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Fonghem P, Pisitkun T, Rattanapinyopituk K, Sirivisoot S, Rungsipipat A. Investigation of proteomic profiles in canine lymphoma using tandem mass tag-based quantitative proteomics approach. Vet World 2022; 15:1333-1340. [PMID: 35765478 PMCID: PMC9210836 DOI: 10.14202/vetworld.2022.1333-1340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Specific tumor biomarkers are useful for the early diagnosis of cancer or can predict the recurrence of neoplastic disease in humans and animals. Lymphoma in dogs could be classified into B-, T-, and NK-cell origins. T-cell lymphoma has the worst prognosis with a shorter survival time and disease-free interval. This study aimed to identify the differential serum protein expressions of canine B- and T-cell lymphomas compared with healthy dogs using a tandem mass tag (TMT)-based quantitative proteomics. Materials and Methods: Serum samples were collected from 20 untreated canine lymphomas (14 B-cells and 6 T-cells) and four healthy control dogs. Sera peptides from each sample were processed for TMT 10-plex tagging and analyzed using liquid chromatography-mass spectrometry (MS). Differential proteome profiling was then compared between lymphoma and control. Results: We discovered 20 elevated and 14 decreased serum proteins in the lymphoma group relative to the healthy group. Six candidate increased proteins in canine lymphomas were beta-actin cytoplasmic 1 (ACTB, p=0.04), haptoglobin (p=0.002), beta-2 microglobulin (aaaaaaaa2M, p=0.007), beta-2 glycoprotein 1 (APOH, p=0.03), metalloproteinase inhibitor 1 (TIMP-1, p=0.03), and CD44 antigen (p=0.02). When compared between B- and T-cell lymphomas, B-cell phenotypes had upregulated immunoglobulin (Ig) heavy chain V region GOM (p=0.02), clusterin (p=0.01), apolipoprotein C1 (APOC1, p=0.05), and plasminogen (p=0.02). Conclusion: These findings were investigated quantitative serum proteomes between B- and T-cell lymphomas using TMT-based MS. ACTB, aaaaaaaa2M, APOH, TIMP-1, CD44 antigen, Ig heavy chain V region GOM, and APOC1 are novel candidate proteins and might serve as a lymphoma biomarker in dogs. However, evaluation with an increased sample size is needed to confirm their diagnostic and prognostic ability.
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Affiliation(s)
- Piyanoot Fonghem
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kasem Rattanapinyopituk
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sirintra Sirivisoot
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Anudep Rungsipipat
- Center of Excellence for Companion Animal Cancer, Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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Parachini-Winter C, Bracha S, Ramsey SA, Yang L, Ho E, Leeper HJ, Curran KM. Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane. J Vet Intern Med 2020; 34:2036-2047. [PMID: 32926463 PMCID: PMC7517837 DOI: 10.1111/jvim.15898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022] Open
Abstract
Background Lymphoma (LSA) is a common malignancy in dogs. Epigenetic changes are linked to LSA pathogenesis and poor prognosis in humans, and LSA pathogenesis in dogs. Sulforaphane (SFN), an epigenetic‐targeting compound, has recently gained interest in relation to cancer prevention and therapy. Objective Examine the impact of oral supplementation with SFN on the lymph node proteome of dogs with multicentric LSA. Animals Seven client‐owned dogs with multicentric LSA. Methods Prospective, nonrandomized, noncontrolled study in treatment‐naïve dogs with intermediate or large cell multicentric LSA. Lymph node cell aspirates were obtained before and after 7 days of oral supplementation with SFN, and analyzed via label‐free mass spectrometry, immunoblots, and Gene Set Enrichment Analysis. Results There was no clinical response and no adverse events attributed to SFN. For individual dogs, the expression of up to 650 proteins changed by at least 2‐fold (range, 2‐100) after supplementation with SFN. When all dogs where analyzed together, 14 proteins were significantly downregulated, and 10 proteins were significantly upregulated after supplementation with SFN (P < .05). Proteins and gene sets impacted by SFN were commonly involved in immunity, response to oxidative stress, gene transcription, apoptosis, protein transport, maturation and ubiquitination. Conclusions and Clinical Importance Sulforaphane is associated with major changes in the proteome of neoplastic lymphocytes in dogs.
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Affiliation(s)
- Cyril Parachini-Winter
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Shay Bracha
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Stephen A Ramsey
- Department of Biomedical Sciences, School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Liping Yang
- Department of Chemistry, College of Science, Oregon State University, Corvallis, Oregon, USA
| | - Emily Ho
- Linus Pauling Institute and College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Haley J Leeper
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlin M Curran
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, USA
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Pisamai S, Roytrakul S, Phaonakrop N, Jaresitthikunchai J, Suriyaphol G. Proteomic analysis of canine oral tumor tissues using MALDI-TOF mass spectrometry and in-gel digestion coupled with mass spectrometry (GeLC MS/MS) approaches. PLoS One 2018; 13:e0200619. [PMID: 30001383 PMCID: PMC6042759 DOI: 10.1371/journal.pone.0200619] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/29/2018] [Indexed: 12/15/2022] Open
Abstract
Oral tumors, including highly invasive and metastatic oral melanoma (OM), non-tonsillar oral squamous cell carcinoma (OSCC) and benign tumors (BN), are common neoplasms in dogs. Although these tumors behave differently, limited data of their protein expression profiles have been exhibited, particularly at the proteome level. The present study aimed to i.) characterize peptide-mass fingerprints (PMFs) and identify potential protein candidates of OM, OSCC, BN and normal control subjects, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS), ii.) identify potential protein candidates associated with the diseases, using in-gel digestion coupled with mass spectrometric analysis (GeLC-MS/MS) and iii.) search for relationships between chemotherapy drugs and disease-perturbed proteins. A distinct cluster of each sample group and unique PMFs with identified protein candidates were revealed. The unique peptide fragment at 2,274 Da of sacsin molecular chaperone (SACS) was observed in early-stage OM whereas the fragment at 1,958 Da of sodium voltage-gated channel alpha subunit 10 (SCN10A) was presented in early- and late-stage OM. The peptide mass at 2,316 Da of Notch1 appeared in early-stage OM and benign oral tumors while the peptide mass at 2,505 Da of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 3A (GRIN3A) was identified in all groups. Markedly expressed proteins from GeLC-MS/MS included Jumonji domain containing 1C (JMJD1C) in benign tumors, inversin (INVS) and rho guanine nucleotide exchange factor 28 (ARHGEF28) in OM, BTB domain-containing 16 (BTBD16) in OSCC, and protein tyrosine phosphatase non-receptor type 1 (PTPN1), BRCA2, DNA repair associated (BRCA2), WW domain binding protein 2 (WBP2), purinergic receptor P2Y1 and proteasome activator subunit 4 (PSME4) in all cancerous groups. The network connections between these proteins and chemotherapy drugs, cisplatin and doxorubicin, were also demonstrated. In conclusion, this study unveiled the unique PMFs and novel candidate protein markers of canine oral tumors.
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Affiliation(s)
- Sirinun Pisamai
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Companion Animal Cancer Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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Ceciliani F, Roccabianca P, Giudice C, Lecchi C. Application of post-genomic techniques in dog cancer research. MOLECULAR BIOSYSTEMS 2017; 12:2665-79. [PMID: 27345606 DOI: 10.1039/c6mb00227g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Omics techniques have been widely applied to veterinary science, although mostly on farm animal productions and infectious diseases. In canine oncology, on the contrary, the use of omics methodologies is still far behind. This review presents the most recent achievement in the application of postgenomic techniques, such as transcriptomics, proteomics, and metabolomics, to canine cancer research. The protocols to recover material suitable for omics analyses from formalin-fixed, paraffin-embedded tissues are presented, and omics applications for biomarker discovery and their potential for cancer diagnostics in veterinary medicine are highlighted.
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Affiliation(s)
- F Ceciliani
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - P Roccabianca
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Giudice
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
| | - C Lecchi
- Department of Veterinary Medicine, Università di Milano, Via Celoria 02, 20133 Milano, Italy.
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Bryan JN. The Current State of Clinical Application of Serum Biomarkers for Canine Lymphoma. Front Vet Sci 2016; 3:87. [PMID: 27747218 PMCID: PMC5042957 DOI: 10.3389/fvets.2016.00087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/13/2016] [Indexed: 11/13/2022] Open
Abstract
Serum biomarkers of canine lymphoma activity for diagnosis, prognosis, and therapy monitoring have been of clinical interest for more than a decade. Tumor products, biochemical enzymes, cytokines, metabolic profiling, leakage enzymes, as well as serum proteins have been studied as biomarkers for lymphoma. Multiple biomarkers combined have been shown to be most sensitive and specific. C-reactive protein, thymidine kinase 1, and haptoglobin have been most extensively studied and commercialized in diagnostic tests, the TK Canine Cancer Panel and the Canine Lymphoma Blood Test. These tests have been evaluated either in cohorts of diseased and healthy dogs or in prospective studies of ill dogs, respectively, for application to clinical decision-making. Some evidence exists for application of these tests, but large-scale studies are lacking in a broad range of lymphoma forms. These biomarkers are commonly elevated at diagnosis and at relapse. Further study is necessary to determine if early intervention guided by biomarker elevation will improve quantity or quality of life for dogs with lymphoma.
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Affiliation(s)
- Jeffrey N Bryan
- Comparative Oncology Radiobiology and Epigenetics Laboratory, Department of Veterinary Medicine and Surgery, University of Missouri , Columbia, MO , USA
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Morris JS. Genomic and proteomic profiling for cancer diagnosis in dogs. Vet J 2016; 215:101-9. [DOI: 10.1016/j.tvjl.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 01/01/2016] [Indexed: 11/25/2022]
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Knapp DW, Ramos-Vara JA, Moore GE, Dhawan D, Bonney PL, Young KE. Urinary Bladder Cancer in Dogs, a Naturally Occurring Model for Cancer Biology and Drug Development. ILAR J 2014; 55:100-18. [DOI: 10.1093/ilar/ilu018] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Abstract
Glycoproteomics, the global analysis of glycoproteins, is a subfield of proteomics with high biological and clinical relevance. Glycoproteomics integrates knowledge and techniques drawing from glycotechnology, separation science, mass spectrometry, and bioinformatics to support systematic identification and quantification of glycoproteins in a complex biological sample. In this chapter, we describe a shotgun proteomics-based glycoproteomics platform that provides precise mapping of protein N-glycosylation sites and quantitative assessment of glycosylation site occupancy on a global scale.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA,
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Abstract
Advancement in electrophoresis and mass spectrometry techniques along with the recent progresses in genomics, culminating in bovine and pig genome sequencing, widened the potential application of proteomics in the field of veterinary medicine. The aim of the present review is to provide an in-depth perspective about the application of proteomics to animal disease pathogenesis, as well as its utilization in veterinary diagnostics. After an overview on the various proteomic techniques that are currently applied to veterinary sciences, the article focuses on proteomic approaches to animal disease pathogenesis. Included as well are recent achievements in immunoproteomics (ie, the identifications through proteomic techniques of antigen involved in immune response) and histoproteomics (ie, the application of proteomics in tissue processed for immunohistochemistry). Finally, the article focuses on clinical proteomics (ie, the application of proteomics to the identification of new biomarkers of animal diseases).
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Hematopoietic Tumors. WITHROW AND MACEWEN'S SMALL ANIMAL CLINICAL ONCOLOGY 2013. [PMCID: PMC7161412 DOI: 10.1016/b978-1-4377-2362-5.00032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pan S, Tamura Y, Chen R, May D, McIntosh MW, Brentnall TA. Large-scale quantitative glycoproteomics analysis of site-specific glycosylation occupancy. MOLECULAR BIOSYSTEMS 2012; 8:2850-6. [PMID: 22892896 PMCID: PMC3463725 DOI: 10.1039/c2mb25268f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Disease-associated aberrant glycosylation may be protein specific and glycosylation site specific. Quantitative assessment of glycosylation changes at a site-specific molecular level may represent one of the initial steps for systematically revealing the glycosylation abnormalities associated with a disease or biological state. Comparative quantitative profiling of glycoproteome to provide accurate quantification of site-specific glycosylation occupancy has been a challenging task, requiring a concerted approach drawing from a variety of techniques. In this report, we present a quantitative glycoproteomics method that allows global scale identification and comparative quantification of glycosylation site occupancy using mass spectrometry. We further demonstrated this approach by quantitatively characterizing the N-glycoproteome of human pancreas.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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Tvarijonaviciute A, Gutiérrez AM, Miller I, Razzazi-Fazeli E, Tecles F, Ceron JJ. A proteomic analysis of serum from dogs before and after a controlled weight-loss program. Domest Anim Endocrinol 2012; 43:271-7. [PMID: 22591953 DOI: 10.1016/j.domaniend.2012.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/07/2012] [Accepted: 04/13/2012] [Indexed: 11/19/2022]
Abstract
The objective of this study was to investigate how weight-loss program would alter the proteome of the serum of Beagle dogs. For this purpose, serum samples from 5 Beagle dogs, before and after weight loss, were analyzed using 2-dimensional electrophoresis. Protein profiles of all samples were obtained, divided into 2 classes (obese and lean), and compared using specific 2-dimensional software, giving a total of 144 spot matches. Statistical analysis revealed 3 spot matches whose expressions were modulated in response to weight loss: 2 protein spots were upregulated and 1 protein spot was downregulated in the obese state in comparison with the lean state of the dogs. Mass spectrometric identification of differentially regulated spots revealed that these protein spots corresponded to retinol-binding protein 4, clusterin precursor, and α-1 antitrypsin, respectively, which could be considered potential markers of obesity and obesity-related disease processes in dogs.
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Affiliation(s)
- A Tvarijonaviciute
- Department of Animal Medicine and Surgery, Faculty of Veterinary Medicine, Regional Campus of International Excellence Campus Mare Nostrum, University of Murcia, 30100 Espinardo, Murcia, Spain
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Pan S, Chen R, Aebersold R, Brentnall TA. Mass spectrometry based glycoproteomics--from a proteomics perspective. Mol Cell Proteomics 2010; 10:R110.003251. [PMID: 20736408 DOI: 10.1074/mcp.r110.003251] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways. Altered glycosylation has been associated with a variety of diseases, including cancer, inflammatory and degenerative diseases. Glycoproteins are becoming important targets for the development of biomarkers for disease diagnosis, prognosis, and therapeutic response to drugs. The emerging technology of glycoproteomics, which focuses on glycoproteome analysis, is increasingly becoming an important tool for biomarker discovery. An in-depth, comprehensive identification of aberrant glycoproteins, and further, quantitative detection of specific glycosylation abnormalities in a complex environment require a concerted approach drawing from a variety of techniques. This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.
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Affiliation(s)
- Sheng Pan
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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