The present study aimed to analyze RNA-seq data of kidney renal clear cell carcinoma (KIRC) to identify prognostic genes. RNA-seq data were downloaded from The Cancer Genome Atlas. Feature genes with a coefficient of variation (CV) >0.5 were selected using the genefilter package in R. Gene co-expression networks were constructed with the WGCNA package. Cox regression analysis was performed using the survive package. Furthermore, a functional enrichment analysis was conducted using Database for Annotation, Visualization and Integrated Discovery tools. A total of 533 KIRC samples were collected, from which 6,758 feature genes with a CV >0.5 were obtained for further analysis. The KIRC samples were divided into two sets: The training set (n=319 samples) and the validation set (n=214 samples). Subsequently, gene co-expression networks were constructed for the two sets. A total of 12 modules were identified, and the green module was significantly associated with survival time. Genes from the green module were revealed to be implicated in the cell cycle and p53 signaling pathway. In addition, a total of 11 hub genes were revealed, and 10 of them (CCNA2, CDC20, CDCA8, GTSE1, KIF23, KIF2C, KIF4A, MELK, TOP2A and TPX2) were validated as possessing prognostic value, as determined by conducting a survival analysis on another gene expression dataset. In conclusion, a total of 10 prognostic genes were identified in KIRC. These findings may help to advance the understanding of this disease, and may also provide potential biomarkers for therapeutic development.

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The oligosaccharide-producing multifunctional amylase-N (OPMA-N) is a novel multifunctional amylase and exhibits both hydrolytic and transglycosyl activities, but the molecular mechanism for its multiple catalytic activities is still unknown. Our research investigates the possible catalytic roles of a Trp residue in OPMA-N (Trp358) which is not only near the catalytic site Glu356 but also highly conserved in glycoside hydrolase subfamily 20 (the neopullulanase subfamily). Site-directed mutageneses at this site reveal that the size and charge of the occupying amino acid directly affect substrate binding, orientation of other crucial catalytic residues, the catalytic specificity, the oligomer formation, as well as the thermal stability of the enzyme. These findings may be useful in elucidating the different mechanisms of the multiple catalytic activities of multifunctional amylase OPMA-N and hence for developing an improved multifunctional amylase for the preparation of isomaltooligosaccharides.

The transcriptional profile of PC-3 human prostate cancer cells infected with tumor-targeting Salmonella typhimurium A1-R (A1-R) was analyzed with by microarray. PC-3 is highly sensitive to A1-R. Numerous genes involved in diverse cellular processes, including apoptosis, necrotic cell death, neutrophil chemotaxis and innate immunity were significantly up-regulated by A1-R bacterial infection. Such up-regulated genes include TNF-a, Fos and JUN which are involved in cell death and IL-1A and CXCL which are involved in neutrophil chemotaxes. Knowledge of the up-regulated gene profile will be exploited for enhancing prostate tumor targeting by A1-R. Keywords: Salmonella typhimurium A1-R, human prostate cancer, microarray, apoptosis, necrotic cell death, neutrophil chemotaxis, tumor-targeting. Citation Format: Ming Zhao, Wen Wu, Chongyi Lu, Yong Zhang, Robert M. Hoffman, Hui Qi, Meng Yang, Yanqin Gu, Yiyu Lu, Shibing Su, Hui Zhang, Qianmei Zhou, Qilong Chen. Microarray gene expression analysis of human prostate cancer PC-3 cells targeted by Salmonella typhimurium A1-R. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4903. doi:10.1158/1538-7445.AM2015-4903