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

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Title: Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives
Authors: Tanca, Alessandro1,2, Addis, Maria Filippa1 addis@portocontericerche.it, Pagnozzi, Daniela1, Cossu-Rocca, Paolo3, Tonelli, Roberto1, Falchi, Giovanni1,4, Eccher, Albino5, Roggio, Tonina1, Fanciulli, Giuseppe6, Uzzau, Sergio1,2
Source: Journal of Proteomics. Mar2011, Vol. 74 Issue 3, p359-370. 12p.
Subjects: Proteomics, Formaldehyde, Paraffin wax, Neuroendocrine tumors, Oxidative stress, Homeostasis, Immunohistochemistry, Hospital records
Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Proteomics is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
An: 57374942
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PubType: Academic Journal
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  Data: Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives
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  Data: <searchLink fieldCode="AR" term="%22Tanca%2C+Alessandro%22">Tanca, Alessandro</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Addis%2C+Maria+Filippa%22">Addis, Maria Filippa</searchLink><relatesTo>1</relatesTo><i> addis@portocontericerche.it</i><br /><searchLink fieldCode="AR" term="%22Pagnozzi%2C+Daniela%22">Pagnozzi, Daniela</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Cossu-Rocca%2C+Paolo%22">Cossu-Rocca, Paolo</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Tonelli%2C+Roberto%22">Tonelli, Roberto</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Falchi%2C+Giovanni%22">Falchi, Giovanni</searchLink><relatesTo>1,4</relatesTo><br /><searchLink fieldCode="AR" term="%22Eccher%2C+Albino%22">Eccher, Albino</searchLink><relatesTo>5</relatesTo><br /><searchLink fieldCode="AR" term="%22Roggio%2C+Tonina%22">Roggio, Tonina</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Fanciulli%2C+Giuseppe%22">Fanciulli, Giuseppe</searchLink><relatesTo>6</relatesTo><br /><searchLink fieldCode="AR" term="%22Uzzau%2C+Sergio%22">Uzzau, Sergio</searchLink><relatesTo>1,2</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Proteomics%22">Journal of Proteomics</searchLink>. Mar2011, Vol. 74 Issue 3, p359-370. 12p.
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  Data: <searchLink fieldCode="DE" term="%22Proteomics%22">Proteomics</searchLink><br /><searchLink fieldCode="DE" term="%22Formaldehyde%22">Formaldehyde</searchLink><br /><searchLink fieldCode="DE" term="%22Paraffin+wax%22">Paraffin wax</searchLink><br /><searchLink fieldCode="DE" term="%22Neuroendocrine+tumors%22">Neuroendocrine tumors</searchLink><br /><searchLink fieldCode="DE" term="%22Oxidative+stress%22">Oxidative stress</searchLink><br /><searchLink fieldCode="DE" term="%22Homeostasis%22">Homeostasis</searchLink><br /><searchLink fieldCode="DE" term="%22Immunohistochemistry%22">Immunohistochemistry</searchLink><br /><searchLink fieldCode="DE" term="%22Hospital+records%22">Hospital records</searchLink>
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  Data: 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. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Journal of Proteomics is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1016/j.jprot.2010.12.001
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      – Code: eng
        Text: English
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        PageCount: 12
        StartPage: 359
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        Type: general
      – SubjectFull: Formaldehyde
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      – SubjectFull: Paraffin wax
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      – SubjectFull: Neuroendocrine tumors
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      – SubjectFull: Immunohistochemistry
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      – SubjectFull: Hospital records
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              Text: Mar2011
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