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

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.**研究目的**：明确编码应激活化型丝裂原活化蛋白激酶（mitogen-activated protein kinase, MAPK）信号通路组分的基因簇内常见DNA序列变异，是否整体与晚期年龄相关性黄斑变性（advanced age-related macular degeneration, AAMD）相关。 **研究方法**：本研究依托3项针对年龄相关性黄斑变性（age-related macular degeneration, AMD）分子遗传学的大规模基因分型项目，纳入1177例AAMD患者与1024例无AMD的老年对照人群，采用元回归与精确检验方法筛选与AAMD相关的单核苷酸多态性（single nucleotide polymorphism, SNP）。针对覆盖独立AAMD相关基因组区域的SNP，采用多位点检验方法（INRICH）分析其在5组编码应激活化型MAPK信号级联反应组分的基因集内的富集情况。 **研究结果**：5组通路基因集合中有4组呈现出与AAMD相关SNP的富集现象；其中2组在校正多重检验后结果仍保持显著。最强的富集信号（P = 0.006）出现在c-Jun氨基末端激酶（c-Jun N-terminal kinase, JNK）/MAPK信号级联（Science Signaling, STKE CMP_10827）中。该通路内7个独立的AAMD相关区域分布于本次检测的25个基因中的6个内，具体包括以下序列变异：1）3个丝裂原活化蛋白激酶激酶激酶（MAP3K4、MAP3K5、MAP3K9），其可磷酸化并激活丝裂原活化蛋白激酶激酶MAP2K4与MAP2K7（这类分子可磷酸化JNK激活环内的苏氨酸与酪氨酸残基）；2）MAP2K7的靶基因JNK3A1，其可激活参与应激相关基因转录调控的复合物，进而影响细胞增殖、凋亡、迁移、代谢与DNA修复；3）NR2C2，一种由JNK1A1激活的转录因子（JNK1A1是可在模型系统中影响视网膜细胞活力的可靶向药物分子）。本研究还观察到与AAMD相关的序列变异存在于编码PPP3CA（一种可灭活MAP3K5的可靶向药物分子）的基因，以及编码参与MAPK感知生长因子/细胞因子的两个基因（TGFB2、TGFBR2）中。 **结论**：不依赖连锁不平衡（linkage disequilibrium, LD）的基因组富集分析显示，AAMD与编码JNK MAPK信号通路组分的功能相关基因集合存在关联。目前已有美国食品药品监督管理局（Food and Drug Administration, FDA）批准的药物可靶向应激活化型MAPK通路的组分，或可为AAMD的预防与治疗提供可行方案。