Dina Ahram and Ben Brett will present their research on 13th September 2012

Dina’s research abstract

Identification and Characterization of Genes Causing Familial Angle Closure Glaucoma in the Basset Hound

Primary angle closure glaucoma (PACG) is a condition that most commonly results from the collapse of the irido-corneal angle due to the anterior movement of the iris. We have identified several Basset Hound pedigrees with characteristic autosomal recessive PACG that closely recapitulates the clinical PACG phenotype observed in human patients and examined the inherent variation in gene-expression patterns in affected and unaffected animals. Gene expression assessment of cultured scleral cells was performed in order to identify genes with potentially significant downregulation or abolished expression without the background effects of inflammatory activity typically found in the glaucomatous eye.
 A primary fibroblast cell culture was established from the sclera of three PACG and three unaffected Bassets. Total RNA extracted from fibroblast cells was assayed using the Affymetrix GeneChip Canine Genome 2.0 Array. The Robust Multichip Average expression summary method was used for background adjustment and normalization. A two class, unpaired, Wilcoxon statistical test was conducted to identify differentially expressed genes. qRT-PCR was performed to validate significantly expressed genes.
PACG fibroblast cultures were observed to display slow growth rates and dysmorphic cell appearance in comparison to wild-type cells. Gene expression analysis revealed over 736 differentially expressed genes based on a minimum two-fold change cutoff in expression level. Genes which revealed significant expression down-regulation in PACG versus control cells include EGFLAM, PSAT1, DRAM1, RASGEF1B, GOLGA1, PCK2 and FAP. Validation of differentially expressed genes using qRT-PCR revealed a significant fold change in genomic DNA quantity in PACG versus control cells.
These studies further suggest that cellular dysfunction is an important aspect in the pathop hysiology of PACG in the dog. Theidentification of genes with significantly altered expression levels does not only provide insight into the molecular pathways associated with the development of PACG but will be helpful in the future characterization of the genetic defect underlying the disease. Ultimately, we anticipate for these studies to also provide valuable insight into the pathophysiology and genetics of human PACG.

Ben’s research abstract

Gene Networks in Mouse Models of Cancer

Cancer is a complex disease caused by the accumulation of multiple somatic mutations in a variety of genes. Genetic heterogeneity within independent tumors has made it challenging to identify conserved genetic events and thus elucidate the biological mechanisms of cancer. To address this problem, we employed a network-based approach to analyze T-ALL tumors generated by a Sleeping Beauty (SB) transposon screen. A genome-wide functional network was generated from known protein-protein interactions and pathways. Based upon the prevalence and distribution of observed SB integration sites, commonly mutated genes were identified as gene-centric common insertion sites (gCISs), and were classified as initiation- or progression-associated. Each initiation gCIS seeds an individual subnetwork. Identifying the most probable paths above a user specified threshold between the seed and remaining gCISs grows the subnetwork. We plan to apply this approach to identify the characteristic difference between the subnetworks of varying tumor types, treatment and response, and primary tumors and metastases and thus elucidate the biological mechanisms of cancer.
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Posted on September 12, 2012, in Student Seminar. Bookmark the permalink. Leave a comment.

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