Literature DB >> 31935107

HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics.

Dylan M Marchione1, Ilyana Ilieva2, Kyle Devins2, Danielle Sharpe2, Darryl J Pappin3,4, Benjamin A Garcia1, John P Wilson4, John B Wojcik2.   

Abstract

Massive formalin-fixed, paraffin-embedded (FFPE) tissue archives exist worldwide, representing an invaluable resource for clinical proteomics research. However, current protocols for FFPE proteomics lack standardization, efficiency, reproducibility, and scalability. Here we present high-yield protein extraction and recovery by direct solubilization (HYPERsol), an optimized workflow using ultrasonication and S-Trap sample processing that enables proteome coverage and quantification from FFPE samples comparable to that achieved from flash-frozen tissue (average R = 0.936). When applied to archival samples, HYPERsol resulted in high-quality data from FFPE specimens in storage for up to 17 years, and may enable the discovery of new immunohistochemical markers.

Entities:  

Keywords:  FFPE; S-Trap; clinical proteomics; immunohistochemistry; sample preparation; tissue

Mesh：

Substances：

Year:  2020        PMID： 31935107      PMCID： PMC7515636          DOI： 10.1021/acs.jproteome.9b00686

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  29 in total

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Journal:  Am J Surg Pathol       Date:  2007-02       Impact factor: 6.394

4.  Archived formalin-fixed paraffin-embedded (FFPE) blocks: A valuable underexploited resource for extraction of DNA, RNA, and protein.

Authors:  Theresa J Kokkat; Miral S Patel; Diane McGarvey; Virginia A LiVolsi; Zubair W Baloch
Journal:  Biopreserv Biobank       Date:  2013-04       Impact factor: 2.300

5.  Improving the Proteomic Analysis of Archival Tissue by Using Pressure-Assisted Protein Extraction: A Mechanistic Approach.

Authors:  Carol B Fowler; Timothy J O'Leary; Jeffrey T Mason
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6.  Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding.

Authors:  Ying Zhang; Markus Muller; Bo Xu; Yutaka Yoshida; Oliver Horlacher; Frederic Nikitin; Samuel Garessus; Sameh Magdeldin; Naohiko Kinoshita; Hidehiko Fujinaka; Eishin Yaoita; Miki Hasegawa; Frederique Lisacek; Tadashi Yamamoto
Journal:  Proteomics       Date:  2015-05-03       Impact factor: 3.984

7.  Loss of H3K27 trimethylation is not suitable for distinguishing malignant peripheral nerve sheath tumor from melanoma: a study of 387 cases including mimicking lesions.

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Journal:  Mod Pathol       Date:  2017-07-28       Impact factor: 7.842

Review 8.  Formaldehyde fixation.

Authors:  C H Fox; F B Johnson; J Whiting; P P Roller
Journal:  J Histochem Cytochem       Date:  1985-08       Impact factor: 2.479

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Journal:  J Clin Pathol       Date:  2001-03       Impact factor: 3.411

10.  Histone H3K27 dimethyl loss is highly specific for malignant peripheral nerve sheath tumor and distinguishes true PRC2 loss from isolated H3K27 trimethyl loss.

Authors:  Dylan M Marchione; Amanda Lisby; Angela N Viaene; Mariarita Santi; MacLean Nasrallah; Li-Ping Wang; Erik A Williams; Ana B Larque; Ivan Chebib; Benjamin A Garcia; John B Wojcik
Journal:  Mod Pathol       Date:  2019-06-07       Impact factor: 7.842
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2.  A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens.

Authors:  Georgia Mitsa; Qianyu Guo; Christophe Goncalves; Samuel E J Preston; Vincent Lacasse; Adriana Aguilar-Mahecha; Naciba Benlimame; Mark Basik; Alan Spatz; Gerald Batist; Wilson H Miller; Sonia V Del Rincon; René P Zahedi; Christoph H Borchers
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3.  Evolution of proteomics technologies for understanding respiratory syncytial virus pathogenesis.

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Journal:  Expert Rev Proteomics       Date:  2021-05-31       Impact factor: 4.250

4.  Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period.

Authors:  Frank Maixner; Mohamed S Sarhan; Kun D Huang; Adrian Tett; Alexander Schoenafinger; Stefania Zingale; Aitor Blanco-Míguez; Paolo Manghi; Jan Cemper-Kiesslich; Wilfried Rosendahl; Ulrike Kusebauch; Seamus R Morrone; Michael R Hoopmann; Omar Rota-Stabelli; Thomas Rattei; Robert L Moritz; Klaus Oeggl; Nicola Segata; Albert Zink; Hans Reschreiter; Kerstin Kowarik
Journal:  Curr Biol       Date:  2021-10-13       Impact factor: 10.834

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