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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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2
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Fahrner M, Bronsert P, Fichtner-Feigl S, Jud A, Schilling O. Proteome biology of primary colorectal carcinoma and corresponding liver metastases. Neoplasia 2021; 23:1240-1251. [PMID: 34768110 PMCID: PMC8591399 DOI: 10.1016/j.neo.2021.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
Colorectal adenocarcinomas (CRC) are one of the most commonly diagnosed tumors worldwide. Colorectal adenocarcinomas primarily metastasize into the liver and (less often) into the peritoneum. Patients suffering from CRC-liver metastasis (CRC-LM) typically present with a dismal overall survival compared to non-metastasized CRC patients. The metastasis process and metastasis-promoting factors in patients with CRC are under intensive debate. However, CRC studies investigating the proteome biology are lacking. Formalin-fixed paraffin-embedded (FFPE) tissue specimens provide a valuable resource for comprehensive proteomic studies of a broad variety of clinical malignancies. The presented pilot study compares the proteome of primary CRC and patient-matched CRC-LM. The applied protocol allows a reproducible and straightforward identification and quantification of over 2,600 proteins within the dissected tumorous tissue. Subsequent unsupervised clustering reveals distinct proteome biologies of the primary CRC and the corresponding CRC-LM. Statistical analysis yields multiple differentially abundant proteins in either primary CRC or their corresponding liver metastases. A more detailed analysis of dysregulated biological processes suggests an active immune response in the liver metastases, including several proteins of the complement system. Proteins with structural roles, e.g. cytoskeleton organization or cell junction assembly appear to be less prominent in liver metastases as compared to primary CRC. Immunohistochemistry corroborates proteomic high expression levels of metabolic proteins in CRC-LM. We further assessed how the in vitro inhibition of two in CRC-LM enriched metabolic proteins affected cell proliferation and chemosensitivity. The presented proteomic investigation in a small clinical cohort promotes a more comprehensive understanding of the distinct proteome biology of primary CRC and their corresponding liver metastases.
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Affiliation(s)
- Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Tumorbank Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg; Core Facility Histopathology and Digital Pathology Freiburg, Medical Center - University of Freiburg
| | - Stefan Fichtner-Feigl
- Department of General and Visceral Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Jud
- Department of General and Visceral Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
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3
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Runge AKW, Hendy J, Richter KK, Masson-MacLean E, Britton K, Mackie M, McGrath K, Collins M, Cappellini E, Speller C. Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome. Proc Biol Sci 2021; 288:20210020. [PMID: 34229485 PMCID: PMC8261203 DOI: 10.1098/rspb.2021.0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.
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Affiliation(s)
- Anne Kathrine W Runge
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany
| | - Kristine K Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | | | - Kate Britton
- Department of Archaeology, University of Aberdeen, Aberdeen, Scotland, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103
| | - Meaghan Mackie
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark.,The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 København N, Denmark
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Prehistory and Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Matthew Collins
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark.,Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Enrico Cappellini
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, 1353 København K, Denmark
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK.,Department of Anthropology, University of British Columbia, 6303 NW Marine Drive, Vancouver, Canada V6T 1Z1
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4
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Leo R, Therachiyil L, Siveen SK, Uddin S, Kulinski M, Buddenkotte J, Steinhoff M, Krishnankutty AR. Protein Expression Profiling Identifies Key Proteins and Pathways Involved in Growth Inhibitory Effects Exerted by Guggulsterone in Human Colorectal Cancer Cells. Cancers (Basel) 2019; 11:E1478. [PMID: 31581454 PMCID: PMC6826505 DOI: 10.3390/cancers11101478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is a leading killer cancer worldwide and one of the most common malignancies with increasing incidences of mortality. Guggulsterone (GS) is a plant sterol used for treatment of various ailments such as obesity, hyperlipidemia, diabetes, and arthritis. In the current study, anti-cancer effects of GS in human colorectal cancer cell line HCT 116 was tested, potential targets identified using mass spectrometry-based label-free shotgun proteomics approach and key pathways validated by proteome profiler antibody arrays. Comprehensive proteomic profiling identified 14 proteins as significantly dysregulated. Proteins involved in cell proliferation/migration, tumorigenesis, cell growth, metabolism, and DNA replication were downregulated while the protein with functional role in exocytosis/tumor suppression was found to be upregulated. Our study evidenced that GS treatment altered expression of Bcl-2 mediated the mitochondrial release of cytochrome c which triggered the formation of apoptosome as well as activation of caspase-3/7 leading to death of HCT 116 cells via intrinsic apoptosis pathway. GS treatment also induced expression of p53 protein while p21 expression was unaltered with no cell cycle arrest. In addition, GS was found to inhibit NF-kB signaling in colon cancer cells by quelling the expression of its regulated gene products Bcl-2, cIAP-1, and survivin.
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Affiliation(s)
- Rari Leo
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Lubna Therachiyil
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
- Department of Pharmaceutical Sciences, College of Pharmacy, Qatar University, Doha 2713, Qatar.
| | - Sivaraman K Siveen
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Joerg Buddenkotte
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha 3050, Qatar.
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha 3050, Qatar.
- Department of Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, Doha 24144, Qatar.
- Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
- College of Medicine, Qatar University, Doha 2713, Qatar.
| | - And Roopesh Krishnankutty
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha 3050, Qatar.
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5
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Chauvin A, Boisvert FM. Clinical Proteomics in Colorectal Cancer, a Promising Tool for Improving Personalised Medicine. Proteomes 2018; 6:proteomes6040049. [PMID: 30513835 PMCID: PMC6313903 DOI: 10.3390/proteomes6040049] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures currently used for detecting this cancer, as well as for predicting the response to treatment and the outcome of a patient's resistance in guiding clinical practice, are key elements driving the search for biomarkers. In the present overview, the different biomarkers (diagnostic, prognostic, treatment resistance) discovered through proteomics studies in various colorectal cancer study models (blood, stool, biopsies), including the different proteomic techniques used for the discovery of these biomarkers, are reviewed, as well as the various tests used in clinical practice and those currently in clinical phase. These studies define the limits and perspectives related to proteomic biomarker research for personalised medicine in colorectal cancer.
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Affiliation(s)
- Anaïs Chauvin
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
| | - François-Michel Boisvert
- Department of Anatomy and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada.
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6
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Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer. Oncotarget 2018; 7:43868-43893. [PMID: 27270312 PMCID: PMC5190065 DOI: 10.18632/oncotarget.9701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/08/2016] [Indexed: 12/14/2022] Open
Abstract
Surgical resection supplemented with adjuvant chemotherapy is the current preferred treatment for Stage III colorectal cancer (CRC). However, as many as 48% of patients who undergo curative resection eventually suffer from incurable distant recurrence. To investigate the molecular mechanisms involved in Stage III CRC post-surgical distant recurrence, we identified a total of 146 differentially expressed proteins (DEPs) associated with distant recurrence in Stage III CRC using TMT-based quantitative mass spectrometry. Among these DEPs, the altered expressions of R-Ras and Transgelin were then validated in 192 individual specimens using immunohistochemistry (IHC). Furthermore, Kaplan-Meier analysis revealed that the levels of R-Ras and Transgelin were significantly associated with 5-year overall survival (OS) and disease-free survival (DFS), and multivariate Cox-regression analyses revealed that R-Ras and Transgelin were independent prognostic factors for OS and DFS, respectively. In conclusion, this study identified potential biochemical players involved in distant recurrence and indicates that R-Ras and Transgelin are potential post-surgical prognostic biomarkers for Stage III CRC. This proteomics data have been submitted to Proteome Xchange under accession number PXD002903.
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7
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Yang Q, Roehrl MH, Wang JY. Proteomic profiling of antibody-inducing immunogens in tumor tissue identifies PSMA1, LAP3, ANXA3, and maspin as colon cancer markers. Oncotarget 2017; 9:3996-4019. [PMID: 29423100 PMCID: PMC5790517 DOI: 10.18632/oncotarget.23583] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/27/2017] [Indexed: 12/13/2022] Open
Abstract
We hypothesized that cancer tissue immunogens - antigens capable of inducing specific antibody production in patients - are promising targets for development of precision diagnostics and humoral immunotherapies. We developed an innovative immuno-proteomic strategy and identified new immunogenic markers of colon cancer. Proteins from cancers and matched normal tissues were separated by 2D gel electrophoresis and blotted with serum antibodies from the same patients. Antibody-reactive proteins were sequenced by mass spectrometry and validated by Western blotting and immunohistochemistry. 170 serum antibody-reactive proteins were identified only in cancerous but not matched normal. Among these, proteasome subunit alpha type 1 (PSA1), leucine aminopeptidase 3 (LAP3), annexin A3 (ANXA3), and maspin (serpin B5) were reproducibly found in tissues from three patients. Differential expression patterns were confirmed in samples from eight patients with various stages of colon adenocarcinoma and liver metastases. These tumor-resident proteins and/or their associated serum antibodies may be promising markers for colon cancer screening and early diagnosis. Furthermore, tumor tissue-specific antibodies could potentially be exploited as immunotherapeutic targets against cancer. More generally, proteomic profiling of antibody-inducing cancer-associated immunogens represents a powerful generic method for uncovering the tumor antigen-ome, i.e., the totality of immunogenic tumor-associated proteins.
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Affiliation(s)
- Qian Yang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Ontario Cancer Institute, University Health Network, Toronto, Canada
| | - Michael H Roehrl
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Ontario Cancer Institute, University Health Network, Toronto, Canada.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julia Y Wang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Ontario Cancer Institute, University Health Network, Toronto, Canada.,Curandis, Boston, MA, USA
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8
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Marolla APC, Waisberg J, Saba GT, Waisberg DR, Margeotto FB, Pinhal MADS. Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry. EINSTEIN-SAO PAULO 2016; 13:510-7. [PMID: 26761548 PMCID: PMC4878623 DOI: 10.1590/s1679-45082015ao3477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/09/2015] [Indexed: 12/15/2022] Open
Abstract
Objective To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Methods Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student’s t test. Results The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). Conclusion The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues.
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Affiliation(s)
| | - Jaques Waisberg
- Hospital do Servidor Público Estadual, São Paulo, SP, Brazil
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9
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Dick JM. Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 2016; 4:e2238. [PMID: 27547546 PMCID: PMC4958012 DOI: 10.7717/peerj.2238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022] Open
Abstract
New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (ZC) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (\documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean ZC or \documentclass[12pt]{minimal}
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}{}${\overline{n}}_{{\mathrm{H}}_{2}\mathrm{O}}$\end{document}n¯H2O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower ZC for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H2O and fugacity of O2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states.
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10
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Wu XY, Huang XE. Clinical Application of Serum Tumor Abnormal Protein (TAP) in Colorectal Cancer Patients. Asian Pac J Cancer Prev 2016; 16:3425-8. [PMID: 25921156 DOI: 10.7314/apjcp.2015.16.8.3425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To explore the association of serum tumor abnormal protein (TAP) with other serological biomarkers e.g. carcinoembryonic antigen (CEA), carbohydrate antigen 125 (CA125), carbohydrate antigen 19-9 (CA19-9) and its clinical application in colorectal cancer (CRC) patients. METHODS Patients (N=98) were enrolled into this study with histologically or cytologically confirmed CRC. Using a test kit, the level of TAP was determined, while chemiluminescence was used to measure the levels of some other common serological biomarkers e.g. CEA, CA125 and CA19-9. RESULTS The area of TAP condensed particulate matter decreased after chemotherapy compared with before chemotherapy when CT or MRI scans showed disease control. In contrast, it increased with disease progression (P<0.05). Furthermore, a statistically significant difference was confirmed in monitoring of TAP and common serological biomarkers e.g. CEA and CA19-9 (p<0.05). CONCLUSIONS Detecting TAP in CRC patients has high sensitivity and specificity and can be used as a new independent indicator for clinically monitoring CRC patients in the course of chemotherapy.
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Affiliation(s)
- Xue-Yan Wu
- Department of Chemotherapy, the Affiliated Jiangsu Cancer Hospital of Nanjing Medical University and Jiangsu Institute of Cancer Research, Nanjing, China E-mail :
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11
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Gemoll T, Meyer R, Habermann JK. Applying Genomics and Proteomics in Translational Surgical Oncology Research. Eur Surg Res 2015; 55:184-97. [PMID: 26339997 DOI: 10.1159/000438860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Translational surgical research can range from investigating clinically oriented basic pathophysiological research via the correlation of molecular findings with a patient's clinical outcome to conducting treatment response studies. Herein, the specialist's opinion as a 'surgeon scientist' plays a pivotal role, e.g. in planning experimental setups focusing on the clinically most relevant needs. SUMMARY AND KEY MESSAGES: This review provides a survey of genomic and proteomic technologies and gives an up-to-date overview of those studies applying these technologies exemplarily in colorectal cancer-based biomarker research. Although current results are promising, future validation studies within multicenter networks are required to promote the translation of 'omics' from bench to bedside. In this endeavor, departments of surgery and institutes of experimental surgery together should play a fundamental role. The program for 'clinician scientists' recently launched by the German Research Society (DFG) could be one tool to promote interdisciplinary networks and surgeons' impact on translational research.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lx00FC;beck and University Medical Center Schleswig-Holstein (UKSH), Lx00FC;beck, Germany
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12
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Label-free quantitative mass spectrometry reveals a panel of differentially expressed proteins in colorectal cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:365068. [PMID: 25699276 PMCID: PMC4324820 DOI: 10.1155/2015/365068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022]
Abstract
To identify potential biomarkers involved in CRC, a shotgun proteomic method was applied to identify soluble proteins in three CRCs and matched normal mucosal tissues using high-performance liquid chromatography and mass spectrometry. Label-free protein profiling of three CRCs and matched normal mucosal tissues were then conducted to quantify and compare proteins. Results showed that 67 of the 784 identified proteins were linked to CRC (28 upregulated and 39 downregulated). Gene Ontology and DAVID databases were searched to identify the location and function of differential proteins that were related to the biological processes of binding, cell structure, signal transduction, cell adhesion, and so on. Among the differentially expressed proteins, tropomyosin-3 (TPM3), endoplasmic reticulum resident protein 29 (ERp29), 18 kDa cationic antimicrobial protein (CAMP), and heat shock 70 kDa protein 8 (HSPA8) were verified to be upregulated in CRC tissue and seven cell lines through western blot analysis. Furthermore, the upregulation of TPM3, ERp29, CAMP, and HSPA8 was validated in 69 CRCs byimmunohistochemistry (IHC) analysis. Combination of TPM3, ERp29, CAMP, and HSPA8 can identify CRC from matched normal mucosal achieving an accuracy of 73.2% using IHC score. These results suggest that TPM3, ERp29, CAMP, and HSPA8 are great potential IHC diagnostic biomarkers for CRC.
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13
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Coghlin C, Murray GI. Biomarkers of colorectal cancer: Recent advances and future challenges. Proteomics Clin Appl 2015; 9:64-71. [DOI: 10.1002/prca.201400082] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/19/2014] [Accepted: 10/07/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Caroline Coghlin
- Department of Pathology; Aberdeen Royal Infirmary; NHS Grampian; Aberdeen UK
| | - Graeme I. Murray
- Pathology Division of Applied Medicine; School of Medicine and Dentistry; University of Aberdeen; Aberdeen UK
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Farrokhi V, McShane AJ, Nemati R, Yao X. Stable isotope dilution mass spectrometry for membrane transporter quantitation. AAPS JOURNAL 2014; 15:1222-31. [PMID: 24022320 DOI: 10.1208/s12248-013-9529-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/16/2013] [Indexed: 11/30/2022]
Abstract
This review provides an introduction to stable isotope dilution mass spectrometry (MS) and its emerging applications in the analysis of membrane transporter proteins. Various approaches and application examples, for the generation and use of quantitation reference standards—either stable isotope-labeled peptides or proteins—are discussed as they apply to the MS quantitation of membrane proteins. Technological considerations for the sample preparation of membrane transporter proteins are also presented.
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Wang K, Huang C, Nice EC. Proteomics, genomics and transcriptomics: their emerging roles in the discovery and validation of colorectal cancer biomarkers. Expert Rev Proteomics 2014; 11:179-205. [PMID: 24611605 DOI: 10.1586/14789450.2014.894466] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the second most common cancer in females and the third in males. Since CRC is often diagnosed at an advanced stage when prognosis is poor, identification of biomarkers for early diagnosis is urgently required. Recent advances in proteomics, genomics and transcriptomics have facilitated high-throughput profiling of data generated from CRC-related genes and proteins, providing a window of information for biomarker discovery and validation. However, transfer of candidate biomarkers from bench to bedside remains a dilemma. In this review, we will discuss emerging proteomic technologies and highlight various sample types utilized for proteomics-based identification of CRC biomarkers. Moreover, recent breakthroughs in genomics and transcriptomics for the identification of CRC biomarkers, with particular emphasis on the merits of emerging methylomic and miRNAomic strategies, will be discussed. Integration of proteomics, genomics and transcriptomics will facilitate the discovery and validation of CRC biomarkers leading to the emergence of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, 610041 , P.R. China
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