Differential Expression Profile Prioritization of Positional Candidate Glaucoma Genes

Abstract

To develop and apply a model for prioritization of candidate glaucoma genes. Methods: This Affymetrix GeneChip (Affymetrix, Santa Clara, Calif) study of gene expression in primary culture human trabecular meshwork cells uses a positional differential expression profile model for prioritization of candidate genes within the GLC1C genetic inclusion interval. Results: Sixteen genes were expressed under all conditions within the GLC1C interval. TMEM22 was the only gene within the interval with differential expression in the same direction under both conditions tested. Two genes, ATP1B3 and COPB2, are of interest in the context of a protein-misfolding model for candidate selection. SLC25A36, PCCB, and FNDC6 are of lesser interest because of moderate expression and changes in expression. Transcription factor ZBTB38 emerges as an interesting candidate gene because of the overall expression level, differential expression, and function. Conclusions: Only 1 gene in the GLC1C interval fits our model for differential expression under multiple glaucoma risk conditions. The use of multiple prioritization models resulted in filtering 7 candidate genes of higher interest out of the 41 known genes in the region. Clinical Relevance: This study identified a small subset of genes that are most likely to harbor mutations that cause glaucoma linked to GLC1C.

Effects of Timolol on MYOC, OPTN, and WDR36 RNA Levels

“…Based on our experience, the variation in dexamethasone-induced MYOC levels, with and without timolol, is consistent with what we usually observe in experiments involving no timolol. 26,27 All of the MYOC values obtained in both treated and untreated samples fall within the range of values normally seen in our cell cultures from unaffected individuals and suggest that timolol is not blocking or reducing MYOC induction by dexamethasone.…”

“…Primary cell cultures of HTM cells, designated HTM10M, HTM12F, and HTM17F, were grown from HTM tissue samples from a 10-year-old white boy (HTM10M), a 12-year-old white girl (HTM12F), and a 17-year-old white girl (HTM17F). 26 The subject previously listed as being 16 years old 26,27 has been reassigned an age of 10 years based on review of records. Corneoscleral buttons 28 were transferred to Optisol 29 at 9 hours, 6 hours 45 minutes, and 13 hours 25 minutes post mortem, respectively.…”

“…Cells were incubated at 0.1µM, 1.0µM, or 10µM timolol 30 with 100nM dexamethasone, 19 combinations of both drugs, or vehicle in Dulbecco modified Eagle medium containing 10% fetal calf serum without bFGF for 21 days, with media changes 3 times per week. The 21-day period that we used in previous dexamethasone experiments 26,27 was selected as a model for long-term treatment.…”

Gene Expression Profile in Human Trabecular Meshwork From Patients With Primary Open-Angle Glaucoma

“…73,74 This approach has been extensively applied with human TMs and/ or cultured TM cells in studies. 29,[31][32][33][34][36][37][38][39][40][41]55,[75][76][77][78][79][80] In comparison, our study includes more POAG cases and controls, and our Illumina array contains probes for more than 47,000 genes and transcripts. Our study used TM samples collected from POAG cases during trabeculectomy, rather than postmortem tissue, as in other studies.…”

“…26,27 A number of studies [28][29][30][31][32][33][34][35][36][37][38][39][40][41] have examined gene expression profiles in TM tissue or cells and provided critical information about POAG. However, it remains unclear how the expression profile is affected in TM Copyright 2013 The Association for Research in Vision and Ophthalmology, Inc. www.iovs.org j ISSN: 1552-5783 tissue from patients with POAG compared with that from healthy control subjects.…”