Targeted RNAseq of Formalin-Fixed Paraffin-Embedded Tissue to Differentiate among Benign and Malignant Adrenal Cortical Tumors

Samuel W. Plaska, Chia Jen Liu, Jung Soo Lim, Juilee Rege, Nolan R. Bick, Antonio M. Lerario, Gary D. Hammer, Thomas J. Giordano, Tobias Else, Scott A. Tomlins, William E. Rainey, Aaron M. Udager

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7 Citations (Scopus)


Lack of routine fresh or frozen tissue is a barrier to widespread transcriptomic analysis of adrenal cortical tumors and an impediment to translational research in endocrinology and endocrine oncology. Our group has previously pioneered the use of targeted amplicon-based next-generation sequencing for archival formalin-fixed paraffin-embedded (FFPE) adrenal tissue specimens to characterize the spectrum of somatic mutations in various forms of primary aldosteronism. Herein, we developed and validated a novel 194-amplicon targeted next-generation RNA sequencing (RNAseq) assay for transcriptomic analysis of adrenal tumors using clinical-grade FFPE specimens. Targeted RNAseq-derived expression values for 27 adrenal cortical tumors, including aldosterone-producing adenomas (APA; n=8), cortisol-producing adenomas (CPA; n=11), and adrenal cortical carcinomas (ACC; n=8), highlighted known differentially-expressed genes (DEGs; i. e., CYP11B2, IGF2, etc.) and tumor type-specific transcriptional modules (i. e., high cell cycle/proliferation transcript expression in ACC, etc.), and a subset of DEGs was validated orthogonally using quantitative reverse transcription PCR (qRT-PCR). Finally, unsupervised hierarchical clustering using a subset of high-confidence DEGs revealed three discrete clusters representing APA, CPA, and ACC tumors with corresponding unique gene expression signatures, suggesting potential clinical utility for a transcriptomic-based approach to tumor classification. Overall, these data support the use of targeted amplicon-based RNAseq for comprehensive transcriptomic profiling of archival FFPE adrenal tumor material and indicate that this approach may facilitate important translational research opportunities for the study of these tumors.

Original languageEnglish
Pages (from-to)607-613
Number of pages7
JournalHormone and Metabolic Research
Issue number8
Publication statusPublished - 2020 Aug 1

Bibliographical note

Funding Information:
W.E.R. is supported by the National Institutes of Health/National Institute ofDiabetes and Digestive and Kidney Diseases (R01 DK106618). G.D.H. is supported by the Department of Defense Congressionally Directed Medical Research Programs (W81XWH-19-1-0623 and W81XWH-19-1-0528).

Publisher Copyright:
© 2020 Georg Thieme Verlag KG Stuttgart New York.

All Science Journal Classification (ASJC) codes

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Endocrinology
  • Clinical Biochemistry
  • Biochemistry, medical


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