title: Impact of in Vivo Ischemic Time on RNA Quality--Experiences from a Colon Cancer Biobank.
abstract: Considerable effort has been made to improve differentiated diagnostics as well as personalized treatment for colorectal cancer patients. High-quality fresh frozen tissue is often required to investigate relevant molecular signatures in these patients. In RNA expression studies, the "RNA integrity number" is widely accepted as a reliable marker of RNA quality. Here, we investigate the feasibility of obtaining high-quality tissue from a colon cancer biobank and the impact of in vivo ischemic time and various technical and clinicopathological factors on RNA quality. Biopsies were obtained immediately following the tumor removal. The time from clamping the main arterial supply to resection and removal of the tumor was used to estimate the in vivo ischemic time. We did not observe a significant difference in RNA quality between normal tissue and tumor tissue. We observed a significant correlation between in vivo ischemic time and RNA quality in normal tissue (r = -0.24, p<0.001) but not in tumor tissue. Male gender and laparoscopic procedure were also significantly associated with lower RNA quality in normal tissue only. In tumor tissue, poor differentiation was associated with low RNA quality. In conclusion, in vivo ischemic time, surgical procedure, and gender have minor but significant effects on the quality of RNA from normal colon tissue but not tumor tissue. Poorly differentiated tumors are associated with lower RNA quality. Although its impact is low, it can still be considered to note in vivo ischemic time in colon cancer specimen procurement.
authors.affiliation: 1 Department of Science, Systems and Models, Roskilde University , Roskilde, Denmark .|2 Department of Surgery, Koege-Roskilde University Hospital , Roskilde, Denmark .
authors.forename: Jesper
authors.initials: J
authors.lastname: Olsen
authors.affiliation: 2 Department of Surgery, Koege-Roskilde University Hospital , Roskilde, Denmark .
authors.forename: Lene T
authors.initials: LT
authors.lastname: Kirkeby
authors.affiliation: 4 Department of Pathology, Roskilde University , Roskilde, Denmark .
authors.forename: Susanne
authors.initials: S
authors.lastname: Eiholm
authors.affiliation: 2 Department of Surgery, Koege-Roskilde University Hospital , Roskilde, Denmark .
authors.forename: Per
authors.initials: P
authors.lastname: Jess
authors.affiliation: 1 Department of Science, Systems and Models, Roskilde University , Roskilde, Denmark .
authors.forename: Jesper T
authors.initials: JT
authors.lastname: Troelsen
authors.affiliation: 2 Department of Surgery, Koege-Roskilde University Hospital , Roskilde, Denmark .|3 Faculty of Health and Medical Sciences, Copenhagen University , Copenhagen, Denmark .
authors.forename: Ismail
authors.initials: I
authors.lastname: Gögenür
authors.affiliation: 3 Faculty of Health and Medical Sciences, Copenhagen University , Copenhagen, Denmark .
authors.forename: Jorgen
authors.initials: J
authors.lastname: Olsen
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D018070:Biological Specimen Banks; D001706:Biopsy; D003106:Colon / Q000473:pathology; D003110:Colonic Neoplasms / Q000473:pathology* / Q000601:surgery*; D005260:Female; D006801:Humans; D007511:Ischemia / Q000473:pathology*; D010535:Laparoscopy; D008297:Male; D008875:Middle Aged; D009361:Neoplasm Invasiveness; D012334:RNA, Neoplasm / Q000032:analysis*; D012044:Regression Analysis; D013048:Specimen Handling / Q000379:methods*; D013997:Time Factors; D014015:Tissue Banks
chemical_list: D012334:RNA, Neoplasm