values stratified according to the genotypes. The difference in gene expression between AA and GG was tested by t-test and P < 0.05 was considered significant. (B) Association of rs1378938 with interleukin 6 levels in response to lipopolysaccharide. The CeD-associated risk allele rs1378938*T (in red) results in lowered interleukin 6 (P = 0.019) cytokine levels upon LPS stimulation of primary mononuclear cells. The x-axis displays the three different genotypes and the number of individuals in each group. The y-axis presents the age and gender corrected cytokine levels.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 3: Validation of the functional role of ULK3 locus in autophagy in celiac disease. (A) Genotype-dependent expression levels of autophagy genes in coeliac disease biopsies. There were 3 AA, 15 AG and 13 GG genotypes. The expression for 217 autophagy genes could be extracted from the microarray data of coeliac disease biopsies and the genotype data at the ULK3 SNP were extracted using Immunochip for 31 CeD patients. The heatmap shows the normalized expression values stratified according to the genotypes. The difference in gene expression between AA and GG was tested by t-test and P < 0.05 was considered significant. (B) Association of rs1378938 with interleukin 6 levels in response to lipopolysaccharide. The CeD-associated risk allele rs1378938*T (in red) results in lowered interleukin 6 (P = 0.019) cytokine levels upon LPS stimulation of primary mononuclear cells. The x-axis displays the three different genotypes and the number of individuals in each group. The y-axis presents the age and gender corrected cytokine levels.
Mentions: To investigate the functional impact of ULK3 locus on autophagy pathway in CeD, we tested whether known autophagy genes were differentially regulated in intestinal biopsies of CeD patients [35]. We indeed observed an enrichment of autophagy genes being differentially expressed (Fig. 3A) compared to a random set of genes in CeD biopsies (P = 2.2 × 10−16). We further confirmed that the ULK3 affecting SNP genotype is correlated with the expression levels of autophagy genes in CeD biopsies (Supplemental Fig. 3). Autophagy is also involved in regulating inflammatory process in response to human pathogens by influencing cytokine production and secretion. We therefore tested whether ULK3 SNP influences the production of cytokines in PBMCs in response to lipopolysaccharide (LPS), a cell-wall component of Gram negative bacteria. We found a significant difference (P = 0.019) in the levels of IL-6 between rs1378938 CC and TT genotypes, where the risk allele T is associated with lower levels of IL-6 in response to LPS (Fig. 3B). This finding indicated that ULK3 dependent autophagy might be involved in regulation of inflammation and emphasizes the importance of studying non-gluten antigens (e.g. host–microbiome interaction) in the context of CeD pathogenesis.

View Article: PubMed Central - PubMed

ABSTRACT

Genome-wide association and fine-mapping studies in 14 autoimmune diseases (AID) have implicated more than 250 loci in one or more of these diseases. As more than 90% of AID-associated SNPs are intergenic or intronic, pinpointing the causal genes is challenging. We performed a systematic analysis to link 460 SNPs that are associated with 14 AID to causal genes using transcriptomic data from 629 blood samples. We were able to link 71 (39%) of the AID-SNPs to two or more nearby genes, providing evidence that for part of the AID loci multiple causal genes exist. While 54 of the AID loci are shared by one or more AID, 17% of them do not share candidate causal genes. In addition to finding novel genes such as ULK3, we also implicate novel disease mechanisms and pathways like autophagy in celiac disease pathogenesis. Furthermore, 42 of the AID SNPs specifically affected the expression of 53 non-coding RNA genes. To further understand how the non-coding genome contributes to AID, the SNPs were linked to functional regulatory elements, which suggest a model where AID genes are regulated by network of chromatin looping/non-coding RNAs interactions. The looping model also explains how a causal candidate gene is not necessarily the gene closest to the AID SNP, which was the case in nearly 50% of cases.

No MeSH data available.


Related in: MedlinePlus