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Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives

Tanca, Alessandro and Addis, Maria Filippa and Pagnozzi, Daniela and Cossu Rocca, Paolo Alessandro and Tonelli, Roberto and Falchi, Giovanni and Eccher, Albino and Roggio, Tonina and Fanciulli, Giuseppe and Uzzau, Sergio (2011) Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives. Journal of Proteomics, Vol. 74 (3), p. 359-370. eISSN 1876-7737. Article.

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DOI: 10.1016/j.jprot.2010.12.001

Abstract

Hospital tissue repositories host an invaluable supply of diseased samples with matched retrospective clinical information. In this work, a recently optimized method for extracting full-length proteins from formalin-fixed, paraffin-embedded (FFPE) tissues was evaluated on lung neuroendocrine tumor (LNET) samples collected from hospital repositories. LNETs comprise a heterogeneous spectrum of diseases, for which subtype-specific diagnostic markers are lacking. Six archival samples diagnosed as typical carcinoid (TC) or small cell lung carcinoma (SCLC) were subjected to a full-length protein extraction followed by a GeLC–MS/MS analysis, enabling the identification of over 300 distinct proteins per tumor subtype. All identified proteins were categorized through DAVID software, revealing a differential distribution of functional classes, such as those involved in RNA processing, response to oxidative stress and ion homeostasis. Moreover, using spectral counting for protein abundance estimation and beta-binomial test as statistical filter, a list of 28 differentially expressed proteins was generated and submitted to pathway analysis by means of Ingenuity Pathway Analysis software. Differential expression of chromogranin-A (more expressed in TCs) and stathmin (more expressed in SCLCs) was consistently confirmed by immunohistochemistry. Therefore, FFPE hospital archival samples can be successfully subjected to proteomic investigations aimed to biomarker discovery following a GeLC–MS/MS label-free approach.

Item Type:Article
ID Code:5443
Status:Published
Refereed:Yes
Uncontrolled Keywords:FFPE, lung neuroendocrine tumors, stathmin, GeLC–MS/MS, spectral counting
Subjects:Area 06 - Scienze mediche > MED/13 Endocrinologia
Area 06 - Scienze mediche > MED/07 Microbiologia e microbiologia clinica
Area 06 - Scienze mediche > MED/08 Anatomia patologica
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > Porto Conte Ricerche, Alghero
001 Università di Sassari > 03 Istituti > Anatomia patologica
002 Altri enti e centri di ricerca del Nord Sardegna > Biosistema s.c.r.l.-Centro di competenza e trasferimento tecnologico biosistema, Sassari
Publisher:Elsevier
eISSN:1876-7737
Copyright Holders:© 2010 Elsevier
Deposited On:18 Feb 2011 13:23

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