A transcriptome-wide association study based on 27 tissues identifies 106 genes potentially relevant for disease pathology in age-related macular degeneration

Abstract

Genome-wide association studies (GWAS) for late stage age-related macular degeneration (AMD) have identified 52 independent genetic variants with genome-wide significance at 34 genomic loci. Typically, such an approach rarely results in the identification of functional variants implicating a defined gene in the disease process. We now performed a transcriptome-wide association study (TWAS) allowing the prediction of effects of AMD-associated genetic variants on gene expression. The TWAS was based on the genotypes of 16,144 late-stage AMD cases and 17,832 healthy controls, and gene expression was imputed for 27 different human tissues which were obtained from 134 to 421 individuals. A linear regression model including each individuals imputed gene expression data and the respective AMD status identified 106 genes significantly associated to AMD variants in at least one tissue (Q-value < 0.001). Gene enrichment analysis highlighted rather systemic than tissue-or cellspecific processes. Remarkably, 31 of the 106 genes overlapped with significant GWAS signals of other complex traits and diseases, such as neurological or autoimmune conditions. Taken together, our study highlights the fact that expression of genes associated with AMD is not restricted to retinal tissue as could be expected for an eye disease of the posterior pole, but instead is rather ubiquitous suggesting processes underlying AMD pathology to be of systemic nature. Age-related macular degeneration (AMD) is a frequent disease of the choroid, Bruch's membrane, retinal pigment epithelium and photoreceptor complex characterized by a progressive loss of vision in older individuals of industrialized countries. For the year 2016, it was estimated that worldwide approximately 162 million were affected by early AMD (prevalence 8.0%) and 10 million people by late AMD (prevalence 0.4%). These numbers were predicted to increase to 260 million patients with early and 19 million with late AMD by the year 2040 1. It is well established that AMD is a complex disease, involving environmental and genetic risk factors. The International AMD Genomics Consortium (IAMDGC) performed a genome-wide association study (GWAS) and reported 7,218 genetic variants to be associated with late-stage AMD at a genome-wide significance level (P-value ≤ 5 × 10 −8). Sequential forward selection finally identified 52 independent association signals, which are distributed over 34 genomic loci 2. An additional 11,768 variants (P-value ≤ 5 × 10 −4) failed to reach genome-wide significance in this study but may well play a role in AMD pathogenesis. These variants may become relevant only with an increase in sample-size in future GWAS, or by gathering additional information on the functional impact of these variants in relation to AMD pathology.

Learning from Fifteen Years of Genome-Wide Association Studies in Age-Related Macular Degeneration

“…Remarkably, with exception of the study by Orozco et al (2020) [ 28 ], an AMD-associated regulation of the genes PILRA and PILRB was reported in all studies and consistently showed an upregulation with increased AMD risk. Another three loci (see “ CFI ”, “ C2/CFB/SKIV2L ”, and “ RDH5/CD63 ”) revealed gene regulatory effects predominantly in retina in comparison to data available from extraocular tissues [ 31 , 33 ] (category 2). The gene HLA-DQB1 (locus “ C2/CFB/SKIV2L ”) is part of the major histocompatibility complex and was explicitly excluded in the TWAS by Strunz et al (2020).…”

“…Strunz et al (2020) performed an eQTL mega-analysis using three datasets based on 311 retinal tissue samples of exclusively healthy donor eyes, including 94 control samples of Ratnapriya et al (2019) [ 25 , 32 ]. Two further studies targeted gene expression regulation in extraocular tissues including 588 liver tissue samples from four independent studies [ 31 ], and various tissues originating from the GTEx database as well as individual genotype data from the IAMDGC sample set [ 8 , 33 ] ( Table 1 ).…”

“…The latter threshold was set arbitrarily to enable a more focused interpretation of regulatory effects. It should be mentioned that there were partially overlapping samples used in the studies, e.g., the mega-analysis by Strunz et al (2018) [ 31 ] included some GTEx samples which were also enrolled in the subsequent TWAS [ 33 ].…”

“…The gene HLA-DQB1 (locus “ C2/CFB/SKIV2L ”) is part of the major histocompatibility complex and was explicitly excluded in the TWAS by Strunz et al (2020). Consequently, no conclusions about gene expression regulation in extraocular tissues can be drawn [ 33 ]. Eight AMD loci (category 3: “ CFH ”, “ COL8A1 ”, “ TNFRSF10A ”, “ CETP ”, “ CTRB2/CTRB1 ”, “ C3 ”, “ CNN2 ”, and “ MMP9 ”) revealed gene expression regulation effects only in extraocular tissues while five of these harbor multiple genes which were assigned to different categories.…”

“…The correction for multiple testing was done as described for Ratnapriya et al (2019). Third, a TWAS based on 27 tissues from GTEx and the individual genotypes of all samples from the IAMDGC with European ethnicity [ 8 , 33 ]. AMD-associated genes were identified separately for each tissue and adjustment for multiple testing used a Benjamini and Hochberg FDR threshold of 0.001.…”