Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues

Formalin‐fixed paraffin‐embedded (FFPE) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow‐up.

[1]  Shuji Yamashita,et al.  Heat-induced antigen retrieval: mechanisms and application to histochemistry. , 2007, Progress in histochemistry and cytochemistry.

[2]  Daniel C. Liebler,et al.  Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis* , 2009, Molecular & Cellular Proteomics.

[3]  R. Klopfleisch,et al.  Excavation of a buried treasure--DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. , 2011, Histology and histopathology.

[4]  Daniela Berg,et al.  Molecular profiling of signalling pathways in formalin-fixed and paraffin-embedded cancer tissues. , 2010, European journal of cancer.

[5]  R. Casadonte,et al.  Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry , 2011, Nature Protocols.

[6]  T. Godfrey,et al.  Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction. , 2000, The Journal of molecular diagnostics : JMD.

[7]  T. Veenstra,et al.  Mass spectrometric analysis of formalin‐fixed paraffin‐embedded tissue: Unlocking the proteome within , 2006, Proteomics.

[8]  J. Eng,et al.  Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues , 2007, Oncogene.

[9]  P. Selby,et al.  Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin‐fixed paraffin‐embedded tissues using western blotting , 2009, The Journal of pathology.

[10]  Yuan Tian,et al.  Isolation of proteins by heat-induced extraction from formalin-fixed, paraffin-embedded tissue and preparation of tryptic peptides for mass spectrometric analysis. , 2010, Current protocols in molecular biology.

[11]  A. Tanca,et al.  Generation of high‐quality protein extracts from formalin‐fixed, paraffin‐embedded tissues , 2009, Proteomics.

[12]  Heath C. Thomas,et al.  Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry , 2009, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[13]  T. Veenstra,et al.  Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry , 2004, Proteomics.

[14]  Li Yang,et al.  Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. , 2008, Journal of proteome research.

[15]  R. E. Cunningham,et al.  ‘Tissue surrogates’ as a model for archival formalin-fixed paraffin-embedded tissues , 2007, Laboratory Investigation.

[16]  M. Aubele,et al.  Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. , 2010, Journal of proteome research.

[17]  Lixin Xu,et al.  Modeling formalin fixation and antigen retrieval with bovine pancreatic RNase A II. Interrelationship of cross-linking, immunoreactivity, and heat treatment , 2004, Laboratory Investigation.

[18]  C. Dani,et al.  Extreme instability of myc mRNA in normal and transformed human cells. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[19]  B. Balgley,et al.  Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. , 2009, Journal of proteome research.

[20]  Andrea Urbani,et al.  Protein unlocking procedures of formalin‐fixed paraffin‐embedded tissues: Application to MALDI‐TOF Imaging MS investigations , 2008, Proteomics.

[21]  J. Solassol,et al.  KRAS Mutation Detection in Paired Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Colorectal Cancer Tissues , 2011, International journal of molecular sciences.

[22]  K. Smalley,et al.  Using quantitative proteomic analysis to understand genotype specific intrinsic drug resistance in melanoma , 2011, Oncotarget.

[23]  C. Röcken,et al.  Comparison of different tissue sampling methods for protein extraction from formalin-fixed and paraffin-embedded tissue specimens. , 2010, Experimental and molecular pathology.

[24]  M. Mann,et al.  Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. , 2010, Journal of proteome research.

[25]  E. Petricoin,et al.  Evaluation of ethanol‐fixed, paraffin‐embedded tissues for proteomic applications , 2003, Proteomics.

[26]  György Marko-Varga,et al.  Preferential expression of potential markers for cancer stem cells in large cell neuroendocrine carcinoma of the lung. An FFPE proteomic study , 2011, Journal of Clinical Bioinformatics.

[27]  J. Eng,et al.  Proteomics Analysis of Human Coronary Atherosclerotic Plaque , 2007, Molecular & Cellular Proteomics.

[28]  N Seta,et al.  Protein glycosylation and diseases: blood and urinary oligosaccharides as markers for diagnosis and therapeutic monitoring. , 2000, Clinical chemistry.

[29]  Matthias Mann,et al.  High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. , 2011, Journal of proteome research.

[30]  S. Schully,et al.  Use of Oncotype DX in Women with Node-Positive Breast Cancer , 2011, PLoS currents.

[31]  T. O'Leary,et al.  Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates , 2010, PloS one.

[32]  S. Kornfeld Diseases of abnormal protein glycosylation: an emerging area. , 1998, The Journal of clinical investigation.

[33]  Chang-Won Lee,et al.  Proteome analysis of human stomach tissue: Separation of soluble proteins by two‐dimensional polyacrylamide gel electrophoresis and identification by mass spectrometry , 2002, Electrophoresis.

[34]  B. Balgley,et al.  Protein Extraction from Formalin-fixed, Paraffin-embedded Tissue Sections: Quality Evaluation by Mass Spectrometry , 2006, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[35]  M. Chung,et al.  Differential recovery of membrane proteins after extraction by aqueous methanol and trifluoroethanol , 2007, Proteomics.

[36]  P. Roller,et al.  Formaldehyde fixation. , 1985, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[37]  J. Nährig,et al.  Quantitative protein analysis from formalin‐fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis , 2007, The Journal of pathology.

[38]  A. Tanca,et al.  Impact of fixation time on GeLC-MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues. , 2011, Journal of proteomics.

[39]  S. Bogen,et al.  A molecular mechanism of formalin fixation and antigen retrieval. , 2004, American journal of clinical pathology.

[40]  Rohit Bhargava,et al.  Histopathologic variables predict Oncotype DX™ Recurrence Score , 2008, Modern Pathology.

[41]  Y. Okada,et al.  Mechanisms of heat-induced antigen retrieval: analyses in vitro employing SDS-PAGE and immunohistochemistry. , 2005, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[42]  T. Griffin,et al.  Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae. , 2005, Analytical Chemistry.

[43]  Nathan L. Avaritt,et al.  A quantitative proteomic analysis of FFPE melanoma , 2011, Journal of cutaneous pathology.

[44]  Carsten Denkert,et al.  Quantitative Determination of Estrogen Receptor, Progesterone Receptor, and HER2 mRNA in Formalin-fixed Paraffin-embedded Tissue—A New Option for Predictive Biomarker Assessment in Breast Cancer , 2011, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[45]  S. Hewitt,et al.  Histo-proteomic profiling of formalin-fixed, paraffin-embedded tissue , 2010, Expert review of proteomics.

[46]  Yongheng Chen,et al.  Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry , 2010, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[47]  B. Leyland-Jones,et al.  Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform , 2011, British Journal of Cancer.

[48]  T. Conrads,et al.  Differential proteomic analysis of late-stage and recurrent breast cancer from formalin-fixed paraffin-embedded tissues. , 2011, Journal of proteome research.

[49]  K. Elenitoba-Johnson,et al.  Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS , 2005, Laboratory Investigation.

[50]  Juergen Kast,et al.  Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. , 2008, Analytica chimica acta.

[51]  K. Becker,et al.  Producing reverse phase protein microarrays from formalin-fixed tissues. , 2011, Methods in molecular biology.

[52]  D. DeVoe,et al.  Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens , 2007, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[53]  E. Espinosa,et al.  Protein phosphorylation analysis in archival clinical cancer samples by shotgun and targeted proteomics approaches. , 2011, Molecular bioSystems.

[54]  Ronald J Moore,et al.  Development and evaluation of a micro- and nanoscale proteomic sample preparation method. , 2005, Journal of proteome research.

[55]  T. O'Leary,et al.  Effects of formaldehyde fixation on protein secondary structure: a calorimetric and infrared spectroscopic investigation. , 1991, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[56]  P. Selby,et al.  Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. , 2008, Molecular bioSystems.

[57]  H. Kocher,et al.  Proteome of formalin‐fixed paraffin‐embedded pancreatic ductal adenocarcinoma and lymph node metastases , 2012, The Journal of pathology.

[58]  H. Puchtler,et al.  On the chemistry of formaldehyde fixation and its effects on immunohistochemical reactions , 2004, Histochemistry.

[59]  S. Merchant,et al.  Efficient method for the proteomic analysis of fixed and embedded tissues. , 2005, Journal of proteome research.

[60]  P. Cohen The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. , 2001, European journal of biochemistry.

[61]  Linda S. Lee,et al.  Proteomic Analysis of Formalin-Fixed Paraffin-Embedded Pancreatic Tissue Using Liquid Chromatography Tandem Mass Spectrometry , 2012, Pancreas.

[62]  R. Tonelli,et al.  Proteomic analysis of formalin-fixed, paraffin-embedded lung neuroendocrine tumor samples from hospital archives. , 2011, Journal of proteomics.

[63]  Yuan Tian,et al.  N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. , 2009, Journal of proteome research.

[64]  M. Buck,et al.  Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins , 1998, Quarterly Reviews of Biophysics.

[65]  Pornpimol Charoentong,et al.  Mathematical models for translational and clinical oncology , 2013, Journal of Clinical Bioinformatics.

[66]  A. Adai,et al.  Global microRNA expression profiling of microdissected tissues identifies miR‐135b as a novel biomarker for pancreatic ductal adenocarcinoma , 2012, International journal of cancer.

[67]  R. Langer,et al.  Protein Microarray-based Comparison of HER2, Estrogen Receptor, and Progesterone Receptor Status in Core Biopsies and Surgical Specimens From FFPE Breast Cancer Tissues , 2011, Applied immunohistochemistry & molecular morphology : AIMM.

[68]  S. Hewitt,et al.  A well‐based reverse‐phase protein array applicable to extracts from formalin‐fixed paraffin‐embedded tissue , 2008, Proteomics. Clinical applications.

[69]  R. Langer,et al.  Discovery of New Molecular Subtypes in Oesophageal Adenocarcinoma , 2011, PloS one.

[70]  H. Zou,et al.  Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. , 2007, Journal of proteome research.

[71]  J. Garin,et al.  Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins , 2000, Electrophoresis.

[72]  M. Monden,et al.  Extraction and Analysis of Diagnostically Useful Proteins from Formalin-fixed, Paraffin-embedded Tissue Sections , 1998, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.