title: Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers.
abstract: For patients with locally advanced rectal cancer (LARC) treated with preoperation chemoradiation (pCRT), identifying differentially expressed (DE) genes between non-responders and responders is a common approach for investigating mechanisms of chemoradiation resistance. However, some of such DE genes might be irrelevant to cancer itself but simply reflect the pharmacokinetic differences of the normal tissues. In this study, we adopted the RankComp algorithm to identify DE genes for each of LARC sample compared with its own normal state. Then, we identified genes with significantly different deregulation frequencies between the non-responders and responders, defined as cancer-related pCRT-response genes. Pathway enrichment and protein-protein interaction analyses showed that these genes specifically and intensively interacted with currently known effective genes of pCRT, involving in DNA replication, cell cycle and DNA repair. In contrast, after excluding the cancer-related pCRT-response genes, the other DE genes between non-responders and responders were enriched in many pathways of drug and protein metabolisms and transports, and interacted with both the known effective genes and pharmacokinetic genes. Hence, these two types of DE genes should be distinguished for investigating mechanisms of pCRT response in LARCs.
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.|Department of Preventive Medicine, School of Basic Medicine Sciences, Gannan Medical University, Ganzhou, China, 341000.
authors.forename: You
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Jun
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Lu
authors.initials: L
authors.lastname: Ao
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Qingzhou
authors.initials: Q
authors.lastname: Guan
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Juan
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Haidan
authors.initials: H
authors.lastname: Yan
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Hao
authors.initials: H
authors.lastname: Cai
authors.affiliation: Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China, 350001.
authors.forename: Qiao
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China, 350001.
authors.forename: Weizhong
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University Fuzhou, China, 350001.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: D000368:Aged; D000465:Algorithms; D004260:DNA Repair / Q000235:genetics; D005260:Female; D005472:Fluorouracil / Q000627:therapeutic use / Q000633:toxicity; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D060066:Protein Interaction Maps / Q000187:drug effects; D012004:Rectal Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology / Q000532:radiotherapy; D012007:Rectum / Q000378:metabolism
chemical_list: D005472:Fluorouracil