101 research outputs found

    Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration

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    PURPOSE. Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability. METHODS. We performed pathway analyses using summary statistics from the International AMD Genomics Consortium’s 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis. RESULTS. We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) ‘‘drive’’ the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways. CONCLUSIONS. We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD

    Peripheral blood mononuclear cells from neovascular age-related macular degeneration patients produce higher levels of chemokines CCL2 (MCP-1) and CXCL8 (IL-8)

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    Flow cytometry analysis of PBMCs. PBMCs were first divided into CD11b+CD3−, CD11b−CD3+ and CD11b−CD3− cells (A) and the average percentage of all samples (n = 55) was analysed before and after stimulation with PMA/ionomycin (B). Figure S2. Percentage of total IL-4 and IL-10 producing PBMCs and percentage of CD11b−CD3+ IL-17A and IFNγ producing PBMCs (almost all of IL-17A and IFNγ producing PBMCs were CD11b−CD3+) from controls and nAMD patients under non-stimulated culture conditions and after stimulation with PMA/ionomycin. Controls n = 27, nAMD = 28; mean + SEM are shown. (PDF 413 kb

    A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.

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    This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.3448Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.We thank all participants of all the studies included for enabling this research by their participation in these studies. Computer resources for this project have been provided by the high-performance computing centers of the University of Michigan and the University of Regensburg. Group-specific acknowledgments can be found in the Supplementary Note. The Center for Inherited Diseases Research (CIDR) Program contract number is HHSN268201200008I. This and the main consortium work were predominantly funded by 1X01HG006934-01 to G.R.A. and R01 EY022310 to J.L.H

    New insights into the genetic etiology of Alzheimer's disease and related dementias.

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    Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

    New insights into the genetic etiology of Alzheimer's disease and related dementias

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    Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

    Исследование уровня экспрессии генов-маркеров пролиферативной активности в слизистой оболочке толстой кишки при различной патологии

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    Background. The search for molecular markers of colon diseases allowing highly specific and sensitive identification and differentiation of pathological processes is a clinically important problem. Expression levels of genes responsible for proliferation can reflect the changes in the affected tissues. The study objective is to perform comparative analysis of molecular and genetic markers of proliferative activity in benign and malignant neoplasms of the colon. Materials and methods. Analysis of the changes in proliferation markers (CCND1, с-MYC, Ki-67, HER2neu, TERT) in adenocarcinoma of the colon (n = 259), resection margin (about 15–20 cm from the tumor lesion) (n = 251), unchanged colon mucosa from healthy donors (n = 247), polyps (n = 28), unchanged colon mucosa intestinal polyposis (10–15 cm from the polyp) (n = 75) was performed using RT-PCR. Results and conclusion. It was shown that morphologically unchanged tissue of intestinal mucosa in malignant tumors has significant differences from normal tissue of healthy donors. Significant differences in the level of expression of genes responsible for the processes of proliferation, с-MYC, CCND1, TERT were found in benign hyperproliferative diseases (polyps). Moreover, these changes were specific to the type of pathological process, which allows us to consider these genes as the most promising candidates in the development of a differential method for diagnosing colon diseases.Введение. Поиск молекулярных маркеров диагностики заболеваний толстой кишки, способных с высокой чувствительностью и специфичностью выявлять и дифференцировать патологический процесс, является актуальной клинически важной задачей. Уровень экспрессии генов, ответственных за процессы пролиферации, может отражать картину изменений в тканях пораженного органа. Цель исследования – сравнительный анализ молекулярно-генетических маркеров пролиферативной активности при доброкачественных и злокачественных новообразованиях толстой кишки. Материалы и методы. Методом полимеразной цепной реакции в реальном времени проведен анализ изменений экспрессии маркеров пролиферации (CCND1, с-MYC, Ki-67, HER2neu, TERT) в следующих тканях: аденокарциномы толстой кишки (n = 259), края резекции (около 15–20 см от опухолевого узла) (n = 251), неизмененной слизистой оболочки толстой кишки здоровых доноров (n = 247), полипов (n = 28), неизмененной слизистой оболочки толстой кишки при полипах (10–15 см от полипа) (n = 75). Результаты и заключение. Установлено, что в тканях полипов толстой кишки наблюдаются достоверные различия в уровне экспрессии генов, ответственных за процессы пролиферации (с-MYC, CCND1, TERT). Выявленные различия специфичны для типа патологического процесса, что позволяет рассматривать данные гены в качестве наиболее перспективных кандидатов при разработке дифференциального метода диагностики заболеваний толстой кишки
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