Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

// Jun Fan 1 , Raya Khanin 2 , Hitomi Sakamoto 1 , Yi Zhong 1 , Chelsea Michael 3 , Derwin Pena 3 , Breanna Javier 1 , Laura D. Wood 6 , Christine A. Iacobuzio-Donahue 3, 4, 5 1 Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA 2 Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA 3 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA 4 Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA 5 David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA 6 Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA Correspondence to: Christine A. Iacobuzio-Donahue, email: iacobuzc@mskcc.org Keywords: autopsy, RNA, post-mortem, RNA sequencing, metastasis Received: July 22, 2016      Accepted: August 31, 2016      Published: September 02, 2016 ABSTRACT The last decade has seen a marked rise in the use of cancer tissues obtained from research autopsies. Such resources have been invaluable for studying cancer evolution or the mechanisms of therapeutic resistance to targeted therapies. Degradation of biomolecules is a potential challenge to usage of cancer tissues obtained in the post-mortem setting and remains incompletely studied. We analysed the nucleic acid quality in 371 different frozen tissue samples collected from 80 patients who underwent a research autopsy, including eight normal tissue types, primary and metastatic tumors. Our results indicate that RNA integrity number (RIN) of normal tissues decline with the elongation of post-mortem interval (PMI) in a tissue-type specific manner. Unlike normal tissues, the RNA quality of cancer tissues is highly variable with respect to post-mortem interval. The kinetics of DNA damage also has tissue type-specific features. Moreover, while DNA degradation is an indicator of low RNA quality, the converse is not true. Finally, we show that despite RIN values as low as 5.0, robust data can be obtained by RNA sequencing that reliably discriminates expression signatures.