1
|
Cruz-Monserrate Z, Gumpper K, Kaul S, Badi N, Terhorst S, Dubay K, Lesinski GB, Fisher W, McElhany A, Lara LF, Krishna S, Mace T, Higuita-Castro N, Ortega-Pineda L, Freitas MA, Hinton A, Yadav D, Hart PA, Pandol SJ, Ahmed S, Fatou B, Steen H, Conwell DL. Delayed Processing of Secretin-Induced Pancreas Fluid Influences the Quality and Integrity of Proteins and Nucleic Acids. Pancreas 2021; 50:17-28. [PMID: 33370019 PMCID: PMC7883383 DOI: 10.1097/mpa.0000000000001717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES Endoscopic pancreatic function tests are used to diagnose pancreatic diseases and are a viable source for the discovery of biomarkers to better characterize pancreatic disorders. However, pancreatic fluid (PF) contains active enzymes that degrade biomolecules. Therefore, we tested how preservation methods and time to storage influence the integrity and quality of proteins and nucleic acids. METHODS We obtained PF from 9 subjects who underwent an endoscopic pancreatic function test. Samples were snap frozen at the time of collection; after 1, 2, and 4 hours on ice; or after storage overnight at 4°C with or without RNase or protease inhibitors (PIs). Electrophoresis and mass spectrometry analysis determined protein abundance and quality, whereas nucleic acid integrity values determined DNA and RNA degradation. RESULTS Protein degradation increased after 4 hours on ice and DNA degradation after 2 hours on ice. Adding PIs delayed degradation. RNA was significantly degraded under all conditions compared with the snap frozen samples. Isolated RNA from PF-derived exosomes exhibited similar poor quality as RNA isolated from matched PF samples. CONCLUSIONS Adding PIs immediately after collecting PF and processing the fluid within 4 hours of collection maintains the protein and nucleic acid integrity for use in downstream molecular analyses.
Collapse
Affiliation(s)
- Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Kristyn Gumpper
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Sabrina Kaul
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Niharika Badi
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Samantha Terhorst
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Kelly Dubay
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Gregory B. Lesinski
- Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University, Atlanta, GA
| | - William Fisher
- The Elkins Pancreas Center, Michael E. DeBakey Department of Surgery, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Amy McElhany
- The Elkins Pancreas Center, Michael E. DeBakey Department of Surgery, and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Luis F. Lara
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Somashekar Krishna
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Thomas Mace
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Natalia Higuita-Castro
- Department of Biomedical Engineering and Department of Surgery, The Ohio State University, Columbus, OH
| | | | - Michael A. Freitas
- The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Alice Hinton
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH
| | - Dhiraj Yadav
- University of Pittsburgh, Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Pittsburgh, PA
| | - Phil A. Hart
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Stephen J. Pandol
- Digestive Disease Center, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Saima Ahmed
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Benoit Fatou
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Hanno Steen
- Departments of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Darwin L. Conwell
- Division of Gastroenterology, Hepatology, and Nutrition, The Ohio State University Wexner Medical Center, Columbus, OH
| |
Collapse
|
2
|
Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
Collapse
Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| |
Collapse
|
3
|
Molecular architecture of mouse and human pancreatic zymogen granules: protein components and their copy numbers. BIOPHYSICS REPORTS 2018; 4:94-103. [PMID: 29756009 PMCID: PMC5937866 DOI: 10.1007/s41048-018-0055-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/17/2017] [Indexed: 01/15/2023] Open
Abstract
A molecular model of pancreatic zymogen granule (ZG) is critical for understanding its functions. We have extensively characterized the composition and membrane topology of rat ZG proteins. In this study, we report the development of targeted proteomics approaches to quantify representative mouse and human ZG proteins using LC-SRM and heavy isotope-labeled synthetic peptides. The absolute quantities of mouse Rab3D and VAMP8 were determined as 1242 ± 218 and 2039 ± 151 (mean ± SEM) copies per ZG. The size distribution and the averaged diameter of ZGs 750 ± 23 nm (mean ± SEM) were determined by atomic force microscopy. The absolute quantification of Rab3D was then validated using semi-quantitative Western blotting with purified GST-Rab3D proteins as an internal standard. To extend our proteomics analysis to human pancreas, ZGs were purified using human acini obtained from pancreatic islet transplantation center. One hundred and eighty human ZG proteins were identified for the first time including both the membrane and the content proteins. Furthermore, the copy number per ZG of human Rab3D and VAMP8 were determined to be 1182 ± 45 and 485 ± 15 (mean ± SEM). The comprehensive proteomic analyses of mouse and human pancreatic ZGs have the potential to identify species-specific ZG proteins. The determination of protein copy numbers on pancreatic ZGs represents a significant advance towards building a quantitative molecular model of a prototypical secretory vesicle using targeted proteomics approaches. The identification of human ZG proteins lays a foundation for subsequent studies of altered ZG compositions and secretion in pancreatic diseases.
Collapse
|
4
|
Yu SL, Han S, Kim HR, Park JW, Jin DI, Kang J. Phosphorylation of carboxypeptidase B1 protein regulates β-cell proliferation. Int J Mol Med 2017; 40:1397-1404. [PMID: 28949379 PMCID: PMC5627887 DOI: 10.3892/ijmm.2017.3141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/11/2017] [Indexed: 11/24/2022] Open
Abstract
A reduction in pancreatic islet β-cells leads to the onset of diabetes. Hence, the identification of the mechanisms inducing β-cell proliferation is important for developing a treatment course against the disease. It has been well established that post-translational modifications (PTMs) of proteins affect their functionality. In addition, PTMs have been suggested to play important roles in organ regeneration. Therefore, in this study, we investigated PTMs associated with pancreatic regeneration using two-dimensional electrophoresis. Four carboxypeptidase B1 (CPB1) proteins were identified at different isoelectric points, with the same molecular weight. The motif of CPB1 PTMs was identified by mass spectrophotometry, and the downregulation of CPB1 phosphorylation in pancreatectomy was confirmed. The dephosphorylation of CPB1 induced β-cell proliferation. We thus surmise that the altered PTM of CPB1 is associated with pancreatic regeneration.
Collapse
Affiliation(s)
- Seong-Lan Yu
- Department of Pharmacology, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea
| | - Seungyun Han
- Department of Anatomy, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea
| | - Hong Rye Kim
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jong Woo Park
- Department of Pharmacology, SungKyunKwan University, Suwon 16419, Republic of Korea
| | - Dong Il Jin
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jaeku Kang
- Department of Pharmacology, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea
| |
Collapse
|
5
|
Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
Collapse
Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
| | | |
Collapse
|
6
|
Abstract
Chronic pancreatitis (CP) represents a significant health care burden in the United States. Diagnosing it early and accurately is important for the efficient management of these patients. However, the early diagnosis of CP, when structural and functional pancreatic changes are subtle, remains difficult. Complicating this is the large cohort of patients with nonspecific abdominal pain who are often suspected of having early CP and who utilize significant health care resources in attempts at diagnosis and management. We present a review of the current diagnostic tests available for making an early diagnosis of CP. We further report our approach to patients suspected of having CP based on the available literature.
Collapse
|
7
|
Krishnamoorthy S, Liu Z, Hong A, Zhu R, Chen H, Li T, Zhou X, Gao X. A Novel Phosphopeptide Microarray Based Interactome Map in Breast Cancer Cells Reveals Phosphoprotein-GRB2 Cell Signaling Networks. PLoS One 2013; 8:e67634. [PMID: 23826330 PMCID: PMC3694890 DOI: 10.1371/journal.pone.0067634] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 05/21/2013] [Indexed: 11/23/2022] Open
Abstract
The architecture of cellular proteins connected to form signaling pathways in response to internal and external cues is much more complex than a group of simple protein-protein interactions. Post translational modifications on proteins (e.g., phosphorylation of serine, threonine and tyrosine residues on proteins) initiate many downstream signaling events leading to protein-protein interactions and subsequent activation of signaling cascades leading to cell proliferation, cell differentiation and cell death. As evidenced by a rapidly expanding mass spectrometry database demonstrating protein phosphorylation at specific motifs, there is currently a large gap in understanding the functional significance of phosphoproteins with respect to their specific protein connections in the signaling cascades. A comprehensive map that interconnects phospho-motifs in pathways will enable identification of nodal protein interactions that are sensitive signatures indicating a disease phenotype from the physiological hemostasis and provide clues into control of disease. Using a novel phosphopeptide microarray technology, we have mapped endogenous tyrosine-phosphoproteome interaction networks in breast cancer cells mediated by signaling adaptor protein GRB2, which transduces cellular responses downstream of several RTKs through the Ras-ERK signaling cascade. We have identified several previously reported motif specific interactions and novel interactions. The peptide microarray data indicate that various phospho-motifs on a single protein are differentially regulated in various cell types and shows global downregulation of phosphoprotein interactions specifically in cells with metastatic potential. The study has revealed novel phosphoprotein mediated signaling networks, which warrants further detailed analysis of the nodes of protein-protein interaction to uncover their biomarker or therapeutic potential.
Collapse
Affiliation(s)
- Srinivasan Krishnamoorthy
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail: (SK); (XG)
| | - Zhonghua Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Ailing Hong
- LC Sciences, Houston, Texas, United States of America
| | - Ruijuan Zhu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Haosi Chen
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Tongbin Li
- LC Sciences, Houston, Texas, United States of America
| | | | - Xiaolian Gao
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail: (SK); (XG)
| |
Collapse
|