Oncotarget

Research Papers:

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

Jun Fan, Raya Khanin, Hitomi Sakamoto, Yi Zhong, Chelsea Michael, Derwin Pena, Breanna Javier, Laura D. Wood and Christine A. Iacobuzio-Donahue _

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Oncotarget. 2016; 7:66906-66921. https://doi.org/10.18632/oncotarget.11836

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Abstract

Jun Fan1, Raya Khanin2, Hitomi Sakamoto1, Yi Zhong1, Chelsea Michael3, Derwin Pena3, Breanna Javier1, Laura D. Wood6, Christine A. Iacobuzio-Donahue3,4,5

1Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA

2Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA

3Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA

4Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA

5David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA

6Department 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.


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