AMD-Associated Genes Encoding Stress-Activated MAPK Pathway Constituents Are Identified by Interval-Based Enrichment Analysis

John Paul Sangiovanni,Phil H Lee,Yi-Hsiang Hsu

doi:10.1371/journal.pone.0071239

Abstract

PurposeTo determine whether common DNA sequence variants within groups of genes encoding elements of stress-activated mitogen-activated protein kinase (MAPK) signaling pathways are, in aggregate, associated with advanced AMD (AAMD).MethodsWe used meta-regression and exact testing methods to identify AAMD-associated SNPs in 1177 people with AAMD and 1024 AMD-free elderly peers from 3 large-scale genotyping projects on the molecular genetics of AMD. SNPs spanning independent AAMD-associated genomic intervals were examined with a multi-locus-testing method (INRICH) for enrichment within five sets of genes encoding constituents of stress-activated MAPK signaling cascades.ResultsFour-of-five pathway gene sets showed enrichment with AAMD-associated SNPs; findings persisted after adjustment for multiple testing in two. Strongest enrichment signals (P = 0.006) existed in a c-Jun N-terminal kinase (JNK)/MAPK cascade (Science Signaling, STKE CMP_10827). In this pathway, seven independent AAMD-associated regions were resident in 6 of 25 genes examined. These included sequence variants in: 1) three MAP kinase kinase kinases (MAP3K4, MAP3K5, MAP3K9) that phosphorylate and activate the MAP kinase kinases MAP2K4 and MAP2K7 (molecules that phosphorylate threonine and tyrosine residues within the activation loop of JNK); 2) a target of MAP2K7 (JNK3A1) that activates complexes involved in transcriptional regulation of stress related genes influencing cell proliferation, apoptosis, motility, metabolism and DNA repair; and 3) NR2C2, a transcription factor activated by JNK1A1 (a drugable molecule influencing retinal cell viability in model systems). We also observed AAMD-related sequence variants resident in genes encoding PPP3CA (a drugable molecule that inactivates MAP3K5), and two genes (TGFB2, TGFBR2) encoding factors involved in MAPK sensing of growth factors/cytokines.ConclusionsLinkage disequilibrium (LD)-independent genomic enrichment analysis yielded associations of AAMD with aggregates of functionally related genes encoding constituents of the JNK MAPK signaling pathway. FDA-approved drugs now exist to target constituents of stress-activated MAPK pathways and may offer reasonable approaches to preventing or treating AAMD.

Highlights

We have previously reported single locus associations for advanced AMD (AAMD) with DNA sequence variants resident in genes encoding constituents of mitogen-activated protein kinase (MAPK) pathways. [21,22] AAMD-associated single nucleotide polymorphisms (SNPs) exist in genes encoding cell surface and nuclear receptors known to act in MAPK pathways – such genes include the members of the: 1) peroxisome proliferator activator receptor (PPAR)/retinoid X receptor (RXR) complex [22]; 2) VEGF signaling system[22,25,26,27]; and, 3) insulin signaling system. [28]
We applied findings from a genome-wide association project (NEI-AMD, the NEI Study of Age-Related Macular Degeneration) to a pathway-based genome-wide analytic method (INRICH) [11] to test for enriched association signals in five published sets of genes encoding MAPK pathway constituents including SAPKs. In this process we examined linkage disequilibrium (LD)-independent genomic intervals to determine whether common DNA sequence variants within groups of genes encoding constituents of MAPK pathways were, in aggregate, more strongly associated with AAMD than expected by chance alone
AAMD-associated genomic regions were significantly enriched for genes encoding constituents of four-offive MAPK pathway gene sets (Table 1)

Summary

Introduction

Neovascular AMD) and neurodegeneration of the retinal pigment epithelial (RPE) cell-photoreceptor complex Geographic atrophy).[4,5,6] AMD is a common complex disease and its polygenic nature has been partially characterized from 19 strongly-associated (P#161028) loci in a multi-center study on over 77,000 people. [7] Ward & Kellis [8] review works demonstrating the influence of common alleles contributing small, but meaningful effects in traits or disease risk [9] – as in the present work, loci associated with complex traits at P-values far below those considered significant on a genome-wide level have clustered across the genome within DNA sequence encoding constituents of biological pathways implicated in disease pathogenesis.

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