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

Plaska, Samuel; Liu, Chia-Jen; Lim, Jung Soo; Rege, Juilee; Bick, Nolan; Lerário, Antônio M.; Hammer, Gary D.; Giordano, Thomas J.; Else, Tobias; Tomlins, Scott A.; Rainey, William E.; Udager, Aaron M.

doi:10.1055/a-1212-8803

Cited by 9 publications

(11 citation statements)

References 27 publications

(40 reference statements)

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“…As the rate limiting step for aldosterone synthesis, CYP11B2 overexpression is present in a number of studies investigating gene expression profiles in APAs [ 14 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 ]. Interestingly, several studies have observed heterogeneity in CYP11B2 expression in APAs, with one subgroup overexpressed and another group with either unchanged or even reduced CYP11B2 expression [ 47 , 55 , 56 , 57 ].…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, VSNL1 expression in APAs harboring KCNJ5 mutations is significantly higher than in wild-type tumors [ 52 ]. Glutathione S-Transferase Alpha 1 ( GSTA1 ), an enzyme protecting cells from reactive oxygen species which also serving as transmitter of calcium signaling, presents significantly lower expression in APAs compared to non-aldosterone producing adenomas, while KCNJ5 mutated APAs had significantly lower expression of this gene than did wild-type APAs [ 45 , 69 ].…”

Section: Resultsmentioning

confidence: 99%

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Transcriptomics, Epigenetics, and Metabolomics of Primary Aldosteronism

Spyroglou

Piaditis

Kaltsas

et al. 2021

Cancers

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Introduction: Primary aldosteronism (PA) is the most common cause of endocrine hypertension, mainly caused by aldosterone-producing adenomas or hyperplasia; understanding its pathophysiological background is important in order to provide ameliorative treatment strategies. Over the past several years, significant progress has been documented in this field, in particular in the clarification of the genetic and molecular mechanisms responsible for the pathogenesis of aldosterone-producing adenomas (APAs). Methods: Systematic searches of the PubMed and Cochrane databases were performed for all human studies applying transcriptomic, epigenetic or metabolomic analyses to PA subjects. Studies involving serial analysis of gene expression and microarray, epigenetic studies with methylome analyses and micro-RNA expression profiles, and metabolomic studies focused on improving understanding of the regulation of autonomous aldosterone production in PA were all included. Results: In this review we summarize the main findings in this area and analyze the interplay between primary aldosteronism and several signaling pathways with differential regulation of the RNA and protein expression of several factors involved in, among others, steroidogenesis, calcium signaling, and nuclear, membrane and G-coupled protein receptors. Distinct transcriptomic and metabolomic patterns are also presented herein, depending on the mutational status of APAs. In particular, two partially opposite transcriptional and steroidogenic profiles appear to distinguish APAs carrying a KCNJ5 mutation from all other APAs, which carry different mutations. Conclusions: These findings can substantially contribute to the development of personalized treatment in patients with PA.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Transcriptomics, Epigenetics, and Metabolomics of Primary Aldosteronism

Spyroglou

Piaditis

Kaltsas

et al. 2021

Cancers

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“…In this study, we showed that gene expression profiles from FFPE samples were highly similar to those from fresh frozen samples of the same adrenocortical tumors (ACC, APA, and CPA). In transcriptome profiling using FFPE samples, targeted RNA-seq is often used because of the low yield and quality of RNA extracted from such samples (35,36). Plaska et al reported that targeted RNA-seq (194 target genes) using FFPE samples of adrenocortical tumors (ACC, APA, and CPA) could distinguish between benign and malignant tumors (36).…”

Section: Discussionmentioning

confidence: 99%

“…In transcriptome profiling using FFPE samples, targeted RNA-seq is often used because of the low yield and quality of RNA extracted from such samples (35,36). Plaska et al reported that targeted RNA-seq (194 target genes) using FFPE samples of adrenocortical tumors (ACC, APA, and CPA) could distinguish between benign and malignant tumors (36). However, targeted RNA-seq is not suitable for comprehensive genetic analysis (e.g., detection of novel pathogenic genes) because it restricts the genes that can be analyzed.…”

Section: Discussionmentioning

confidence: 99%

Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples

et al. 2022

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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.

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“…This technology is robust, cheaper and simpler to run compared to full length RNA sequencing 19 . Other gene expression techniques starting from FFPE have been reported in ACC [34][35][36] . However these techniques have not emerged yet as optimal for prognostic determination in ACC.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma

Jouinot

Lippert²,

Sibony

et al. 2022

European Journal of Endocrinology

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Design: Molecular classification is important for diagnosis and prognosis of adrenocortical tumors (ACT). Transcriptome profiles separate adrenocortical adenomas “C2” from carcinomas, and identify two groups of carcinomas “C1A” and “C1B”, of poor and better prognosis respectively. However, many ACT cannot be profiled because of improper or absent freezing procedure, a mandatory requirement so far. The main aim was to determine transcriptome profiles on formalin-fixed paraffin-embedded (FFPE) samples, using the new 3’-end RNA-sequencing technology. A secondary aim was to demonstrate the ability of this technique to explore large FFPE archives, by focusing on the rare oncocytic ACT variants. Methods: We included 131 ACT: a training cohort from Cochin hospital and an independent validation cohort from Wuerzburg hospital. The 3’ transcriptome was generated from FFPE samples using QuantSeq (Lexogen) and NextSeq500 (Illumina). Results: In the training cohort, unsupervised clustering identified 3 groups: “C1A” aggressive carcinomas (N=28, 29%), “C1B” more indolent carcinomas (N=28, 29%), and “C2” adenomas (N=39, 41%). The prognostic value of FFPE transcriptome was confirmed in the validation cohort (5-year OS: 26% in “C1A” (N=26) and 100% in “C1B” (N=10), p=0.003). FFPE transcriptome was an independent prognostic factor in multivariable model including tumor stage and Ki-67 (OS HR 7.5, p=0.01). Oncocytic ACT (N=19) did not form any specific cluster. Oncocytic carcinomas (N=6) and oncocytic ACT of uncertain malignant potential (N=4) were all in “C1B”. Conclusions: The 3’ RNA-sequencing represents a convenient solution for determining ACT molecular class from FFPE samples. This technique should facilitate routine use and large retrospective studies.

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

Cited by 9 publications

References 27 publications

Transcriptomics, Epigenetics, and Metabolomics of Primary Aldosteronism

Transcriptomics, Epigenetics, and Metabolomics of Primary Aldosteronism

Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples

Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma

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