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

Anne Jouinot; Juliane Lippert; Mathilde Sibony; Florian Violon; Lindsay Jeanpierre; Daniel De Murat; Roberta Armignacco; Amandine Septier; Karine Perlemoine; Franck Letourneur; Brigitte Izac; Bruno Ragazzon; Karen Leroy; Eric Pasmant; Marie-odile North; Sébastien Gaujoux; Bertrand Dousset; Lionel Groussin; Rossella Libe; Benoit Terris; Martin Fassnacht; Cristina L Ronchi; Jérôme Bertherat; Guillaume Assie

doi:10.1530/EJE-21-1228

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

Anne Jouinot, Juliane Lippert, Mathilde Sibony, Florian Violon, Lindsay Jeanpierre, Daniel De Murat, Roberta Armignacco, Amandine Septier, Karine Perlemoine, Franck Letourneur, Brigitte Izac, Bruno Ragazzon, Karen Leroy, Eric Pasmant, Marie-odile North, Sébastien Gaujoux, Bertrand Dousset, Lionel Groussin, Rossella Libe, Benoit TerrisMartin Fassnacht, Cristina L Ronchi, Jérôme Bertherat, Guillaume Assie

Metabolism and Systems Science

Research output: Contribution to journal › Article › peer-review

70 Downloads (Pure)

Abstract

Design: Molecular classification is important for the 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 procedures, 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, Vienna, Austria) and NextSeq500 (Illumina, San Diego, CA, USA).

Results: In the training cohort, unsupervised clustering identified three 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 a 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.

Original language	English
Pages (from-to)	607-617
Number of pages	11
Journal	European Journal of Endocrinology
Volume	186
Issue number	6
DOIs	https://doi.org/10.1530/EJE-21-1228
Publication status	Published - 21 Apr 2022

Bibliographical note

Funding Information:
This work was supported by the Programme de Recherche Translationnelle en Cancérologie to the COMETE network (PRT-K COMETE-TACT 阀C and PRT-K COMETE-CARE), the CARPEM (CAncer Research for PErsonalized Medicine), the 阀TMO Cancer of AV 阀ESAN (Alliance pour les Sciences de la Vie et de la Santé) on funds administrated by 阀NSERM (A J received a PhD and post-doctoral grant), the Deutsche Krebshilfe (70112969 to C L R and M F) and Deutsche Forschungsgemeinschaft (no. 314061271 – CRC/TRR 205, .FA-466/4-2 and FA-466/8-1 to M F, and RO-5435/3-1 to C L R).

Publisher Copyright:
© 2022 The authors Published by Bioscientifica Ltd.

Keywords

Adrenal Cortex Neoplasms/diagnosis
Adrenocortical Carcinoma/diagnosis
Formaldehyde
Gene Expression Profiling/methods
Humans
Paraffin
Paraffin Embedding/methods
Prognosis
RNA
Retrospective Studies
Tissue Fixation/methods
Transcriptome

Access to Document

10.1530/EJE-21-1228Licence: Creative Commons: Attribution (CC BY)

JouinotA2022TranscriptomeFinal published version, 3.94 MBLicence: Creative Commons: Attribution (CC BY)

Cite this

Jouinot, A., Lippert, J., Sibony, M., Violon, F., Jeanpierre, L., De Murat, D., Armignacco, R., Septier, A., Perlemoine, K., Letourneur, F., Izac, B., Ragazzon, B., Leroy, K., Pasmant, E., North, M., Gaujoux, S., Dousset, B., Groussin, L., Libe, R., ... Assie, G. (2022). Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma. European Journal of Endocrinology, 186(6), 607-617. https://doi.org/10.1530/EJE-21-1228

@article{abecf786407c4d4d870d7d13c8b8ea63,

title = "Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma",

abstract = "Design: Molecular classification is important for the 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 procedures, 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, Vienna, Austria) and NextSeq500 (Illumina, San Diego, CA, USA). Results: In the training cohort, unsupervised clustering identified three 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 a 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.",

keywords = "Adrenal Cortex Neoplasms/diagnosis, Adrenocortical Carcinoma/diagnosis, Formaldehyde, Gene Expression Profiling/methods, Humans, Paraffin, Paraffin Embedding/methods, Prognosis, RNA, Retrospective Studies, Tissue Fixation/methods, Transcriptome",

author = "Anne Jouinot and Juliane Lippert and Mathilde Sibony and Florian Violon and Lindsay Jeanpierre and {De Murat}, Daniel and Roberta Armignacco and Amandine Septier and Karine Perlemoine and Franck Letourneur and Brigitte Izac and Bruno Ragazzon and Karen Leroy and Eric Pasmant and Marie-odile North and S{\'e}bastien Gaujoux and Bertrand Dousset and Lionel Groussin and Rossella Libe and Benoit Terris and Martin Fassnacht and Ronchi, {Cristina L} and J{\'e}r{\^o}me Bertherat and Guillaume Assie",

note = "Funding Information: This work was supported by the Programme de Recherche Translationnelle en Canc{\'e}rologie to the COMETE network (PRT-K COMETE-TACT 阀C and PRT-K COMETE-CARE), the CARPEM (CAncer Research for PErsonalized Medicine), the 阀TMO Cancer of AV 阀ESAN (Alliance pour les Sciences de la Vie et de la Sant{\'e}) on funds administrated by 阀NSERM (A J received a PhD and post-doctoral grant), the Deutsche Krebshilfe (70112969 to C L R and M F) and Deutsche Forschungsgemeinschaft (no. 314061271 – CRC/TRR 205, .FA-466/4-2 and FA-466/8-1 to M F, and RO-5435/3-1 to C L R). Publisher Copyright: {\textcopyright} 2022 The authors Published by Bioscientifica Ltd.",

year = "2022",

month = apr,

day = "21",

doi = "10.1530/EJE-21-1228",

language = "English",

volume = "186",

pages = "607--617",

journal = "European Journal of Endocrinology",

issn = "0804-4643",

publisher = "BioScientifica",

number = "6",

}

Jouinot, A, Lippert, J, Sibony, M, Violon, F, Jeanpierre, L, De Murat, D, Armignacco, R, Septier, A, Perlemoine, K, Letourneur, F, Izac, B, Ragazzon, B, Leroy, K, Pasmant, E, North, M, Gaujoux, S, Dousset, B, Groussin, L, Libe, R, Terris, B, Fassnacht, M, Ronchi, CL, Bertherat, J & Assie, G 2022, 'Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma', European Journal of Endocrinology, vol. 186, no. 6, pp. 607-617. https://doi.org/10.1530/EJE-21-1228

TY - JOUR

T1 - Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma

AU - Jouinot, Anne

AU - Lippert, Juliane

AU - Sibony, Mathilde

AU - Violon, Florian

AU - Jeanpierre, Lindsay

AU - De Murat, Daniel

AU - Armignacco, Roberta

AU - Septier, Amandine

AU - Perlemoine, Karine

AU - Letourneur, Franck

AU - Izac, Brigitte

AU - Ragazzon, Bruno

AU - Leroy, Karen

AU - Pasmant, Eric

AU - North, Marie-odile

AU - Gaujoux, Sébastien

AU - Dousset, Bertrand

AU - Groussin, Lionel

AU - Libe, Rossella

AU - Terris, Benoit

AU - Fassnacht, Martin

AU - Ronchi, Cristina L

AU - Bertherat, Jérôme

AU - Assie, Guillaume

N1 - Funding Information: This work was supported by the Programme de Recherche Translationnelle en Cancérologie to the COMETE network (PRT-K COMETE-TACT 阀C and PRT-K COMETE-CARE), the CARPEM (CAncer Research for PErsonalized Medicine), the 阀TMO Cancer of AV 阀ESAN (Alliance pour les Sciences de la Vie et de la Santé) on funds administrated by 阀NSERM (A J received a PhD and post-doctoral grant), the Deutsche Krebshilfe (70112969 to C L R and M F) and Deutsche Forschungsgemeinschaft (no. 314061271 – CRC/TRR 205, .FA-466/4-2 and FA-466/8-1 to M F, and RO-5435/3-1 to C L R). Publisher Copyright: © 2022 The authors Published by Bioscientifica Ltd.

PY - 2022/4/21

Y1 - 2022/4/21

N2 - Design: Molecular classification is important for the 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 procedures, 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, Vienna, Austria) and NextSeq500 (Illumina, San Diego, CA, USA). Results: In the training cohort, unsupervised clustering identified three 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 a 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.

AB - Design: Molecular classification is important for the 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 procedures, 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, Vienna, Austria) and NextSeq500 (Illumina, San Diego, CA, USA). Results: In the training cohort, unsupervised clustering identified three 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 a 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.

KW - Adrenal Cortex Neoplasms/diagnosis

KW - Adrenocortical Carcinoma/diagnosis

KW - Formaldehyde

KW - Gene Expression Profiling/methods

KW - Humans

KW - Paraffin

KW - Paraffin Embedding/methods

KW - Prognosis

KW - RNA

KW - Retrospective Studies

KW - Tissue Fixation/methods

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=85128801282&partnerID=8YFLogxK

U2 - 10.1530/EJE-21-1228

DO - 10.1530/EJE-21-1228

M3 - Article

C2 - 35266879

SN - 0804-4643

VL - 186

SP - 607

EP - 617

JO - European Journal of Endocrinology

JF - European Journal of Endocrinology

IS - 6

ER -

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

Abstract

Bibliographical note

Keywords

Access to Document

Fingerprint

Cite this