Abstract
Whole transcriptome profiling is a promising technique in adrenal studies; however, whole transcriptome profiling of adrenal disease using formalin-fixed paraffin-embedded (FFPE) samples has to be further explored. The aim of this study was to evaluate the utility of transcriptome data from FFPE samples of adrenocortical tumors. We performed whole transcriptome profiling of FFPE and fresh frozen samples of adrenocortical carcinoma (ACC, n = 3), aldosterone-producing adenoma (APA, n = 3), and cortisol-producing adenoma (CPA, n = 3), and examined the similarity between the transcriptome data. We further examined whether the transcriptome data of FFPE samples could be used to distinguish tumor types and detect marker genes. The number of read counts was smaller in FFPE samples than in fresh frozen samples (P < 0.01), while the number of genes detected was similar (P = 0.39). The gene expression profiles of FFPE and fresh frozen samples were highly correlated (r = 0.93, P < 0.01). Tumor types could be distinguished by consensus clustering and principal component analysis using transcriptome data from FFPE samples. In the differential expression analysis between ACC and APA-CPA, known marker genes of ACC (e.g., CCNB2, TOP2A, and MAD2L1) were detected in FFPE samples of ACC. In the differential expression analysis between APA and CPA, known marker genes of APA (e.g., CYP11B2, VSNL1, and KCNJ5) were detected in the APA of FFPE samples. The results suggest that FFPE samples may be a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors.
Highlights
The adrenal cortex produces a variety of steroid hormones and maintains metabolic homeostasis [1]
Total RNA extracted from formalin-fixed paraffin-embedded (FFPE) samples had lower RNA yield and quality parameters compared to those from fresh frozen samples (RNA concentration [mean 36.0 vs 464.5 mL, Wilcoxon rank sum test: P value < 0.01], RNA integrity number (RIN) [mean 2.2 vs 7.9, P value < 0.01], DV200 [mean 47.6 vs 71.0, P value < 0.01])
To evaluate the utility of transcriptome data obtained from FFPE samples in adrenocortical tumors, we compared transcriptome data from FFPE samples of Adrenocortical carcinoma (ACC), Aldosterone-producing adenoma (APA), and cortisol-producing adenoma (CPA) with those from fresh frozen samples of the same tumors
Summary
The adrenal cortex produces a variety of steroid hormones and maintains metabolic homeostasis [1]. Aldosterone, produced in the zona glomerulosa, is involved in the regulation of both the Na/K balance and blood pressure, while cortisol, produced in the zona fasciculata, plays an important role in the regulation of glucose metabolism and the immune response. Some adrenocortical adenomas produce these steroid hormones inappropriately and cause a variety of clinical syndromes. Aldosterone-producing adenoma (APA) causes primary aldosteronism, and cortisol-producing adenoma (CPA) causes Cushing’s syndrome [2, 3]. Adrenocortical carcinoma (ACC) is a rare malignant tumor that arises in the adrenal cortex and has a very poor prognosis [4]. Previous transcriptome studies have shown that APA, CPA, and ACC have distinct gene expression profiles, suggesting that transcriptome profiling can contribute to the accurate diagnosis of adrenocortical tumors [5, 6]. Transcriptome profiling is a promising technique for elucidating the pathogenesis of adrenal diseases in terms of endocrine function and adrenal differentiation [7, 8]
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