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 Delong Wood, Christine A. Iacobuzio-Donahue

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)66906-66921
Number of pages16
JournalOncotarget
Volume7
Issue number41
DOIs
StatePublished - 2016

Fingerprint

Nucleic Acids
Autopsy
Research
Neoplasms
RNA
RNA Sequence Analysis
DNA Damage
DNA
Therapeutics

Keywords

  • Autopsy
  • Metastasis
  • Post-mortem
  • RNA
  • RNA sequencing

ASJC Scopus subject areas

  • Oncology

Cite this

Fan, J., Khanin, R., Sakamoto, H., Zhong, Y., Michael, C., Pena, D., ... Iacobuzio-Donahue, C. A. (2016). Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program. Oncotarget, 7(41), 66906-66921. https://doi.org/10.18632/oncotarget.11836

Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program. / Fan, Jun; Khanin, Raya; Sakamoto, Hitomi; Zhong, Yi; Michael, Chelsea; Pena, Derwin; Javier, Breanna; Wood, Laura Delong; Iacobuzio-Donahue, Christine A.

In: Oncotarget, Vol. 7, No. 41, 2016, p. 66906-66921.

Research output: Contribution to journalArticle

Fan, J, Khanin, R, Sakamoto, H, Zhong, Y, Michael, C, Pena, D, Javier, B, Wood, LD & Iacobuzio-Donahue, CA 2016, 'Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program', Oncotarget, vol. 7, no. 41, pp. 66906-66921. https://doi.org/10.18632/oncotarget.11836
Fan, Jun ; Khanin, Raya ; Sakamoto, Hitomi ; Zhong, Yi ; Michael, Chelsea ; Pena, Derwin ; Javier, Breanna ; Wood, Laura Delong ; Iacobuzio-Donahue, Christine A. / Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program. In: Oncotarget. 2016 ; Vol. 7, No. 41. pp. 66906-66921.
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