Translational genomics of acquired laryngotracheal stenosis.

Objectives/Hypothesis Acquired laryngotracheal stenosis (ALTS) results from abnormal mucosal wound healing after laryngeal and/or tracheal injury. Patients with ALTS often present late after significant reduction of the airway lumen and onset of symptoms. Motivated by the need for earlier detection of affected patients, we sought to investigate genetic markers for ALTS that would identify susceptible patients. Study Design Pilot Case-Control Study. Methods Seventy-six patients were recruited, 40 patients with ALTS and 36 control patients with airway injury but without ALTS. DNA was isolated from whole blood and formalin-fixed paraffin-embedded specimens from patients. Custom primers were designed and the TaqMan assay employing allele-specific polymerase chain reaction was used to interrogate single nucleotide polymorphisms (SNPs): rs2569190, rs1799750, and rs1800469 located in candidate genes CD14, matrix metalloproteinase-1 (MMP-1), and transforming growth factor-β1 (TGF-β1), respectively. A logistic regression model was used to examine the association of candidate gene polymorphisms with the presence or absence of ALTS. Results All 76 patients were successfully genotyped at the three loci of interest by optimizing the genotyping protocol. MMP-1 SNP rs1799750 was most significantly associated with development of ALTS (P = 0.005). Conclusion Identification of SNPs associated with development of ALTS will provide new experimental targets to study wound healing in human subjects. The association found in the current study between ALTS and SNP rs1799750 is being validated in a larger population examining an expanded set of relevant SNPs. Identifying patients with genetic susceptibility to ALTS and poor wound healing in the upper airway will be useful for management of patients after upper-airway injury. Level of Evidence N/A. Laryngoscope, 124:E175–E179, 201

Glyceraldehyde 3-Phosphate Dehydrogenase Depletion Induces Cell Cycle Arrest and Resistance to Antimetabolites in Human Carcinoma Cell LinesS⃞

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a multifunctional protein that acts at the intersection of energy metabolism and stress response in tumor cells. To elucidate the role of GAPDH in chemotherapy-induced stress, we analyzed its activity, protein level, intracellular distribution, and intranuclear mobility in human carcinoma cells A549 and UO31 after treatment with cytarabine, doxorubicin, and mercaptopurine. After treatment with cytosine arabinoside (araC), enzymatically inactive GAPDH accumulated in the nucleus. Experiments on fluorescence recovery after photobleaching with green fluorescent protein-GAPDH fusion protein in the live cells treated with araC demonstrated reduced mobility of green fluorescent protein-GAPDH inside the nucleus, indicative of interactions with nuclear macromolecular components after genotoxic stress. Depletion of GAPDH with RNA interference stopped cell proliferation, and induced cell cycle arrest in G1 phase via p53 stabilization, and accumulation of p53-inducible CDK inhibitor p21. Neither p21 accumulation nor cell cycle arrest was detected in GAPDH-depleted p53-null NCI-H358 cells. GAPDH-depleted A549 cells were 50-fold more resistant to treatment with cytarabine (1.68 ± 0.182 μM versus 0.03 ± 0.015 μM in control). Depletion of GAPDH did not significantly alter cellular sensitivity to doxorubicin (0.05 ± 0.023 μM versus 0.035 ± 0.0154 μM in control). Induction of cell cycle arrest in p53-proficient carcinoma cells via GAPDH abrogation suggests that GAPDH-depleting agents may have a cytostatic effect in cancer cells. Our results define GAPDH as an important determinant of cellular sensitivity to antimetabolite chemotherapy because of its regulatory functions

156 Exploring Genetic Variability in Drug Therapy by Selecting a Minimum Subset of the Most Informative Single Nucleotide Polymorphisms through Approximation of a Markov Blanket in a Kernel-induced Space

Abstract—Genome-wide analysis of single nucleotide polymorphisms (SNP) can potentially be helpful in exploring the role of genetic variability in drug therapy. However, two major problems with such an analysis are the need for a large number of interrogated genomes, and the resulting high-dimensional data where the number of SNPs used as features is much larger than the number of subjects. The aim of this study is to identify informative SNPs associated with clinical efficacy and side effects of domperidone treatment for gastroparesis from DNA microarray experiments by applying our feature selection method, which approximates the Markov Blanket in a kernelinduced space. DNA samples extracted from the saliva of 46 patients treated with domperidone were analyzed using Affymetrix 6.0 SNP microarrays. Experimental evaluations on this SNP microarray dataset provide evidence that our feature selection method can remove useless SNP features more accurately than existing Markov Blanket based alternatives. Keywords-genetic variability; feature selection; drug therapy; SNP I