Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples
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 sam...
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| Format: | Article |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Endocrinology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fendo.2022.808331/full |
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| author | Norifusa Iwahashi Hironobu Umakoshi Masatoshi Ogata Tazuru Fukumoto Hiroki Kaneko Eriko Terada Shunsuke Katsuhara Naohiro Uchida Katsuhiko Sasaki Maki Yokomoto-Umakoshi Yayoi Matsuda Ryuichi Sakamoto Yoshihiro Ogawa |
| author_facet | Norifusa Iwahashi Hironobu Umakoshi Masatoshi Ogata Tazuru Fukumoto Hiroki Kaneko Eriko Terada Shunsuke Katsuhara Naohiro Uchida Katsuhiko Sasaki Maki Yokomoto-Umakoshi Yayoi Matsuda Ryuichi Sakamoto Yoshihiro Ogawa |
| author_sort | Norifusa Iwahashi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T19:34:51Z |
| format | Article |
| id | doaj.art-26c01cd022f74660b5f18ef080dd8da4 |
| institution | Directory Open Access Journal |
| issn | 1664-2392 |
| language | English |
| last_indexed | 2024-04-11T19:34:51Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Endocrinology |
| spelling | doaj.art-26c01cd022f74660b5f18ef080dd8da42022-12-22T04:06:53ZengFrontiers Media S.A.Frontiers in Endocrinology1664-23922022-02-011310.3389/fendo.2022.808331808331Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded SamplesNorifusa Iwahashi0Hironobu Umakoshi1Masatoshi Ogata2Tazuru Fukumoto3Hiroki Kaneko4Eriko Terada5Shunsuke Katsuhara6Naohiro Uchida7Katsuhiko Sasaki8Maki Yokomoto-Umakoshi9Yayoi Matsuda10Ryuichi Sakamoto11Yoshihiro Ogawa12Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanClinical Laboratory Department, Kyushu Pro Search Limited Liability Partnership, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanDepartment of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JapanWhole 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.https://www.frontiersin.org/articles/10.3389/fendo.2022.808331/fullwhole transcriptome profilingRNA sequencing (RNAseq)formalin-fixed paraffin-embedded samples (FFPE samples)adrenal diseasesadrenocortical tumors |
| spellingShingle | Norifusa Iwahashi Hironobu Umakoshi Masatoshi Ogata Tazuru Fukumoto Hiroki Kaneko Eriko Terada Shunsuke Katsuhara Naohiro Uchida Katsuhiko Sasaki Maki Yokomoto-Umakoshi Yayoi Matsuda Ryuichi Sakamoto Yoshihiro Ogawa Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples Frontiers in Endocrinology whole transcriptome profiling RNA sequencing (RNAseq) formalin-fixed paraffin-embedded samples (FFPE samples) adrenal diseases adrenocortical tumors |
| title | Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples |
| title_full | Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples |
| title_fullStr | Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples |
| title_full_unstemmed | Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples |
| title_short | Whole Transcriptome Profiling of Adrenocortical Tumors Using Formalin-Fixed Paraffin-Embedded Samples |
| title_sort | whole transcriptome profiling of adrenocortical tumors using formalin fixed paraffin embedded samples |
| topic | whole transcriptome profiling RNA sequencing (RNAseq) formalin-fixed paraffin-embedded samples (FFPE samples) adrenal diseases adrenocortical tumors |
| url | https://www.frontiersin.org/articles/10.3389/fendo.2022.808331/full |
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