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Kane LE, Mellotte GS, Mylod E, Dowling P, Marcone S, Scaife C, Kenny EM, Henry M, Meleady P, Ridgway PF, MacCarthy F, Conlon KC, Ryan BM, Maher SG. Multi-omic biomarker panel in pancreatic cyst fluid and serum predicts patients at a high risk of pancreatic cancer development. Sci Rep 2025; 15:129. [PMID: 39747972 PMCID: PMC11696309 DOI: 10.1038/s41598-024-83742-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 12/17/2024] [Indexed: 01/04/2025] Open
Abstract
Integration of multi-omic data for the purposes of biomarker discovery can provide novel and robust panels across multiple biological compartments. Appropriate analytical methods are key to ensuring accurate and meaningful outputs in the multi-omic setting. Here, we extensively profile the proteome and transcriptome of patient pancreatic cyst fluid (PCF) (n = 32) and serum (n = 68), before integrating matched omic and biofluid data, to identify biomarkers of pancreatic cancer risk. Differential expression analysis, feature reduction, multi-omic data integration, unsupervised hierarchical clustering, principal component analysis, spearman correlations and leave-one-out cross-validation were performed using RStudio and CombiROC software. An 11-feature multi-omic panel in PCF [PIGR, S100A8, REG1A, LGALS3, TCN1, LCN2, PRSS8, MUC6, SNORA66, miR-216a-5p, miR-216b-5p] generated an AUC = 0.806. A 13-feature multi-omic panel in serum [SHROOM3, IGHV3-72, IGJ, IGHA1, PPBP, APOD, SFN, IGHG1, miR-197-5p, miR-6741-5p, miR-3180, miR-3180-3p, miR-6782-5p] produced an AUC = 0.824. Integration of the strongest performing biomarkers generated a 10-feature cross-biofluid multi-omic panel [S100A8, LGALS3, SNORA66, miR-216b-5p, IGHV3-72, IGJ, IGHA1, PPBP, miR-3180, miR-3180-3p] with an AUC = 0.970. Multi-omic profiling provides an abundance of potential biomarkers. Integration of data from different omic compartments, and across biofluids, produced a biomarker panel that performs with high accuracy, showing promise for the risk stratification of patients with pancreatic cystic lesions.
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Affiliation(s)
- Laura E Kane
- Department of Surgery, Trinity St. James's Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland
| | - Gregory S Mellotte
- Department of Gastroenterology, Tallaght University Hospital, Dublin 24, Ireland
| | - Eimear Mylod
- Department of Surgery, Trinity St. James's Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Simone Marcone
- Department of Surgery, Trinity St. James's Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland
| | - Caitriona Scaife
- Mass Spectrometry Facility, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Elaine M Kenny
- ELDA Biotech, Newhall, M7 Business Park, Co. Kildare, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paul F Ridgway
- Department of Surgery, Centre for Pancreatico-Biliary Diseases, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland
| | - Finbar MacCarthy
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland
| | - Kevin C Conlon
- Department of Surgery, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Barbara M Ryan
- Department of Gastroenterology, Tallaght University Hospital, Dublin 24, Ireland
| | - Stephen G Maher
- Department of Surgery, Trinity St. James's Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin 8, Ireland.
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2
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Sun X, Wang S, Wong CC. Mass spectrometry–based proteomics technology in pancreatic cancer research. JOURNAL OF PANCREATOLOGY 2024; 7:145-163. [DOI: 10.1097/jp9.0000000000000152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2025] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has become a significant health concern with increasing incidence and mortality rates over the past few decades. Researchers have turned their attention to cutting-edge mass spectrometry (MS) technology due to its high-throughput and accurate detection capacity, which plays a vital role in understanding the mechanisms and discovering biomarkers for pancreatic diseases. In this review, we comprehensively investigate various methodologies of quantitative and qualitative proteomics MS technologies, alongside bioinformatical platforms employed in pancreatic cancer research. The integration of these optimized approaches provides novel insights into the molecular mechanisms underlying tumorigenesis and disease progression, ultimately facilitating the discovery of potential diagnostic, prognostic biomarkers, and therapeutic targets. The robust MS-based strategy shows promise in paving the way for early diagnosis and personalized medicine for pancreatic cancer patients.
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Affiliation(s)
- Xue Sun
- First School of Clinical Medicine, Peking University Health Science Center, Peking University, Beijing 100871, China
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Siyuan Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Catherine C.L. Wong
- First School of Clinical Medicine, Peking University Health Science Center, Peking University, Beijing 100871, China
- State Key Laboratory of Complex Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- Tsinghua-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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3
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Rossi R, Mereuta OM, Barbachan e Silva M, Molina Gil S, Douglas A, Pandit A, Gilvarry M, McCarthy R, O'Connell S, Tierney C, Psychogios K, Tsivgoulis G, Szikora I, Tatlisumak T, Rentzos A, Thornton J, Ó Broin P, Doyle KM. Potential Biomarkers of Acute Ischemic Stroke Etiology Revealed by Mass Spectrometry-Based Proteomic Characterization of Formalin-Fixed Paraffin-Embedded Blood Clots. Front Neurol 2022; 13:854846. [PMID: 35518205 PMCID: PMC9062453 DOI: 10.3389/fneur.2022.854846] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
Background and Aims Besides the crucial role in the treatment of acute ischemic stroke (AIS), mechanical thrombectomy represents a unique opportunity for researchers to study the retrieved clots, with the possibility of unveiling biological patterns linked to stroke pathophysiology and etiology. We aimed to develop a shotgun proteomic approach to study and compare the proteome of formalin-fixed paraffin-embedded (FFPE) cardioembolic and large artery atherosclerotic (LAA) clots. Methods We used 16 cardioembolic and 15 LAA FFPE thrombi from 31 AIS patients. The thrombus proteome was analyzed by label-free quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS). MaxQuant v1.5.2.8 and Perseus v.1.6.15.0 were used for bioinformatics analysis. Protein classes were identified using the PANTHER database and the STRING database was used to predict protein interactions. Results We identified 1,581 protein groups as part of the AIS thrombus proteome. Fourteen significantly differentially abundant proteins across the two etiologies were identified. Four proteins involved in the ubiquitin-proteasome pathway, blood coagulation or plasminogen activating cascade were identified as significantly abundant in LAA clots. Ten proteins involved in the ubiquitin proteasome-pathway, cytoskeletal remodeling of platelets, platelet adhesion or blood coagulation were identified as significantly abundant in cardioembolic clots. Conclusion Our results outlined a set of 14 proteins for a proof-of-principle characterization of cardioembolic and LAA FFPE clots, advancing the proteome profile of AIS human thrombi and understanding the pathophysiology of ischemic stroke.
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Affiliation(s)
- Rosanna Rossi
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Oana Madalina Mereuta
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Mariel Barbachan e Silva
- School of Mathematical and Statistical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sara Molina Gil
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Andrew Douglas
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Abhay Pandit
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | | | | | - Shane O'Connell
- School of Mathematical and Statistical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Ciara Tierney
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
| | | | - Georgios Tsivgoulis
- Second Department of Neurology, National and Kapodistrian University of Athens, “Attikon” University Hospital, Athens, Greece
| | - István Szikora
- Department of Neurointerventions, National Institute of Clinical Neurosciences, Budapest, Hungary
| | - Turgut Tatlisumak
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Alexandros Rentzos
- Department of Interventional and Diagnostic Neuroradiology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, Sweden
| | - John Thornton
- Department of Radiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Karen M. Doyle
- Department of Physiology and Galway Neuroscience Centre, School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM–SFI Research Centre for Medical Devices, National University of Ireland Galway, Galway, Ireland
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Chen L, Orr CE, Wang T. Prevalence of histological features resembling autoimmune pancreatitis in neoplastic pancreas resections. Histopathology 2020; 77:673-677. [PMID: 32608526 DOI: 10.1111/his.14197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
AIMS Types 1 and 2 autoimmune pancreatitis (AIP) can mimic pancreatic neoplasia. Due to the small quantity of tissue in mass-targeted pancreas biopsies, inflammatory features may raise the differential of AIP. However, the frequency of AIP-like histology in neoplastic pancreas is not well characterised. Therefore, the specificity of inflammatory lesions on biopsy with respect to the diagnosis of AIP is uncertain. METHODS AND RESULTS Neoplastic pancreas resections performed at our institution between 2008 and 2019 were retrospectively reviewed. Features of AIP types 1 and 2 were assessed in the non-neoplastic areas. If features of immunoglobulin (Ig)G4-associated AIP were seen, IgG4 immunohistochemistry was performed. We identified 163 neoplastic pancreas resections. Of these, 34 had one or more types of inflammatory lesions in non-neoplastic pancreatic tissue. Dense lymphoplasmacytic inflammation mimicking type 1 AIP was found in six cases with mild to moderately increased IgG4-positive plasma cells. Neutrophilic infiltrates in small intralobular ducts were found in 20 cases. Mild extralobular ductitis or duct microabscess was found in 10 specimens. Marked neutrophilic duct destruction that resembled granulocytic epithelial lesions was found in 12 cases. Some cases showed multiple features. CONCLUSION Approximately 20% of neoplastic pancreas resections showed focal areas that could raise the differential of AIP. More cases showed neutrophilic predominant inflammation as seen in type 2 autoimmune pancreatitis, compared to dense lymphoplasmacytic infiltrates seen in type 1 AIP. Pathologists must be cautious when making a diagnosis of AIP on biopsy tissue based on histological findings alone.
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Affiliation(s)
- Lina Chen
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Christine E Orr
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tao Wang
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
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5
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Burian A, Lujber L, Gerlinger I, Jarai T, Orosz E, Turiak L, Acs A, Hegedus Z, Peter AK, Tornoczki T, Gombos K, Mark L. Label-Free Semiquantitative Liquid Chromatography-Tandem Mass Spectrometry Proteomics Analysis of Laryngeal/Hypopharyngeal Squamous Cell Carcinoma on Formalin-Fixed, Paraffin-Embedded Tissue Samples - a Pilot Study. Pathol Oncol Res 2020; 26:2801-2807. [PMID: 32564264 PMCID: PMC7471140 DOI: 10.1007/s12253-020-00849-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Squamous cell carcinoma (SCC) of the head and neck region is the sixth most frequent malignancy with high mortality rate. Due to its poor prognosis it is considered a growing public health problem worldwide inspite of existing treatment modalities. Thus, early diagnosis of new diseases and recurrences is emerging on one hand, but on the other hand troublesome in the lack of reliable tumor markers in this field. The rapid development of proteomics has opened new perspectives in tumor marker discovery. Liquid chromatography/mass spectrometry (LC/MS) as the gold standard in proteomics enables the semi-quantitative analysis of proteins within various tissues. Abundance differences between tumor and normal tissue also can be interpreted as tumor specific changes. The aim of this study was to identify potential tumor markers of laryngeal/hypopharyngeal SCC by revealing abundance changes between cancerous and the surrounding phenotypically healthy tissue. After separating the phenotypically cancerous and healthy parts of formalin-fixed paraffin-embedded tissues, each sample underwent protein recovery process and tryptic digestion for label-free semi-quantitative LC/MS analysis. Eight proteins showed significantly higher abundance in tumor including tenascin, transmembrane emp24 domain-containing protein 2, cytoplasmic dynein light chain 1, coactosin-like protein, small proline-rich protein 2D, nucleolin, U5 small nuclear RNP 200-kDa helicase and fatty aldehyde dehydrogenase. Desmoglein-1 and keratin type I cytoskeletal 9 were down-regulated in tumor. Using Ingenuity Pathway Analysis we mapped the signaling pathways these proteins play role in regarding other tumors. Based on these findings these proteins may serve as promising biomarkers in the fight against laryngeal/hypopharyngeal SCCs.
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Affiliation(s)
- Andras Burian
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Laszlo Lujber
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Imre Gerlinger
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Tamas Jarai
- Tolna County Balassa Janos Hospital, Beri Balogh Adam Str 5-7, Szekszard, H-7100, Hungary
| | - Eva Orosz
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Lilla Turiak
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok Blvd 2, Budapest, H-1117, Hungary
| | - Andras Acs
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok Blvd 2, Budapest, H-1117, Hungary.,Ph.D. School of Pharmaceutical Sciences, Semmelweis University, Ulloi Str 26, Budapest, H-1085, Hungary
| | - Zoltan Hegedus
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Temesvari Blvd 62, Szeged, H-6726, Hungary.,Medical School, Institute of Biochemistry and Medical Chemistry, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary
| | - Aniko Konigne Peter
- Medical School, Institute of Bioanalysis, University of Pecs, Honved Str 1, Pecs, H-7624, Hungary
| | - Tamas Tornoczki
- Medical School, Institute of Pathology, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary
| | - Katalin Gombos
- Clinical Centre, Department of Laboratory Medicine, University of Pecs, Ifjusag Str 13, Pecs, H-7624, Hungary
| | - Laszlo Mark
- Medical School, Institute of Biochemistry and Medical Chemistry, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary. .,MTA-PTE Human Reproduction Research Group, Edesanyak str. 1, Pecs, H-7624, Hungary.
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6
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Benedetto A, Pezzolato M, Beltramo C, Audino V, Ingravalle F, Pillitteri C, Foschini S, Peletto S, Bozzetta E. Real-time PCR assay for detecting illicit steroid administration in veal calves allows reliable biomarker profiling of formalin-fixed, paraffin-embedded (FFPE) archival tissue samples. Food Chem 2020; 312:126061. [DOI: 10.1016/j.foodchem.2019.126061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 11/14/2019] [Accepted: 12/13/2019] [Indexed: 11/30/2022]
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7
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González-Borja I, Viúdez A, Goñi S, Santamaria E, Carrasco-García E, Pérez-Sanz J, Hernández-García I, Sala-Elarre P, Arrazubi V, Oyaga-Iriarte E, Zárate R, Arévalo S, Sayar O, Vera R, Fernández-Irigoyen J. Omics Approaches in Pancreatic Adenocarcinoma. Cancers (Basel) 2019; 11:cancers11081052. [PMID: 31349663 PMCID: PMC6721316 DOI: 10.3390/cancers11081052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma, which represents 80% of pancreatic cancers, is mainly diagnosed when treatment with curative intent is not possible. Consequently, the overall five-year survival rate is extremely dismal—around 5% to 7%. In addition, pancreatic cancer is expected to become the second leading cause of cancer-related death by 2030. Therefore, advances in screening, prevention and treatment are urgently needed. Fortunately, a wide range of approaches could help shed light in this area. Beyond the use of cytological or histological samples focusing in diagnosis, a plethora of new approaches are currently being used for a deeper characterization of pancreatic ductal adenocarcinoma, including genetic, epigenetic, and/or proteo-transcriptomic techniques. Accordingly, the development of new analytical technologies using body fluids (blood, bile, urine, etc.) to analyze tumor derived molecules has become a priority in pancreatic ductal adenocarcinoma due to the hard accessibility to tumor samples. These types of technologies will lead us to improve the outcome of pancreatic ductal adenocarcinoma patients.
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Affiliation(s)
- Iranzu González-Borja
- OncobionaTras Lab, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA) Irunlarrea 3, 31008 Pamplona, Spain
| | - Antonio Viúdez
- OncobionaTras Lab, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA) Irunlarrea 3, 31008 Pamplona, Spain.
- Medical Oncology Department, Complejo Hospitalario de Navarra, Irunlarrea 3, 31008 Pamplona, Spain.
| | - Saioa Goñi
- OncobionaTras Lab, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA) Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaria
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Estefania Carrasco-García
- Grupo de Oncología Celular, Instituto de Investigación Sanitaria Biodonostia, 20014 San Sebastián, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), 28029 Madrid, Spain
| | - Jairo Pérez-Sanz
- OncobionaTras Lab, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA) Irunlarrea 3, 31008 Pamplona, Spain
| | - Irene Hernández-García
- Medical Oncology Department, Complejo Hospitalario de Navarra, Irunlarrea 3, 31008 Pamplona, Spain
| | - Pablo Sala-Elarre
- Medical Oncology Department, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Virginia Arrazubi
- Medical Oncology Department, Complejo Hospitalario de Navarra, Irunlarrea 3, 31008 Pamplona, Spain
| | | | - Ruth Zárate
- OncobionaTras Lab, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA) Irunlarrea 3, 31008 Pamplona, Spain
| | - Sara Arévalo
- Grupo de Oncología Celular, Instituto de Investigación Sanitaria Biodonostia, 20014 San Sebastián, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), 28029 Madrid, Spain
| | | | - Ruth Vera
- Medical Oncology Department, Complejo Hospitalario de Navarra, Irunlarrea 3, 31008 Pamplona, Spain
| | - Joaquin Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
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8
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Aoyama T, Takasawa A, Takasawa K, Ono Y, Emori M, Murata M, Hayasaka T, Fujitani N, Osanai M, Yamashita T, Hasegawa T, Sawada N. Identification of Coiled-Coil Domain-Containing Protein 180 and Leucine-Rich Repeat-Containing Protein 4 as Potential Immunohistochemical Markers for Liposarcoma Based on Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded Tissue. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1015-1028. [PMID: 30790560 DOI: 10.1016/j.ajpath.2019.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/04/2019] [Accepted: 01/24/2019] [Indexed: 12/17/2022]
Abstract
Recent technical improvements in both mass spectrometry and protein extraction have made it possible to use formalin-fixed, paraffin-embedded (FFPE) tissues for proteome analysis. In this study, comparable proteome analysis of FFPE tissues revealed multiple candidate marker molecules for differentiating atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDL) from lipoma. A total of 181 unique proteins were identified for ALT/WDL. Of the identified proteins, coiled-coil domain-containing protein 180 (CCDC180) and leucine-rich repeat-containing protein 4 (LRRC4) were studied as candidate markers of ALT/WDL. CCDC180 and LRRC4 immunohistochemistry clearly stained tumor cells of ALT/WDL and dedifferentiated liposarcoma and could differentiate them from lipoma with high accuracy. Cell biological methods were used to further examine the expression of the candidate marker molecules in liposarcoma cells. In liposarcoma cells, knockdown of CCDC180 and LRRC4 inhibited cell proliferation. CCDC180 inhibited cell migration, invasion, and apoptosis resistance in WDL cells. Adipogenic differentiation suppressed the expression of CCDC180 and LRRC4 in WDL cells. These results indicated that LRRC4 and CCDC180 are novel immunohistochemical markers for differentiating ALT/WDLs. Their expression was associated with adipocyte differentiation and contributed to malignant potentials of WDL cells. Proteome analysis using a standard stock of FFPE tissues can reveal novel biomarkers for various diseases, which contributes to the progress of molecular pathology.
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Affiliation(s)
- Tomoyuki Aoyama
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Akira Takasawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan.
| | - Kumi Takasawa
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yusuke Ono
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Makoto Emori
- Department of Orthopedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masaki Murata
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takahiro Hayasaka
- Department of Gastroenterological Surgery I, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Naoki Fujitani
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Makoto Osanai
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toshihiko Yamashita
- Department of Orthopedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Norimasa Sawada
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
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9
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Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
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Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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Holfeld A, Valdés A, Malmström PU, Segersten U, Lind SB. Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods. Anal Chem 2018; 90:5841-5849. [PMID: 29624047 DOI: 10.1021/acs.analchem.8b00379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) and optimal cutting temperature (OCT)-embedded and frozen tissue specimens in biobanks are highly valuable in clinical studies but proteomic and post-translational modification (PTM) studies using mass spectrometry (MS) have been limited due to structural arrangement of proteins and contaminations from embedding material. This study aims to develop a parallel proteomic workflow for FFPE and OCT/frozen samples that allows for large-scale, quick, reproducible, qualitative, and quantitative high-resolution MS analysis. The optimized protocol gives details on removal of embedding material, protein extraction, and multienzyme digestion using filter-aided sample preparation method. The method was evaluated by investigating the protein expression levels in nonmuscle-invasive and muscle-invasive bladder cancer samples in two cohorts and MS spectra were carefully reviewed for contaminations. More than 2000 and 3000 proteins in FFPE and OCT/frozen samples, respectively, were identified, and samples could be clustered in different tumor stages based on their protein expression. Furthermore, more than 250 and 400 phosphopeptides could be identified from specific patient samples of FFPE and OCT/frozen, respectively, using titanium dioxide enrichment. The paper presents unique data describing the similarities and differences observed in FFPE and OCT/frozen samples and shows the feasibility to detect proteins and site-specific phosphorylation even after long-term storage of clinical samples.
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11
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Saraswat M, Joenväärä S, Seppänen H, Mustonen H, Haglund C, Renkonen R. Comparative proteomic profiling of the serum differentiates pancreatic cancer from chronic pancreatitis. Cancer Med 2017; 6:1738-1751. [PMID: 28573829 PMCID: PMC5504330 DOI: 10.1002/cam4.1107] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/23/2017] [Accepted: 04/24/2017] [Indexed: 02/06/2023] Open
Abstract
Finland ranks sixth among the countries having highest incidence rate of pancreatic cancer with mortality roughly equaling incidence. The average age of diagnosis for pancreatic cancer is 69 years in Nordic males, whereas the average age of diagnosis of chronic pancreatitis is 40–50 years, however, many cases overlap in age. By radiology, the evaluation of a pancreatic mass, that is, the differential diagnosis between chronic pancreatitis and pancreatic cancer is often difficult. Preoperative needle biopsies are difficult to obtain and are demanding to interpret. New blood based biomarkers are needed. The accuracy of the only established biomarker for pancreatic cancer, CA 19‐9 is rather poor in differentiating between benign and malignant mass of the pancreas. In this study, we have performed mass spectrometry analysis (High Definition MSE) of serum samples from patients with chronic pancreatitis (13) and pancreatic cancer (22). We have quantified 291 proteins and performed detailed statistical analysis such as principal component analysis, orthogonal partial least square discriminant analysis and receiver operating curve analysis. The proteomic signature of chronic pancreatitis versus pancreatic cancer samples was able to separate the two groups by multiple statistical techniques. Some of the enriched pathways in the proteomic dataset were LXR/RXR activation, complement and coagulation systems and inflammatory response. We propose that multiple high‐confidence biomarker candidates in our pilot study including Inter‐alpha‐trypsin inhibitor heavy chain H2 (Area under the curve, AUC: 0.947), protein AMBP (AUC: 0.951) and prothrombin (AUC: 0.917), which should be further evaluated in larger patient series as potential new biomarkers for differential diagnosis.
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Affiliation(s)
- Mayank Saraswat
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
| | - Sakari Joenväärä
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
| | - Hanna Seppänen
- Department of SurgeryUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Harri Mustonen
- Department of SurgeryUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Caj Haglund
- Department of SurgeryUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Translational Cancer Biology ProgramResearch Programs UnitUniversity of HelsinkiHelsinkiFinland
| | - Risto Renkonen
- Transplantation LaboratoryHaartman InstituteUniversity of HelsinkiHelsinkiFinland
- HUSLABHelsinki University HospitalHelsinkiFinland
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12
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Advances in Pancreatic Biomarker Measures: A Novel Approach to An Obscure Organ. Clin Transl Gastroenterol 2016; 7:e194. [PMID: 27735921 PMCID: PMC5288586 DOI: 10.1038/ctg.2016.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/06/2016] [Indexed: 11/08/2022] Open
Abstract
The pancreas remains a challenging organ to assess because of its retroperitoneal locations and cost of accessing the pancreatic duct for collection of biological samples. A novel and potentially useful approach to analysis of pancreatic juice proteins has been developed by Rocker et al. (Clin Transl Gastroenterol 7: e174; doi:10.1038/ctg.2016.27) using whole-gut lavage fluid from a colonoscopy prep. The widespread use of colonoscopy for colon cancer screening provides the opportunity to also screen the patient for benign and malignant pancreatic diseases using the fluid waste. New approaches are needed to assessing the pancreas, and wastes should not be wasted.
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13
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Yamamoto T, Kudo M, Peng WX, Takata H, Takakura H, Teduka K, Fujii T, Mitamura K, Taga A, Uchida E, Naito Z. Identification of aldolase A as a potential diagnostic biomarker for colorectal cancer based on proteomic analysis using formalin-fixed paraffin-embedded tissue. Tumour Biol 2016; 37:13595-13606. [PMID: 27468721 PMCID: PMC5097088 DOI: 10.1007/s13277-016-5275-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/15/2016] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide, and many patients are already at an advanced stage when they are diagnosed. Therefore, novel biomarkers for early detection of colorectal cancer are required. In this study, we performed a global shotgun proteomic analysis using formalin-fixed and paraffin-embedded (FFPE) CRC tissue. We identified 84 candidate proteins whose expression levels were differentially expressed in cancer and non-cancer regions. A label-free semiquantitative method based on spectral counting and gene ontology (GO) analysis led to a total of 21 candidate proteins that could potentially be detected in blood. Validation studies revealed cyclophilin A, annexin A2, and aldolase A mRNA and protein expression levels were significantly higher in cancer regions than in non-cancer regions. Moreover, an in vitro study showed that secretion of aldolase A into the culture medium was clearly suppressed in CRC cells compared to normal colon epithelium. These findings suggest that decreased aldolase A in blood may be a novel biomarker for the early detection of CRC.
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Affiliation(s)
- Tetsushi Yamamoto
- Pathological and Biomolecule Analyses Laboratory, Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Mitsuhiro Kudo
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Wei-Xia Peng
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Hideyuki Takata
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.,Departments of Gastrointestinal Hepato Biliary Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Hideki Takakura
- Pathological and Biomolecule Analyses Laboratory, Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Kiyoshi Teduka
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Takenori Fujii
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Kuniko Mitamura
- Pathological and Biomolecule Analyses Laboratory, Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Atsushi Taga
- Pathological and Biomolecule Analyses Laboratory, Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Eiji Uchida
- Departments of Gastrointestinal Hepato Biliary Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Zenya Naito
- Department of Integrated Diagnostic Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.
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14
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. EUPA OPEN PROTEOMICS 2016; 10:9-18. [PMID: 29900094 PMCID: PMC5988570 DOI: 10.1016/j.euprot.2015.10.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/19/2015] [Accepted: 10/25/2015] [Indexed: 01/14/2023]
Abstract
Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.
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Key Words
- CAN, acetonitrile
- DF, directly-frozen
- FA, formic acid
- FASP, filter-aided sample preparation
- FDR, false discovery rate
- FFPE, formalin-fixed
- Formalin-fixed
- HLA-A class I, histocompatibility antigen A-23 alpha chain
- HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain
- Human colon mucosa
- LFQ, label-free quantification
- Mass spectrometry
- PCA, principle component analysis
- PSM, peptide spectral match
- PTM, post-translational modification
- Paraffin-embedded
- Preservation
- Proteomics
- RNAlater
- SDC, sodium deoxycholate
- SDS, sodium dodecyl sulfate
- TEAB, triethylammonium bicarbonate
- iFFPE, immediately formalin-fixed
- s, standard deviation
- sFFPE, stored for 30 min prior to formalin-fixed
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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15
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Gustafsson OJR, Arentz G, Hoffmann P. Proteomic developments in the analysis of formalin-fixed tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:559-80. [PMID: 25315853 DOI: 10.1016/j.bbapap.2014.10.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/22/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Retrospective proteomic studies, including those which aim to elucidate the molecular mechanisms driving cancer, require the assembly and characterization of substantial patient tissue cohorts. The difficulty of maintaining and accessing native tissue archives has prompted the development of methods to access archives of formalin-fixed tissue. Formalin-fixed tissue archives, complete with patient meta data, have accumulated for decades, presenting an invaluable resource for these retrospective studies. This review presents the current knowledge concerning formalin-fixed tissue, with descriptions of the mechanisms of formalin fixation, protein extraction, top-down proteomics, bottom-up proteomics, quantitative proteomics, phospho- and glycoproteomics as well as imaging mass spectrometry. Particular attention has been given to the inclusion of proteomic investigations of archived tumour tissue. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Georgia Arentz
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005.
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16
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Ansari D, Aronsson L, Sasor A, Welinder C, Rezeli M, Marko-Varga G, Andersson R. The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. J Transl Med 2014; 12:87. [PMID: 24708694 PMCID: PMC3998064 DOI: 10.1186/1479-5876-12-87] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic era, it has become evident that genetic changes alone are not sufficient to understand most disease processes including pancreatic cancer. Genome sequencing has revealed a complex set of genetic alterations in pancreatic cancer such as point mutations, chromosomal losses, gene amplifications and telomere shortening that drive cancerous growth through specific signaling pathways. Proteome-based approaches are important complements to genomic data and provide crucial information of the target driver molecules and their post-translational modifications. By applying quantitative mass spectrometry, this is an alternative way to identify biomarkers for early diagnosis and personalized medicine. We review the current quantitative mass spectrometric technologies and analyses that have been developed and applied in the last decade in the context of pancreatic cancer. Examples of candidate biomarkers that have been identified from these pancreas studies include among others, asporin, CD9, CXC chemokine ligand 7, fibronectin 1, galectin-1, gelsolin, intercellular adhesion molecule 1, insulin-like growth factor binding protein 2, metalloproteinase inhibitor 1, stromal cell derived factor 4, and transforming growth factor beta-induced protein. Many of these proteins are involved in various steps in pancreatic tumor progression including cell proliferation, adhesion, migration, invasion, metastasis, immune response and angiogenesis. These new protein candidates may provide essential information for the development of protein diagnostics and targeted therapies. We further argue that new strategies must be advanced and established for the integration of proteomic, transcriptomic and genomic data, in order to enhance biomarker translation. Large scale studies with meta data processing will pave the way for novel and unexpected correlations within pancreatic cancer, that will benefit the patient, with targeted treatment.
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Affiliation(s)
- Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Linus Aronsson
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Agata Sasor
- Department of Pathology, Clinical Sciences Lund, Lund University, and Skåne University Hospital, Lund, Sweden
| | - Charlotte Welinder
- Department of Oncology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Center, Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University, and Skåne University Hospital, SE-221 85 Lund, Sweden
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17
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Iuga C, Seicean A, Iancu C, Buiga R, Sappa PK, Völker U, Hammer E. Proteomic identification of potential prognostic biomarkers in resectable pancreatic ductal adenocarcinoma. Proteomics 2014; 14:945-955. [PMID: 24459066 DOI: 10.1002/pmic.201300402] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 12/17/2022]
Abstract
Pancreatic cancer is a devastating disease with a mortality rate almost identical with its incidence. In this context, the investigation of the pancreatic cancer proteome has gained considerable attention because profiles of proteins may be able to identify disease states and progression more accurately. Therefore, our objective was to investigate the changes in the proteome of patients suffering from pancreatic ductal adenocarcinoma (PDAC) by a comprehensive quantitative approach. Comparative proteomic profiling by label-free LC-MS/MS analysis of nine matched pairs of tumor and nontumor pancreas samples was used to identify differences in protein levels characteristic for PDAC. In this analysis, 488 proteins were quantified by at least two peptides of which 99 proteins displayed altered levels in PDAC (p < 0.01, fold change >1.3). Screening of data revealed a number of molecules that had already been related to PDAC such as galectin-1 (LEG1), major vault protein, adenylyl cyclase-associated protein 1 (CAP1), but also a potential new prognostic biomarker prolargin (PRELP). The Kaplan-Meier survival analysis revealed a significant correlation of protein abundance of PRELP with postoperative survival of patients with PDAC. For selected proteins the findings were verified by targeted proteomics (SRM), validated by immunohistochemistry and Western blotting and their value as candidate biomarkers is discussed.
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Affiliation(s)
- Cristina Iuga
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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18
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Lin F, Tan HJ, Guan JS, Lim YP. Divide and conquer: subproteomic approaches toward gastric cancer biomarker and drug target discovery. Expert Rev Proteomics 2014; 11:515-30. [PMID: 24684179 DOI: 10.1586/14789450.2014.904751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The discovery of biomarkers for early detection and treatment for gastric cancer are two important gaps that proteomics have the potential to fill. Advancements in mass spectrometry, sample preparation and separation strategies are crucial to proteomics-based discoveries and subsequent translations from bench to bedside. A great number of studies exploiting various subproteomic approaches have emerged for higher-resolution analysis (compared with shotgun proteomics) that permit interrogation of different post-translational and subcellular compartmentalized forms of the same proteins as determinants of disease phenotypes. This is a unique and key strength of proteomics over genomics. In this review, the salient features, competitive edges and pitfalls of various subproteomic approaches are discussed. We also highlight valuable insights from several subproteomic studies that have increased our understanding of the molecular etiology of gastric cancer and the findings that led to the discovery of potential biomarkers/drug targets that were otherwise not revealed by conventional shotgun expression proteomics.
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Affiliation(s)
- Fan Lin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, level 1, 5 Science Drive 2, Singapore
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19
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Fowler CB, O'Leary TJ, Mason JT. Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2014; 10:389-400. [PMID: 23992421 DOI: 10.1586/14789450.2013.820531] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue and their associated diagnostic records represent an invaluable source of retrospective proteomic information on diseases for which the clinical outcome and response to treatment are known. However, analysis of archival FFPE tissues by high-throughput proteomic methods has been hindered by the adverse effects of formaldehyde fixation and subsequent tissue histology. This review examines recent methodological advances for extracting proteins from FFPE tissue suitable for proteomic analysis. These methods, based largely upon heat-induced antigen retrieval techniques borrowed from immunohistochemistry, allow at least a qualitative analysis of the proteome of FFPE archival tissues. The authors also discuss recent advances in the proteomic analysis of FFPE tissue; including liquid-chromatography tandem mass spectrometry, reverse phase protein microarrays and imaging mass spectrometry.
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Affiliation(s)
- Carol B Fowler
- Laboratory of Proteomics and Protein Science, Washington DC Veterans Affairs Medical Center, Washington, DC, USA.
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20
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Giusti L, Lucacchini A. Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013; 10:165-77. [PMID: 23573783 DOI: 10.1586/epr.13.3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable informational resource of histologically characterized specimens for proteomic studies. In this article, the authors review the advancement performed in the field of FFPE proteomics focusing on formaldehyde treatment and on strategies addressed to obtain the best recovery in the protein/peptide extraction. A variety of approaches have been used to characterize protein tissue extracts, and many efforts have been performed demonstrating the comparability between fresh/frozen and FFPE proteomes. Finally, the authors report and discuss the large numbers of works aimed at developing new strategies and sophisticated platforms in the analysis of FFPE samples to validate known potential biomarkers and to discover new ones.
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Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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21
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Abstract
Proteomics is an approach to looking at the identity, amount, proteolysis, compartmentalization, and posttranslational modification of a large number of proteins simultaneously in a cell or tissue. Recently, proteomics has begun to be applied to the study of pancreatitis to ascertain mechanisms of disease and search for biomarkers of disease. Most mechanistic work has been carried out in animal models of acute pancreatitis. In 8 studies, 97 proteins have been reported to increase, 55 to decrease, and 23 to undergo proteolysis. Proteins showing increases are most often related to stress, inflammation, or the cytoskeleton, whereas decreases are seen in digestive enzymes and proteins related to metabolism. Many protein changes however, are not consistent between studies and only the most recent studies are rigorous and quantitative. By contrast, biomarker studies have focused on pancreatic juice and plasma of humans with disease and often are directed at distinguishing chronic pancreatitis from cancer. Chronic pancreatitis has also been investigated in tissue sections of histological samples. In this review, the results of studies to date are described as well as coverage of the methods used and special issues that must be considered. Areas are pointed out that are worthy of future study.
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22
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Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer. JOP : JOURNAL OF THE PANCREAS 2013; 14:405-414. [PMID: 23846938 PMCID: PMC4506757 DOI: 10.6092/1590-8577/1508] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/15/2013] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
CONTEXT Formalin-fixed paraffin-embedded (FFPE) tissue is a standard for specimen preservation, and as such FFPE tissue banks are an untapped resource of histologically-characterized specimens for retrospective biomarker investigation for pancreatic disease. OBJECTIVES We use liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to compare FFPE specimens from three different diseases of the exocrine pancreas. DESIGN We investigated the proteomic profile of FFPE pancreatic tissue from 9 archived specimens that were histologically classified as: autoimmune pancreatitis (n=3), chronic pancreatitis (n=3), and pancreatic cancer (n=3), using LC-MS/MS. SETTING This is a proteomic analysis experiment of FFPE pancreatic tissue in an academic center. PATIENTS FFPE tissue specimens were provided by Dana-Farber/Harvard Cancer Center (Boston, MA, USA). INTERVENTIONS FFPE tissue specimens were collected via routine surgical resection procedures. MAIN OUTCOME MEASURES We compared proteins identified from chronic pancreatitis, autoimmune pancreatitis, and pancreatic cancer FFPE pancreatic tissue. RESULTS We identified 386 non-redundant proteins from 9 specimens. Following our filtering criteria, 73, 29, and 53 proteins were identified exclusively in autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer specimens, respectively. CONCLUSIONS We report that differentially-expressed proteins can be identified among FFPE tissues specimens originating from individuals with different histological diagnoses. These proteins merit further confirmation with a greater number of specimens and orthogonal validation, such as immunohistochemistry. The mass spectrometry-based methodology used herein has the potential to enhance diagnostic biomarker and therapeutic target discovery, further advancing pancreatic research.
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Affiliation(s)
- Joao A Paulo
- Department of Pathology, Children’s Hospital Boston
- Proteomics Center, Children’s Hospital Boston
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Vivek Kadiyala
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Scott Brizard
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Peter A Banks
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Hanno Steen
- Department of Pathology, Children’s Hospital Boston
- Proteomics Center, Children’s Hospital Boston
| | - Darwin L Conwell
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
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23
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Ulmasov B, Oshima K, Rodriguez MG, Cox RD, Neuschwander-Tetri BA. Differences in the degree of cerulein-induced chronic pancreatitis in C57BL/6 mouse substrains lead to new insights in identification of potential risk factors in the development of chronic pancreatitis. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:692-708. [PMID: 23845568 DOI: 10.1016/j.ajpath.2013.05.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 03/25/2013] [Accepted: 05/11/2013] [Indexed: 12/26/2022]
Abstract
A frequently used experimental model of chronic pancreatitis (CP) recapitulating human disease is repeated injection of cerulein into mice. C57BL/6 is the most commonly used inbred mouse strain for biomedical research, but widespread demand has led to generation of several substrains with subtly different phenotypes. In this study, two common substrains, C57BL/6J and C57BL/6NHsd, exhibited different degrees of CP, with C57BL/6J being more susceptible to repetitive cerulein-induced CP as assessed by pancreatic atrophy, pancreatic morphological changes, and fibrosis. We hypothesized that the deficiency of nicotinamide nucleotide transhydrogenase (NNT) protein in C57BL/6J is responsible for the more severe C57BL/6J phenotype but the parameters of CP in NNT-expressing transgenic mice generated on a C57BL6/J background do not differ with those of wild-type C57BL/6J. The highly similar genetic backgrounds but different CP phenotypes of these two substrains presents a unique opportunity to discover genes important in pathogenesis of CP. We therefore performed whole mouse genome Affymetrix microarray analysis of pancreatic gene expression of C57BL/6J and C57BL/6NHsd before and after induction of CP. Genes with differentially regulated expression between the two substrains that might be candidates in CP progression included Mmp7, Pcolce2, Itih4, Wdfy1, and Vtn. We also identified several genes associated with development of CP in both substrains, including RIKEN cDNA 1810009J06 gene (trypsinogen 5), Ccl8, and Ccl6.
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Affiliation(s)
- Barbara Ulmasov
- Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, USA.
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Kadiyala V, Lee LS, Banks PA, Suleiman S, Paulo JA, Wang W, Rosenblum J, Sainani NI, Mortele K, Conwell DL. Cigarette smoking impairs pancreatic duct cell bicarbonate secretion. JOP : JOURNAL OF THE PANCREAS 2013; 14:31-8. [PMID: 23306332 DOI: 10.6092/1590-8577/1195] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/24/2012] [Accepted: 11/27/2012] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To compare pancreatic duct cell function in smokers (current and past) and never smokers by measurement of secretin-stimulated peak bicarbonate concentration ([HCO3-]) in endoscopic collected pancreatic fluid (PF). METHODS This retrospective study was cross-sectional in design, recording demographic information (age, gender, etc.), smoking status (former, current, never), alcohol intake, clinical data (imaging, endoscopy), and laboratory results (peak PF [HCO3-]) from subjects evaluated for pancreatic disease at a tertiary pancreas center. Univariate and multivariate statistical analysis (SAS Version 9.2, Cary, NC, USA) was performed to assess the relationship between cigarette smoking and secretin-stimulated pancreatic fluid bicarbonate concentration. RESULTS A total of 131 subjects underwent pancreatic fluid collection (endoscopic pancreatic function test, ePFT) for bicarbonate analysis: 25.2% (33 out of 131) past smokers, 31.3% (41 out of 131) current smokers, and 43.5% (57 out of 131) were never smokers. Measures of Association: The mean peak PF [HCO3-] in never smokers (81.3 ± 18.5 mEq/L) was statistically higher (indicating better duct cell function) when compared to past smokers (66.8 ± 24.7 mEq/L, P=0.005) and current smokers (70.0 ± 20.2 mEq/L, P=0.005). However, the mean peak [HCO3-] in past smokers was not statistically different from that in current smokers (P=0.575), and therefore, the two smoking groups were combined to form a single "smokers cohort". When compared to the never smokers, the smokers cohort was older (P=0.037) and had a greater proportion of subjects with definite chronic pancreatitis imaging (P=0.010), alcohol consumption ≥20 g/day (P=0.012), and abnormal peak PF [HCO3-] (P<0.001). Risk-Based Estimates: Cigarette smoking (risk ratio, RR: 2.2, 95% CI: 1.3-3.5; P<0.001), diagnosis of definite chronic pancreatitis imaging (RR: 2.2, 95% CI: 1.6-3.2; P<0.001) and alcohol consumption ≥20 g/day (RR: 1.6, 95% CI: 1.1-2.4; P=0.033) were all associated with low mean peak PF [HCO3-] (indicating duct cell secretory dysfunction). Multivariate Analysis: Smoking (odds ratio, OR: 3.8, 95% CI: 1.6-9.1; P=0.003) and definite chronic pancreatitis imaging (OR: 5.7, 95% CI: 2.2-14.8; P<0.001) were determined to be independent predictors of low peak PF [HCO3-], controlling for age, gender, and alcohol intake. Furthermore there was no interaction between smoking status and alcohol intake in predicting duct cell dysfunction (P=0.571). CONCLUSION Measurement of pancreatic fluid bicarbonate in smokers reveals that cigarette smoking (past and current) is an independent risk factor for pancreatic duct cell secretory dysfunction (low PF [HCO3-]). Furthermore, the risk of duct cell dysfunction in subjects who smoked was approximately twice the risk (RR: 2.2) in never smokers. Further in depth, translational research approaches to pancreatic fluid analysis may help unravel mechanisms of cigarette smoking induced pancreatic duct cell injury.
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Affiliation(s)
- Vivek Kadiyala
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Magdeldin S, Yamamoto T. Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012; 12:1045-58. [PMID: 22318899 PMCID: PMC3561704 DOI: 10.1002/pmic.201100550] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
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Paulo JA, Kadiyala V, Banks PA, Steen H, Conwell DL. Mass spectrometry-based proteomics for translational research: a technical overview. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2012; 85:59-73. [PMID: 22461744 PMCID: PMC3313540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mass spectrometry-based investigation of clinical samples enables the high-throughput identification of protein biomarkers. We provide an overview of mass spectrometry-based proteomic techniques that are applicable to the investigation of clinical samples. We address sample collection, protein extraction and fractionation, mass spectrometry modalities, and quantitative proteomics. Finally, we examine the limitations and further potential of such technologies. Liquid chromatography fractionation coupled with tandem mass spectrometry is well suited to handle mixtures of hundreds or thousands of proteins. Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease.
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Affiliation(s)
- Joao A Paulo
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA.
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