1
|
Repetto O, Vettori R, Steffan A, Cannizzaro R, De Re V. Circulating Proteins as Diagnostic Markers in Gastric Cancer. Int J Mol Sci 2023; 24:16931. [PMID: 38069253 PMCID: PMC10706891 DOI: 10.3390/ijms242316931] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing targeted prevention strategies. Markers are necessary for early detection and to guide clinicians to the best personalized treatment. The current semi-invasive endoscopic methods to detect GC are invasive, costly, and time-consuming. Recent advances in proteomics technologies have enabled the screening of many samples and the detection of novel biomarkers and disease-related signature signaling networks. These biomarkers include circulating proteins from different fluids (e.g., plasma, serum, urine, and saliva) and extracellular vesicles. We review relevant published studies on circulating protein biomarkers in GC and detail their application as potential biomarkers for GC diagnosis. Identifying highly sensitive and highly specific diagnostic markers for GC may improve patient survival rates and contribute to advancing precision/personalized medicine.
Collapse
Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Roberto Vettori
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Renato Cannizzaro
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy;
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
| |
Collapse
|
2
|
Liu D, Wang Y, Li X, Wang Y, Zhang Z, Wang Z, Zhang X. Participation of protein metabolism in cancer progression and its potential targeting for the management of cancer. Amino Acids 2023; 55:1223-1246. [PMID: 37646877 DOI: 10.1007/s00726-023-03316-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023]
Abstract
Cancer malignancies may broadly be described as heterogeneous disorders manifested by uncontrolled cellular growth/division and proliferation. Tumor cells utilize metabolic reprogramming to accomplish the upregulated nutritional requirements for sustaining their uncontrolled growth, proliferation, and survival. Metabolic reprogramming also called altered or dysregulated metabolism undergoes modification in normal metabolic pathways for anabolic precursor's generation that serves to continue biomass formation that sustains the growth, proliferation, and survival of carcinogenic cells under a nutrition-deprived microenvironment. A wide range of dysregulated/altered metabolic pathways encompassing different metabolic regulators have been described; however, the current review is focused to explain deeply the metabolic pathways modifications inducing upregulation of proteins/amino acids metabolism. The essential modification of various metabolic cycles with their consequent outcomes meanwhile explored promising therapeutic targets playing a pivotal role in metabolic regulation and is successfully employed for effective target-specific cancer treatment. The current review is aimed to understand the metabolic reprogramming of different proteins/amino acids involved in tumor progression along with potential therapeutic perspective elucidating targeted cancer therapy via these targets.
Collapse
Affiliation(s)
- Dalong Liu
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yun Wang
- Department of Thoracic Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Xiaojiang Li
- Department of Orthopedics, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China
| | - Yan Wang
- Department of Neurosurgery, People's Hospital of Jilin City, Jilin, 136200, China
| | - Zhiqiang Zhang
- Department of Orthopedics, Baishan Hospital of Traditional Chinese Medicine, Baishan, 134300, China
| | - Zhifeng Wang
- Department of Traditional Chinese Medicine, Changchun Chaoyang District Hospital of Traditional Chinese Medicine, Changchun, 130000, China
| | - Xudong Zhang
- Department of Brain Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, 130000, China.
| |
Collapse
|
3
|
Wang Z, Fang Z, Liu L, Zhu H, Wang Y, Zhao C, Guo Z, Qin H, Nie Y, Liang X, Dong M, Ye M. Development of an Integrated Platform for the Simultaneous Enrichment and Characterization of N- and O-Linked Intact Glycopeptides. Anal Chem 2023; 95:7448-7457. [PMID: 37146305 DOI: 10.1021/acs.analchem.2c04305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Both N-linked glycosylation and O-linked glycosylation play essential roles in the onset and progression of various diseases including cancer, and N-/O-linked site-specific glycans have been proven to be promising biomarkers for the discrimination of cancer. However, the micro-heterogeneity and low abundance nature of N-/O-linked glycosylation, as well as the time-consuming and tedious procedures for the enrichment of O-linked intact glycopeptides, pose great challenges for their efficient and accurate characterization. In this study, we developed an integrated platform for the simultaneous enrichment and characterization of N- and O-linked intact glycopeptides from the same serum sample. By fine-tuning the experimental conditions, we demonstrated that this platform allowed the selective separation of N- and O-linked intact glycopeptides into two fractions, with 85.1% O-linked intact glycopeptides presented in the first fraction and 93.4% N-linked intact glycopeptides presented in the second fraction. Determined with high reproducibility, this platform was further applied to the differential analysis of serum samples of gastric cancer and health control, which revealed 17 and 181 significantly changed O-linked and N-linked intact glycopeptides. Interestingly, five glycoproteins containing both significant regulation of N- and O-glycosylation were observed, hinting potential co-regulation of different types of glycosylation during tumor progress. In summary, this integrated platform opened a potentially useful avenue for the global analysis of protein glycosylation and can serve as a useful tool for the characterization of N-/O-linked intact glycopeptides at the proteomics scale.
Collapse
Affiliation(s)
- Zhongyu Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyao Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Changrui Zhao
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Zhimou Guo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Mingming Dong
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| |
Collapse
|
4
|
Cao W, Bruening ML. Analysis of Protein Glycosylation after Rapid Digestion Using Protease-Containing Membranes in Spin Columns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37127550 DOI: 10.1021/jasms.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important protein post-translational modification that plays a pivotal role in the bioactivity of therapeutic proteins and in the infectivity of viral proteins. Liquid chromatography with tandem mass spectrometry readily identifies protein glycans with site specificity. However, the overnight incubation used in conventional in-solution proteolysis leads to high turnaround times for glycosylation analysis, particularly when sequential in-solution digestions are needed for site-specific glycan identification. Using bovine fetuin as a model glycoprotein, this work first shows that in-membrane digestion in ∼3 min yields similar glycan identification and quantitation when compared to overnight in-solution digestion. Protease-containing membranes in a spin column enable digestion of therapeutic proteins (trastuzumab and erythropoietin) and a viral protein (SARS-CoV-2 receptor binding domain) in ∼30 s. Glycan identification is similar after in-solution and in-membrane digestion, and limited in-membrane digestion enhances the identification of high-mannose glycans in trastuzumab. Finally, stacked membranes containing trypsin and chymotrypsin allow fast sequential proteolytic digestion to site-specifically identify the glycans of SARS-CoV-2 receptor binding domain. One can easily assemble the protease-containing membranes in commercial spin columns, and spinning multiple columns simultaneously will facilitate parallel analyses.
Collapse
Affiliation(s)
- Weikai Cao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
5
|
Characterization and Vaccine Potential of Outer Membrane Vesicles from Photobacterium damselae subsp. piscicida. Int J Mol Sci 2023; 24:ijms24065138. [PMID: 36982212 PMCID: PMC10049053 DOI: 10.3390/ijms24065138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Photobacterium damselae subsp. piscicida (Phdp) is a Gram-negative fish pathogen with worldwide distribution and broad host specificity that causes heavy economic losses in aquaculture. Although Phdp was first identified more than 50 years ago, its pathogenicity mechanisms are not completely understood. In this work, we report that Phdp secretes large amounts of outer membrane vesicles (OMVs) when cultured in vitro and during in vivo infection. These OMVs were morphologically characterized and the most abundant vesicle-associated proteins were identified. We also demonstrate that Phdp OMVs protect Phdp cells from the bactericidal activity of fish antimicrobial peptides, suggesting that secretion of OMVs is part of the strategy used by Phdp to evade host defense mechanisms. Importantly, the vaccination of sea bass (Dicentrarchus labrax) with adjuvant-free crude OMVs induced the production of anti-Phdp antibodies and resulted in partial protection against Phdp infection. These findings reveal new aspects of Phdp biology and may provide a basis for developing new vaccines against this pathogen.
Collapse
|
6
|
Hassan T, Firdous P, Nissar K, Ahmad MB, Imtiyaz Z. Role of proteomics in surgical oncology. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
7
|
Trbojević-Akmačić I, Lageveen-Kammeijer GSM, Heijs B, Petrović T, Deriš H, Wuhrer M, Lauc G. High-Throughput Glycomic Methods. Chem Rev 2022; 122:15865-15913. [PMID: 35797639 PMCID: PMC9614987 DOI: 10.1021/acs.chemrev.1c01031] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycomics aims to identify the structure and function of the glycome, the complete set of oligosaccharides (glycans), produced in a given cell or organism, as well as to identify genes and other factors that govern glycosylation. This challenging endeavor requires highly robust, sensitive, and potentially automatable analytical technologies for the analysis of hundreds or thousands of glycomes in a timely manner (termed high-throughput glycomics). This review provides a historic overview as well as highlights recent developments and challenges of glycomic profiling by the most prominent high-throughput glycomic approaches, with N-glycosylation analysis as the focal point. It describes the current state-of-the-art regarding levels of characterization and most widely used technologies, selected applications of high-throughput glycomics in deciphering glycosylation process in healthy and disease states, as well as future perspectives.
Collapse
Affiliation(s)
| | | | - Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tea Petrović
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Helena Deriš
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Gordan Lauc
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
- Faculty
of Pharmacy and Biochemistry, University
of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
| |
Collapse
|
8
|
Tarfeen N, Nisa KU, Nisa Q. MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9340741 DOI: 10.1007/s43538-022-00085-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.
Collapse
|
9
|
Relevance of miR-223 as Potential Diagnostic and Prognostic Markers in Cancer. BIOLOGY 2022; 11:biology11020249. [PMID: 35205115 PMCID: PMC8869096 DOI: 10.3390/biology11020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
In 1993, the discovery of microRNAs in Caenorhabditis elegans (C. elegans) altered the paradigmatic view of RNA biology and post-transcriptional gene regulation. Further study revealed the role of microRNAs in disease development and progression. In particular, this review highlights microRNA-223 (miR-223 or miRNA-223) expression in malignant neoplastic disorders. miR-223 expression controls aspects of hematopoiesis and apoptosis, and cell proliferation, migration, and invasion. miR-223 regulates a number of gene targets, including cytoplasmic activation/proliferation-associated protein-1 (Caprin-1), insulin-like growth factor-1 receptor (IGF-1R), and other cell proliferation- and cell cycle-associated genes. Several studies have proposed miR-223 as a novel biomarker for early cancer diagnosis. Here, we emphasize miR-223′s role in the development and progression of cancer.
Collapse
|
10
|
Tvaroška I. Glycosyltransferases as targets for therapeutic intervention in cancer and inflammation: molecular modeling insights. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-02026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Marques MS, Costa AC, Osório H, Pinto ML, Relvas S, Dinis-Ribeiro M, Carneiro F, Leite M, Figueiredo C. Helicobacter pylori PqqE is a new virulence factor that cleaves junctional adhesion molecule A and disrupts gastric epithelial integrity. Gut Microbes 2021; 13:1-21. [PMID: 33970782 PMCID: PMC8115454 DOI: 10.1080/19490976.2021.1921928] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Helicobacter pylori infects approximately half of the world's population and is the strongest risk factor for peptic ulcer disease and gastric cancer, representing a major global health concern. H. pylori persistently colonizes the gastric epithelium, where it subverts the highly organized structures that maintain epithelial integrity. Here, a unique strategy used by H. pylori to disrupt the gastric epithelial junctional adhesion molecule-A (JAM-A) is disclosed, using various experimental models that include gastric cell lines, primary human gastric cells, and biopsy specimens of infected and non-infected individuals. H. pylori preferentially cleaves the cytoplasmic domain of JAM-A at Alanine 285. Cells stably transfected with full-length JAM-A or JAM-A lacking the cleaved sequence are used in a range of functional assays, which demonstrate that the H. pylori cleaved region is critical to the maintenance of the epithelial barrier and of cell-cell adhesion. Notably, by combining chromatography techniques and mass spectrometry, PqqE (HP1012) is purified and identified as the H. pylori virulence factor that cleaves JAM-A, uncovering a previously unreported function for this bacterial protease. These findings propose a novel mechanism for H. pylori to disrupt epithelial integrity and functions, breaking new ground in the understanding of the pathogenesis of this highly prevalent and clinically relevant infection.
Collapse
Affiliation(s)
- Miguel S. Marques
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Ana C. Costa
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Hugo Osório
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Marta L. Pinto
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Sandra Relvas
- Department of Pathology, Centro Hospitalar Universitário S. João, Porto, Portugal
| | - Mário Dinis-Ribeiro
- Faculty of Medicine of the University of Porto, Porto, Portugal,Instituto Português de Oncologia, Porto, Portugal,Center for Health Technology and Services Research (CINTESIS), Porto, Portugal
| | - Fátima Carneiro
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal,Department of Pathology, Centro Hospitalar Universitário S. João, Porto, Portugal
| | - Marina Leite
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Ceu Figueiredo
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Ipatimup – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal,Faculty of Medicine of the University of Porto, Porto, Portugal,CONTACT Ceu Figueiredo i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| |
Collapse
|
12
|
Aziz F, Khan I, Shukla S, Dey DK, Yan Q, Chakraborty A, Yoshitomi H, Hwang SK, Sonwal S, Lee H, Haldorai Y, Xiao J, Huh YS, Bajpai VK, Han YK. Partners in crime: The Lewis Y antigen and fucosyltransferase IV in Helicobacter pylori-induced gastric cancer. Pharmacol Ther 2021; 232:107994. [PMID: 34571111 DOI: 10.1016/j.pharmthera.2021.107994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 02/05/2023]
Abstract
Helicobacter pylori (H. pylori) is a major causative agent of chronic gastritis, gastric ulcer and gastric carcinoma. H. pylori cytotoxin associated antigen A (CagA) plays a crucial role in the development of gastric cancer. Gastric cancer is associated with glycosylation alterations in glycoproteins and glycolipids on the cell surface. H. pylori cytotoxin associated antigen A (CagA) plays a significant role in the progression of gastric cancer through post-translation modification of fucosylation to develop gastric cancer. The involvement of a variety of sugar antigens in the progression and development of gastric cancer has been investigated, including type II blood group antigens. Lewis Y (LeY) is overexpressed on the tumor cell surface either as a glycoprotein or glycolipid. LeY is a difucosylated oligosaccharide, which is catalyzed by fucosyltransferases such as FUT4 (α1,3). FUT4/LeY overexpression may serve as potential correlative biomarkers for the prognosis of gastric cancer. We discuss the various aspects of H. pylori in relation to fucosyltransferases (FUT1-FUT9) and its fucosylated Lewis antigens (LeY, LeX, LeA, and LeB) and gastric cancer. In this review, we summarize the carcinogenic effect of H. pylori CagA in association with LeY and its synthesis enzyme FUT4 in the development of gastric cancer as well as discuss its importance in the prognosis and its inhibition by combination therapy of anti-LeY antibody and celecoxib through MAPK signaling pathway preventing gastric carcinogenesis.
Collapse
Affiliation(s)
- Faisal Aziz
- The Hormel Institute-University of Minnesota, Austin, MN 55912, USA; Department of Biochemistry and Molecular Biology, Dalian Medical University, Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, Dalian 116044, PR China.
| | - Imran Khan
- The Hormel Institute-University of Minnesota, Austin, MN 55912, USA
| | - Shruti Shukla
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gwal Pahari, Gurugram, Haryana 122003, India
| | - Debasish Kumar Dey
- Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Qiu Yan
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, Dalian 116044, PR China
| | | | - Hisae Yoshitomi
- The Hormel Institute-University of Minnesota, Austin, MN 55912, USA
| | - Seung-Kyu Hwang
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Nam-gu, Incheon 22212, Republic of Korea
| | - Sonam Sonwal
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Nam-gu, Incheon 22212, Republic of Korea
| | - Hoomin Lee
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Nam-gu, Incheon 22212, Republic of Korea
| | - Yuvaraj Haldorai
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamilnadu 641046, India
| | - Jianbo Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China; University of Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, E32004 Ourense, Spain.
| | - Yun Suk Huh
- Department of Biological Engineering, NanoBio High-Tech Materials Research Center, Inha University, 100 Inha-ro, Nam-gu, Incheon 22212, Republic of Korea.
| | - Vivek K Bajpai
- Department of Energy and Materials Engineering, Dongguk University-Seoul, 30 Pildong-ro 1-gil, Seoul 04620, Republic of Korea.
| | - Young-Kyu Han
- Department of Energy and Materials Engineering, Dongguk University-Seoul, 30 Pildong-ro 1-gil, Seoul 04620, Republic of Korea.
| |
Collapse
|
13
|
Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
Collapse
Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
| |
Collapse
|
14
|
Santos M, Pereira SB, Flores C, Príncipe C, Couto N, Karunakaran E, Cravo SM, Oliveira P, Tamagnini P. Absence of KpsM (Slr0977) Impairs the Secretion of Extracellular Polymeric Substances (EPS) and Impacts Carbon Fluxes in Synechocystis sp. PCC 6803. mSphere 2021; 6:e00003-21. [PMID: 33504656 PMCID: PMC7885315 DOI: 10.1128/msphere.00003-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/02/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS), composed mainly of heteropolysaccharides, that play a variety of physiological roles, being crucial for cell protection, motility, and biofilm formation. However, due to their complexity, the EPS biosynthetic pathways as well as their assembly and export mechanisms are still far from being fully understood. Here, we show that the absence of a putative EPS-related protein, KpsM (Slr0977), has a pleiotropic effect on Synechocystis sp. strain PCC 6803 physiology, with a strong impact on the export of EPS and carbon fluxes. The kpsM mutant exhibits a significant reduction of released polysaccharides and a smaller decrease of capsular polysaccharides, but it accumulates more polyhydroxybutyrate (PHB) than the wild type. In addition, this strain shows a light/cell density-dependent clumping phenotype and exhibits an altered protein secretion capacity. Furthermore, the most important structural component of pili, the protein PilA, was found to have a modified glycosylation pattern in the mutant compared to the wild type. Proteomic and transcriptomic analyses revealed significant changes in the mechanisms of energy production and conversion, namely, photosynthesis, oxidative phosphorylation, and carbon metabolism, in response to the inactivation of slr0977 Overall, this work shows for the first time that cells with impaired EPS secretion undergo transcriptomic and proteomic adjustments, highlighting the importance of EPS as a major carbon sink in cyanobacteria. The accumulation of PHB in cells of the mutant, without affecting significantly its fitness/growth rate, points to its possible use as a chassis for the production of compounds of interest.IMPORTANCE Most cyanobacteria produce extracellular polymeric substances (EPS) that fulfill different biological roles depending on the strain/environmental conditions. The interest in the cyanobacterial EPS synthesis/export pathways has been increasing, not only to optimize EPS production but also to efficiently redirect carbon flux toward the production of other compounds, allowing the implementation of industrial systems based on cyanobacterial cell factories. Here, we show that a Synechocystis kpsM (slr0977) mutant secretes less EPS than the wild type, accumulating more carbon intracellularly, as polyhydroxybutyrate. Further characterization showed a light/cell density-dependent clumping phenotype, altered protein secretion, and modified glycosylation of PilA. The proteome and transcriptome of the mutant revealed significant changes, namely, in photosynthesis and carbon metabolism. Altogether, this work provides a comprehensive overview of the impact of kpsM disruption on Synechocystis physiology, highlighting the importance of EPS as a carbon sink and showing how cells adapt when their secretion is impaired, and the redirection of the carbon fluxes.
Collapse
Affiliation(s)
- Marina Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Sara B Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Carlos Flores
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Narciso Couto
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Sara M Cravo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Matosinhos, Portugal
- Laboratório de Química Orgânica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Paulo Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Celular e Molecular, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
15
|
Mucin-Type O-GalNAc Glycosylation in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1325:25-60. [PMID: 34495529 DOI: 10.1007/978-3-030-70115-4_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mucin-type GalNAc O-glycosylation is one of the most abundant and unique post-translational modifications. The combination of proteome-wide mapping of GalNAc O-glycosylation sites and genetic studies with knockout animals and genome-wide analyses in humans have been instrumental in our understanding of GalNAc O-glycosylation. Combined, such studies have revealed well-defined functions of O-glycans at single sites in proteins, including the regulation of pro-protein processing and proteolytic cleavage, as well as modulation of receptor functions and ligand binding. In addition to isolated O-glycans, multiple clustered O-glycans have an important function in mammalian biology by providing structural support and stability of mucins essential for protecting our inner epithelial surfaces, especially in the airways and gastrointestinal tract. Here the many O-glycans also provide binding sites for both endogenous and pathogen-derived carbohydrate-binding proteins regulating critical developmental programs and helping maintain epithelial homeostasis with commensal organisms. Finally, O-glycan changes have been identified in several diseases, most notably in cancer and inflammation, where the disease-specific changes can be used for glycan-targeted therapies. This chapter will review the biosynthesis, the biology, and the translational perspectives of GalNAc O-glycans.
Collapse
|
16
|
Fernandes E, Sores J, Cotton S, Peixoto A, Ferreira D, Freitas R, Reis CA, Santos LL, Ferreira JA. Esophageal, gastric and colorectal cancers: Looking beyond classical serological biomarkers towards glycoproteomics-assisted precision oncology. Am J Cancer Res 2020; 10:4903-4928. [PMID: 32308758 PMCID: PMC7163443 DOI: 10.7150/thno.42480] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Esophageal (OC), gastric (GC) and colorectal (CRC) cancers are amongst the digestive track tumors with higher incidence and mortality due to significant molecular heterogeneity. This constitutes a major challenge for patients' management at different levels, including non-invasive detection of the disease, prognostication, therapy selection, patient's follow-up and the introduction of improved and safer therapeutics. Nevertheless, important milestones have been accomplished pursuing the goal of molecular-based precision oncology. Over the past five years, high-throughput technologies have been used to interrogate tumors of distinct clinicopathological natures, generating large-scale biological datasets (e.g. genomics, transcriptomics, and proteomics). As a result, GC and CRC molecular subtypes have been established to assist patient stratification in the clinical settings. However, such molecular panels still require refinement and are yet to provide targetable biomarkers. In parallel, outstanding advances have been made regarding targeted therapeutics and immunotherapy, paving the way for improved patient care; nevertheless, important milestones towards treatment personalization and reduced off-target effects are also to be accomplished. Exploiting the cancer glycoproteome for unique molecular fingerprints generated by dramatic alterations in protein glycosylation may provide the necessary molecular rationale towards this end. Therefore, this review presents functional and clinical evidences supporting a reinvestigation of classical serological glycan biomarkers such as sialyl-Tn (STn) and sialyl-Lewis A (SLeA) antigens from a tumor glycoproteomics perspective. We anticipate that these glycobiomarkers that have so far been employed in non-invasive cancer prognostication may hold unexplored value for patients' management in precision oncology settings.
Collapse
|
17
|
Gomes C, Almeida A, Barreira A, Calheiros J, Pinto F, Abrantes R, Costa A, Polonia A, Campos D, Osório H, Sousa H, Pinto-de-Sousa J, Kolarich D, Reis CA. Carcinoembryonic antigen carrying SLe X as a new biomarker of more aggressive gastric carcinomas. Am J Cancer Res 2019; 9:7431-7446. [PMID: 31695778 PMCID: PMC6831293 DOI: 10.7150/thno.33858] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023] Open
Abstract
Malignant transformation of gastric cells is accompanied by the deregulated expression of glycosyltransferases leading to the biosynthesis of tumor-associated glycans such as the sialyl-Lewis X antigen (SLex). SLex presence on cell surface glycoconjugates increases the invasive capacity of gastric cancer cells and is associated with tumor metastasis. ST3Gal IV enzyme is involved in the synthesis of SLex antigen and overexpressed in gastric carcinomas. Herein, we identified the glycoproteins carrying SLex in gastric cancer cells overexpressing ST3Gal IV enzyme and evaluated their biomarker potential for gastric carcinoma. Methods: SLex modified glycoproteins were identified applying western blot and mass spectrometry. Immunoprecipitation, proximity ligation assay (PLA), E-selectin binding assay and CRISPR/cas9 knockout experiments were performed to characterize the presence of SLex on the identified glycoprotein. Protein N-glycans of the SLex protein carrier were in deep analyzed by porous-graphitized-carbon liquid-chromatography and tandem mass spectrometry glycomics. In silico expression analysis of α2-3 sialyltransferase ST3Gal IV and SLex protein carrier was performed and the conjoint expression of the SLex modified glycoproteins evaluated by immunohistochemistry and PLA in a series of gastric carcinomas. Results: Carcinoembryonic antigen (CEA; CEACAM5) was identified and validated by different methodologies as a major carrier of SLex. N-glycomics of CEA revealed that complex N-glycans are capped with α2-3 linked sialic acid (Neu5Acα2-3Galβ1-4GlcNAc). Data set analysis of ST3Gal IV and CEA showed that ST3Gal IV expression was associated with patient´s poor survival, whereas CEA did not show any prognostic value. The co-expression of both CEA and SLeX was observed in 86,3% of gastric carcinoma cases and 74,5% of the total cases displayed the conjoint CEA+SLexin situ PLA expression. This expression was associated with clinicopathological features of the tumors, including infiltrative pattern of tumor growth, presence of venous invasion and patient's poor survival. CEA immunoprecipitation from gastric carcinoma tissues also confirmed the presence of SLex. Conclusion: CEA is the major glycoprotein carrying SLex in gastric carcinoma and the conjoint detection of CEA-SLex is associated with aggressive tumor features highlighting its PLA detection as a biomarker of gastric cancer patient prognosis for theranostic applications.
Collapse
|
18
|
Freitas D, Balmaña M, Poças J, Campos D, Osório H, Konstantinidi A, Vakhrushev SY, Magalhães A, Reis CA. Different isolation approaches lead to diverse glycosylated extracellular vesicle populations. J Extracell Vesicles 2019; 8:1621131. [PMID: 31236201 PMCID: PMC6571546 DOI: 10.1080/20013078.2019.1621131] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/17/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of small secreted particles involved in intercellular communication and mediating a broad spectrum of biological functions. EVs cargo is composed of a large repertoire of molecules, including glycoconjugates. Herein, we report the first study on the impact of the isolation strategy on the EV populations’ glycosylation profile. The use of different state-of-the-art protocols, namely differential ultracentrifugation (UC), total exosome isolation (TEI), OptiPrepTM density gradient (ODG) and size exclusion chromatography (SEC) resulted in EV populations displaying different sets of glycoconjugates. The EV populations obtained by UC, ODG and SEC methods displayed similar protein and glycan profiles, whereas TEI methodology isolated the most distinct EV population. In addition, ODG and SEC isolation protocols provided an enhanced EV glycoproteins detection. Remarkably, proteins displaying the tumour-associated glycan sialyl-Tn (STn) were identified as packaged cargo into EVs independently of the isolation methodology. STn carrying EV samples isolated by UC, ODG and SEC presented a considerable set of cancer-related proteins that were not detected in EVs isolated by TEI. Our work demonstrates the impact of using different isolation methodologies in the populations of EVs that are obtained, with consequences in the glycosylation profile of the isolated population. Furthermore, our results highlight the importance of selecting adequate EV isolation protocols and cell culture conditions to determine the structural and functional complexity of the EV glycoconjugates.
Collapse
Affiliation(s)
- Daniela Freitas
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Juliana Poças
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Diana Campos
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Hugo Osório
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Magalhães
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Celso A Reis
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| |
Collapse
|
19
|
Pereira SB, Santos M, Leite JP, Flores C, Eisfeld C, Büttel Z, Mota R, Rossi F, De Philippis R, Gales L, Morais‐Cabral JH, Tamagnini P. The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803. Microbiologyopen 2019; 8:e00753. [PMID: 30675753 PMCID: PMC6562117 DOI: 10.1002/mbo3.753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/10/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS) mainly composed of heteropolysaccharides with unique characteristics that make them suitable for biotechnological applications. However, manipulation/optimization of EPS biosynthesis/characteristics is hindered by a poor understanding of the production pathways and the differences between bacterial species. In this work, genes putatively related to different pathways of cyanobacterial EPS polymerization, assembly, and export were targeted for deletion or truncation in the unicellular Synechocystis sp. PCC 6803. No evident phenotypic changes were observed for some mutants in genes occurring in multiple copies in Synechocystis genome, namely ∆wzy (∆sll0737), ∆wzx (∆sll5049), ∆kpsM (∆slr2107), and ∆kpsM∆wzy (∆slr2107∆sll0737), strongly suggesting functional redundancy. In contrast, Δwzc (Δsll0923) and Δwzb (Δslr0328) influenced both the amount and composition of the EPS, establishing that Wzc participates in the production of capsular (CPS) and released (RPS) polysaccharides, and Wzb affects RPS production. The structure of Wzb was solved (2.28 Å), revealing structural differences relative to other phosphatases involved in EPS production and suggesting a different substrate recognition mechanism. In addition, Wzc showed the ATPase and autokinase activities typical of bacterial tyrosine kinases. Most importantly, Wzb was able to dephosphorylate Wzc in vitro, suggesting that tyrosine phosphorylation/dephosphorylation plays a role in cyanobacterial EPS production.
Collapse
Affiliation(s)
- Sara B. Pereira
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Marina Santos
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - José P. Leite
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carlos Flores
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carina Eisfeld
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Department of Water ManagementDelft University of TechnologyDelftThe Netherlands
| | - Zsófia Büttel
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Rita Mota
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Luís Gales
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - João H. Morais‐Cabral
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Paula Tamagnini
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Faculdade de Ciências, Departamento de BiologiaUniversidade do PortoPortoPortugal
| |
Collapse
|
20
|
Terceti MS, Vences A, Matanza XM, Barca AV, Noia M, Lisboa J, dos Santos NMS, do Vale A, Osorio CR. The RstAB System Impacts Virulence, Motility, Cell Morphology, Penicillin Tolerance and Production of Type II Secretion System-Dependent Factors in the Fish and Human Pathogen Photobacterium damselae subsp. damselae. Front Microbiol 2019; 10:897. [PMID: 31105680 PMCID: PMC6491958 DOI: 10.3389/fmicb.2019.00897] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/08/2019] [Indexed: 01/04/2023] Open
Abstract
The RstB histidine kinase of the two component system RstAB positively regulates the expression of damselysin (Dly), phobalysin P (PhlyP) and phobalysin C (PhlyC) cytotoxins in the fish and human pathogen Photobacterium damselae subsp. damselae, a marine bacterium of the family Vibrionaceae. However, the function of the predicted cognate response regulator RstA has not been studied so far, and the role of the RstAB system in other cell functions and phenotypes remain uninvestigated. Here, we analyzed the effect of rstA and rstB mutations in cell fitness and in diverse virulence-related features. Both rstA and rstB mutants were severely impaired in virulence for sea bream and sea bass fish. Mutants in rstA and rstB genes were impaired in hemolysis and in Dly-dependent phospholipase activity but had intact PlpV-dependent phospholipase and ColP-dependent gelatinase activities. rstA and rstB mutants grown at 0.5% NaCl exhibited impaired swimming motility, enlarged cell size and impaired ability to separate after cell division, whereas at 1% NaCl the mutants exhibited normal phenotypes. Mutation of any of the two genes also impacted tolerance to benzylpenicillin. Notably, rstA and rstB mutants showed impaired secretion of a number of type II secretion system (T2SS)-dependent proteins, which included the three major cytotoxins Dly, PhlyP and PhlyC, as well as a putative delta-endotoxin and three additional uncharacterized proteins which might constitute novel virulence factors of this pathogenic bacterium. The analysis of the T2SS-dependent secretome of P. damselae subsp. damselae also led to the identification of RstAB-independent potential virulence factors as lipoproteins, sialidases and proteases. The RstAB regulon included plasmid, chromosome I and chromosome II-encoded genes that showed a differential distribution among isolates of this subspecies. This study establishes RstAB as a major regulator of virulence and diverse cellular functions in P. damselae subsp. damselae.
Collapse
Affiliation(s)
- Mateus S. Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Ana Vences
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Xosé M. Matanza
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Alba V. Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Manuel Noia
- Departamento de Bioloxía Funcional, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| | - Johnny Lisboa
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Nuno M. S. dos Santos
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carlos R. Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela – USC, Santiago de Compostela, Spain
| |
Collapse
|
21
|
Barros D, Parreira P, Furtado J, Ferreira-da-Silva F, Conde-Sousa E, García AJ, Martins MCL, Amaral IF, Pêgo AP. An affinity-based approach to engineer laminin-presenting cell instructive microenvironments. Biomaterials 2019; 192:601-611. [DOI: 10.1016/j.biomaterials.2018.10.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/14/2018] [Accepted: 10/28/2018] [Indexed: 01/11/2023]
|
22
|
Flores C, Santos M, Pereira SB, Mota R, Rossi F, De Philippis R, Couto N, Karunakaran E, Wright PC, Oliveira P, Tamagnini P. The alternative sigma factor SigF is a key player in the control of secretion mechanisms inSynechocystissp. PCC 6803. Environ Microbiol 2018; 21:343-359. [DOI: 10.1111/1462-2920.14465] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Carlos Flores
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; ICBAS - Instituto de Ciências Biomédicas Abel Salazar; Porto Portugal
| | - Marina Santos
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Departamento de Biologia Molecular; ICBAS - Instituto de Ciências Biomédicas Abel Salazar; Porto Portugal
| | - Sara B. Pereira
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Rita Mota
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental Sciences; University of Florence; Florence Italy
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental Sciences; University of Florence; Florence Italy
| | - Narciso Couto
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Esther Karunakaran
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, University of Sheffield; Sheffield UK
| | - Paulo Oliveira
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
| | - Paula Tamagnini
- Bioengineering and Synthetic Microbiology Group; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto; Porto Portugal
- Bioengineering and Synthetic Microbiology Group; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto; Porto Portugal
- Faculdade de Ciências, Departamento de Biologia; Universidade do Porto; Porto Portugal
| |
Collapse
|
23
|
Barros-Barbosa A, Ferreira MJ, Rodrigues TA, Pedrosa AG, Grou CP, Pinto MP, Fransen M, Francisco T, Azevedo JE. Membrane topologies of PEX13 and PEX14 provide new insights on the mechanism of protein import into peroxisomes. FEBS J 2018; 286:205-222. [PMID: 30414318 DOI: 10.1111/febs.14697] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/19/2018] [Accepted: 11/07/2018] [Indexed: 01/19/2023]
Abstract
PEX13 and PEX14 are two core components of the so-called peroxisomal docking/translocation module, the transmembrane hydrophilic channel through which newly synthesized peroxisomal proteins are translocated into the organelle matrix. The two proteins interact with each other and with PEX5, the peroxisomal matrix protein shuttling receptor, through relatively well characterized domains. However, the topologies of these membrane proteins are still poorly defined. Here, we subjected proteoliposomes containing PEX13 or PEX14 and purified rat liver peroxisomes to protease-protection assays and analyzed the protected protein fragments by mass spectrometry, Edman degradation and western blotting using antibodies directed to specific domains of the proteins. Our results indicate that PEX14 is a bona fide intrinsic membrane protein with a Nin -Cout topology, and that PEX13 adopts a Nout -Cin topology, thus exposing its carboxy-terminal Src homology 3 [SH3] domain into the organelle matrix. These results reconcile several enigmatic findings previously reported on PEX13 and PEX14 and provide new insights into the organization of the peroxisomal protein import machinery. ENZYMES: Trypsin, EC3.4.21.4; Proteinase K, EC3.4.21.64; Tobacco etch virus protease, EC3.4.22.44.
Collapse
Affiliation(s)
- Aurora Barros-Barbosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Cláudia P Grou
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
| | - Manuel P Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal
| | - Marc Fransen
- Departement Cellulaire en Moleculaire Geneeskunde, KU Leuven - Universiteit Leuven, Belgium
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| |
Collapse
|
24
|
Shu J, Yu H, Du H, Zhang J, Zhang K, Li X, Xie H, Li Z. Identification of N- and O-linked glycans recognized by AAL in saliva of patients with atrophic gastritis and gastric cancer. Cancer Biomark 2018; 22:669-681. [PMID: 29865036 DOI: 10.3233/cbm-171087] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIM Gastric cancer (GC) is a common and fatal malignancy with a worldwide occurrence. There still lacks effective biomarkers for precisely evaluating GC. Saliva is a biological fluid with enormous diagnostic potentials which emerged many advantages. We aimed to discover the novel biomarkers for accurately distinguishing early GC based on saliva glycopatterns. METHODS We used Aleuria Aurantia Lectin (AAL)-magnetic particle conjugates to isolate fucosylated glycoproteins in the pooled saliva of healthy volunteers (HV, n= 51) and patients with atrophic gastritis (AG, n= 51) or GC (n= 51), following to release the N- and O-linked glycans from the isolated proteins with PNGase F and NaClO, and further identified the released glycans by MALDI-TOF/TOF-MS, respectively. RESULTS A total of 9/9, 8/11, and 9/9 fucosylated N-/O-linked glycans were annotated in the isolated salivary proteins from HV, AG, and GC, respectively. Among these, six fucosylated N-linked glycansand four O-linked glycans exhibited significantly increased expression levels in GC, while five fucosylated N-linked glycans and ten fucosylated O-linked glycans exhibited significantly decreased expression levels in GC. The proportion of fucosylated N-linked glycans was decreased in GC (41.66%) compared with AG (43.63%) and HV (52.57%), as well as the fucosylated O-linked glycans was apparently decreased in GC (19.58%) compared with AG (25.43%) and HV (55.54%). CONCLUSIONS This study could provide pivotal information to distinguish among HV, AG, and GC, and facilitate the discovery of biomarkers for GC diagnosis based on precise alterations of N- and O-linked glycans in saliva.
Collapse
Affiliation(s)
- Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Haoqi Du
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jiaxu Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Kun Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xiaojie Li
- Department of Pothology, First People's Hospital of Chenzhou, Chenzhou, Hunan, China
| | - Hailong Xie
- Institute of Cancer Research, University of South China, Hengyang, Hunan, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| |
Collapse
|
25
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
Collapse
Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| |
Collapse
|
26
|
Pereira C, Pereira AT, Osório H, Moradas-Ferreira P, Costa V. Sit4p-mediated dephosphorylation of Atp2p regulates ATP synthase activity and mitochondrial function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:591-601. [PMID: 29719209 DOI: 10.1016/j.bbabio.2018.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/13/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022]
Abstract
Sit4p is a type 2A-related protein phosphatase in Saccharomyces cerevisiae involved in a wide spectrum of cellular functions, including the glucose repression of mitochondrial transcription. Here we report that Sit4p is also involved in post-translational regulation of mitochondrial proteins and identified 9 potential targets. One of these, the ATP synthase (FoF1 complex) beta subunit Atp2p, was characterized and two phosphorylation sites, T124 and T317, were identified. Expression of Atp2p-T124 or T317 phosphoresistant versions in sit4Δ cells decreased Atp2p phosphorylation confirming these as Sit4p-regulated sites. Moreover, Sit4p and Atp2p interacted both physically and genetically. Mimicking phosphorylation at T124 or T317 increased Atp2p levels, resulting in higher abundance/activity of ATP synthase. Similar changes were observed in sit4Δ cells in which Atp2p is endogenously more phosphorylated. Expression of Atp2-T124 or T317 phosphomimetics also increased mitochondrial respiration and ATP levels and extended yeast lifespan. These results suggest that Sit4p-mediated dephosphorylation of Atp2p-T124/T317 downregulates Atp2p alongside with ATP synthase and mitochondrial function. Combination of transcriptional with post-translational regulation during fermentative growth may allow for a more efficient Sit4p repression of mitochondrial respiration.
Collapse
Affiliation(s)
- Clara Pereira
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal.
| | - Andreia T Pereira
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal
| | - Hugo Osório
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal; Departamento de Patologia e Oncologia, Faculdade de Medicina, Universidade do Porto, Portugal
| | - Pedro Moradas-Ferreira
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Vítor Costa
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, Universidade do Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal.
| |
Collapse
|
27
|
Shu J, Yu H, Li X, Zhang D, Liu X, Du H, Zhang J, Yang Z, Xie H, Li Z. Salivary glycopatterns as potential biomarkers for diagnosis of gastric cancer. Oncotarget 2018; 8:35718-35727. [PMID: 28415698 PMCID: PMC5482611 DOI: 10.18632/oncotarget.16082] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/28/2017] [Indexed: 01/13/2023] Open
Abstract
Gastric cancer (GC) is still an extremely severe health issue with high mortality due to the lacking of effective biomarkers. In this study, we aimed to investigate the alterations of salivary protein glycosylation related to GC and assess the possibility of salivary glycopatterns as potential biomarkers for the diagnosis of GC. Firstly, 94 patients with GC (n = 64) and atrophic gastritis (AG) (n = 30), as well as 30 age- and sex-matched healthy volunteers (HV) were enrolled in the test group to probe the difference of salivary glycopatterns using lectin microarrays, the results were validated by saliva microarrays and lectin blotting analysis. Then, the diagnostic model of GC (Model GC) and AG (Model AG) were constructed based on 15 candidate lectins which exhibited significant alterations of salivary glycopattern by logistic stepwise regression. Finally, two diagnostic models were assessed in the validation group including HV (n = 30) and patients with GC (n = 23) and AG (n = 24) and achieved high diagnostic power (Model GC (AUC: 0.89, sensitivity: 0.96 and specificity: 0.80), Model AG (AUC: 0.83, sensitivity: 0.92 and specificity: 0.72)). This study provides pivotal information to distinguish HV, AG and GC based on precise alterations in salivary glycopatterns, which have great potential to be biomarkers for diagnosis of GC.
Collapse
Affiliation(s)
- Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaojie Li
- Department of Pothology. First People`s Hospital of Chenzhou, Chenzhou, China
| | - Dandan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiawei Liu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Haoqi Du
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jiaxu Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhao Yang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Hailong Xie
- Institute of Cancer Research, University of South China, Hengyang, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| |
Collapse
|
28
|
Oliveira FMSD, Mereiter S, Lönn P, Siart B, Shen Q, Heldin J, Raykova D, Karlsson NG, Polom K, Roviello F, Reis CA, Kamali-Moghaddam M. Detection of post-translational modifications using solid-phase proximity ligation assay. N Biotechnol 2017; 45:51-59. [PMID: 29101055 DOI: 10.1016/j.nbt.2017.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/21/2023]
Abstract
Post-translational modifications (PTMs) regulate protein activities to help orchestrate and fine-tune cellular processes. Dysregulation of PTMs is often related with disorders and malignancies, and may serve as a precise biomarker of disease. Developing sensitive tools to measure and monitor low-abundant PTMs in tissue lysates or serum will be instrumental for opening up new PTM-based diagnostic avenues. Here, we investigate the use of solid-phase proximity ligation assay (SP-PLA) for detection of different PTMs. The assay depends on the recognition of the target protein molecule and its modification by three affinity binders. Using antibodies and lectins, we applied the method for detection of glycosylated CD44 and E-Cadherin, and phosphorylated p53 and EGFR. The assay was found to have superior dynamic range and limit of detection compared to standard ELISAs. In summary, we have established the use of SP-PLA as an appropriate method for sensitive detection of PTMs in lysates and sera, which may provide a basis for future PTM-based diagnostic and prognostic biomarkers.
Collapse
Affiliation(s)
| | - Stefan Mereiter
- i3S - Instituto de Investigação e Inovação em Saúde and IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Benjamin Siart
- Department of Anthropology, University of Vienna, Austria; Department of Behavioral Biology, University of Vienna, Austria
| | - Qiujin Shen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Heldin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | - Doroteya Raykova
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology at Institute of Biomedicine, Gothenburg University, Sweden
| | - Karol Polom
- Department of Surgical Oncology, Medical University of Gdansk, Poland; General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy
| | - Franco Roviello
- General Surgery and Surgical Oncology Department, Università deli Studi di Siena, Italy
| | - Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde and IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Portugal; Faculty of Medicine of the University of Porto, Portugal
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
29
|
Cairns MT, Gupta A, Naughton JA, Kane M, Clyne M, Joshi L. Glycosylation-related gene expression in HT29-MTX-E12 cells upon infection by Helicobacter pylori. World J Gastroenterol 2017; 23:6817-6832. [PMID: 29085225 PMCID: PMC5645615 DOI: 10.3748/wjg.v23.i37.6817] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 06/09/2017] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To identify glycosylation-related genes in the HT29 derivative cell line, HT29-MTX-E12, showing differential expression on infection with Helicobacter pylori (H. pylori). METHODS Polarised HT29-MTX-E12 cells were infected for 24 h with H. pylori strain 26695. After infection RNA was isolated from both infected and non-infected host cells. Sufficient infections were carried out to provide triplicate samples for microarray analysis and for qRT-PCR analysis. RNA was isolated and hybridised to Affymetrix arrays. Analysis of microarray data identified genes significantly differentially expressed upon infection. Genes were grouped into gene ontology functional categories. Selected genes associated with host glycan structure (glycosyltransferases, hydrolases, lectins, mucins) were validated by real-time qRT-PCR analysis. RESULTS Infection of host cells was confirmed by the isolation of live bacteria after 24 h incubation and by PCR amplification of bacteria-specific genes from the host cell RNA. H. pylori do not survive incubation under the adopted culture conditions unless they associate with the adherent mucus layer of the host cell. Microarray analysis identified a total of 276 genes that were significantly differentially expressed (P < 0.05) upon H. pylori infection and where the fold change in expression was greater than 2. Six of these genes are involved in glycosylation-related processes. Real-time qRT-PCR demonstrated significant downregulation (1.8-fold, P < 0.05) of the mucin MUC20. REG4 was heavily expressed and significantly downregulated (3.1-fold, P < 0.05) upon infection. Gene ontology analysis was consistent with previous studies on H. pylori infection. CONCLUSION Gene expression data suggest that infection with H. pylori causes a decrease in glycan synthesis, resulting in shorter and simpler glycan structures.
Collapse
Affiliation(s)
- Michael T Cairns
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, H91 CF50 Galway, Ireland
| | - Ananya Gupta
- School of Natural Sciences, National University of Ireland Galway, H91 CF50 Galway, Ireland
| | - Julie A Naughton
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Marian Kane
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, H91 CF50 Galway, Ireland
| | - Marguerite Clyne
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Ireland
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, H91 CF50 Galway, Ireland
| |
Collapse
|
30
|
Protein glycosylation in gastric and colorectal cancers: Toward cancer detection and targeted therapeutics. Cancer Lett 2017; 387:32-45. [DOI: 10.1016/j.canlet.2016.01.044] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 12/25/2022]
|
31
|
Ferreirinha P, Correia A, Teixeira-Coelho M, Osório H, Teixeira L, Rocha A, Vilanova M. Mucosal immunization confers long-term protection against intragastrically established Neospora caninum infection. Vaccine 2016; 34:6250-6258. [PMID: 27814932 DOI: 10.1016/j.vaccine.2016.10.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/07/2016] [Accepted: 10/24/2016] [Indexed: 11/25/2022]
Abstract
Neospora caninum is an obligate intracellular protozoan parasite responsible for heavy economic losses in dairy and beef cattle farms worldwide. Although vaccination is widely regarded as the preferable strategy to prevent neosporosis no commercial vaccine is currently available. We have previously shown that intranasal immunization with an N. caninum antigen extract enriched in hydrophobic proteins plus CpG adjuvant protected mice against intragastrically established neosporosis. Nevertheless, the antigen specificity as well as the long-term protective effect of this immunization strategy were not determined. Here, we show that the protective effect of this intranasal immunization procedure lasted for at least 20weeks. Protection was accompanied by long-lasting elevated levels of parasite-specific serum IgG and intestinal IgA. Moreover, spleen and mesenteric lymph node cells obtained from non-infected long-term immunized mice responded by producing interferon-γ following in vitro parasite-antigen recall. Analysis of serum IgG and intestinal IgA antibody reactivity in immunized mice identified dense granule antigen 7 (NcGRA7) and microneme associated protein 1 (NcMIC1) as immunodominant antigens respectively recognized by those antibody fractions. In summary, this work shows that a previously reported mucosal immunization strategy against N. caninum infection established through the gastrointestinal tract is effective in the long term.
Collapse
Affiliation(s)
- Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Correia
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Maria Teixeira-Coelho
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Hugo Osório
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, 4200-135 Porto, Portugal; FMUP - Faculdade de Medicina da Universidade do Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Luzia Teixeira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal; UMIB - Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, Portugal
| | - António Rocha
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
| | - Manuel Vilanova
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal.
| |
Collapse
|
32
|
Fucosyltransferase-4 and Oligosaccharide Lewis Y Antigen as potentially Correlative Biomarkers of Helicobacter pylori CagA Associated Gastric Cancer. Pathol Oncol Res 2016; 23:173-179. [PMID: 27757838 DOI: 10.1007/s12253-016-0122-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 10/04/2016] [Indexed: 12/20/2022]
Abstract
H. pylori cytotoxin associated antigen A (CagA) plays a significant role in the progression of gastric cancer but their effect on fucosylation to develop gastric cancer is unknown. Fucosyltransferase IV (FUT4) is the key enzyme for synthesis of LewisY (LeY) carried by glycoproteins and glycolipids on the cell membrane. Herein, we compare the expression of CagA, p-EGFR, FUT4 and LeY in gastritis (n = 128, 176), gastric ulcer (n = 174, 213), and gastric cancer (n = 323, 261) tissue and serum samples, respectively by IHC and ELISA. Moreover, we investigated the potential correlation of CagA with FUT4 and LeY overexpression through EGFR activation. IHC and ELISA results showed higher positive cases of H. pylori CagA (83, 86 %), p-EGFR (81, 72 %), FUT4 (91, 97 %) and LeY (93, 92 %) in gastric cancer, compared to gastritis and gastric ulcer, H. pylori CagA (58, 67 & 59, 73 %), p-EGFR (52, 63 & 35, 47 %), FUT4 (68, 78 & 67, 82 %) and LeY (62,76 & 65, 85 %), respectively. We found a significant high expression (H-Value) of CagA (1.79, 1.66), p-EGFR (1.53, 1.58), FUT4 (2.14, 1.66) and LeY (1.69, 1.61) in gastric cancer tissues and serum, respectively as compared to chronic gastritis and gastric ulcers, CagA (0.64,1.14), p-EGFR (0.856, 0.678), FUT4 (0.949,1.197) and LeY (0.68,1.008) (P < 0.0001), respectively. Furthermore, H. pylori CagA showed significant correlation with p-EGFR (R-0.62, -0.74), FUT4 (R-0.81, -0.76) and LeY (R-0.82, -0.70) in gastric tissues and serum (P < 0.0001). H. pylori CagA plays key role in the development of gastric cancer with overexpression of FUT4/LeY, serve as potentially correlative biomarkers of H. pylori CagA associated gastric cancer.
Collapse
|
33
|
The promise of protein glycosylation for personalised medicine. Biochim Biophys Acta Gen Subj 2016; 1860:1583-95. [DOI: 10.1016/j.bbagen.2016.03.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/04/2016] [Accepted: 03/05/2016] [Indexed: 12/21/2022]
|
34
|
Duarte HO, Freitas D, Gomes C, Gomes J, Magalhães A, Reis CA. Mucin-Type O-Glycosylation in Gastric Carcinogenesis. Biomolecules 2016; 6:E33. [PMID: 27409642 PMCID: PMC5039419 DOI: 10.3390/biom6030033] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/15/2022] Open
Abstract
Mucin-type O-glycosylation plays a crucial role in several physiological and pathological processes of the gastric tissue. Modifications in enzymes responsible for key glycosylation steps and the consequent abnormal biosynthesis and expression of their glycan products constitute well-established molecular hallmarks of disease state. This review addresses the major role played by mucins and associated O-glycan structures in Helicobacter pylori adhesion to the gastric mucosa and the subsequent establishment of a chronic infection, with concomitant drastic alterations of the gastric epithelium glycophenotype. Furthermore, alterations of mucin expression pattern and glycan signatures occurring in preneoplastic lesions and in gastric carcinoma are also described, as well as their impact throughout the gastric carcinogenesis cascade and in cancer progression. Altogether, mucin-type O-glycosylation alterations may represent promising biomarkers with potential screening and prognostic applications, as well as predictors of cancer patients' response to therapy.
Collapse
Affiliation(s)
- Henrique O Duarte
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira no. 228, Porto 4050-313, Portugal.
| | - Daniela Freitas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira no. 228, Porto 4050-313, Portugal.
| | - Catarina Gomes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
| | - Joana Gomes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
| | - Ana Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
| | - Celso A Reis
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), University of Porto, Rua Jorge Viterbo Ferreira no. 228, Porto 4050-313, Portugal.
- Medical Faculty, University of Porto, Alameda Prof Hernâni Monteiro, Porto 4200-319, Portugal.
| |
Collapse
|
35
|
Barbosa AD, Pereira C, Osório H, Moradas-Ferreira P, Costa V. The ceramide-activated protein phosphatase Sit4p controls lifespan, mitochondrial function and cell cycle progression by regulating hexokinase 2 phosphorylation. Cell Cycle 2016; 15:1620-30. [PMID: 27163342 DOI: 10.1080/15384101.2016.1183846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Sit4p is the catalytic subunit of a ceramide-activated PP2A-like phosphatase that regulates cell cycle, mitochondrial function, oxidative stress resistance and chronological lifespan in yeast. In this study, we show that hexokinase 2 (Hxk2p) is hyperphosphorylated in sit4Δ mutants grown in glucose medium by a Snf1p-independent mechanism and Hxk2p-S15A mutation suppresses phenotypes associated with SIT4 deletion, namely growth arrest at G1 phase, derepression of mitochondrial respiration, H2O2 resistance and lifespan extension. Consistently, the activation of Sit4p in isc1Δ mutants, which has been associated with premature aging, leads to Hxk2p hypophosphorylation, and the expression of Hxk2p-S15E increases the lifespan of isc1Δ cells. The overall results suggest that Hxk2p functions downstream of Sit4p in the control of cell cycle, mitochondrial function, oxidative stress resistance and chronological lifespan.
Collapse
Affiliation(s)
- António Daniel Barbosa
- b IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal.,c ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto , Porto , Portugal
| | - Clara Pereira
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
| | - Hugo Osório
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,d Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP) , Porto , Portugal
| | - Pedro Moradas-Ferreira
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal.,c ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto , Porto , Portugal
| | - Vítor Costa
- a Instituto de Investigação e Inovação em Saúde, Universidade do Porto , Porto , Portugal.,b IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal.,c ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto , Porto , Portugal
| |
Collapse
|
36
|
Xie MZ, He ZM, Huang FJ, Zhou XQ, Wu ZZ. Comparative study of saliva peptide signatures between gastric carcinoma and chronic gastritis. Shijie Huaren Xiaohua Zazhi 2016; 24:1976-1983. [DOI: 10.11569/wcjd.v24.i13.1976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen differential protein expression profiles in saliva between gastric carcinoma and chronic gastritis, and to establish a model for differentiating these groups.
METHODS: Saliva samples from 57 patients with gastric carcinoma and 28 patients with gastritis were purified with weak cationic-exchange magnetic beads (MB-WCX) and then analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Subsequently, we compared the saliva peptide signatures of the two groups and obtained differently expressed peptides by using Biomarker Wizard. Then, we established two diagnostic models to distinguish the gastric carcinoma group from the gastritis group and normal control group by using Biomarker Patterns 5.0.2.
RESULTS: A diagnostic pattern for discriminating between the gastric carcinoma group and gastritis group using three peptides (m/z 4267.09, 6564.85, 2138.14) was established with a 96% (55/57) sensitivity and an 86% (24/28) specificity. A sensitivity of 89%(51/57) and a specificity of 75% (21/28) were obtained in cross validation.
CONCLUSION: The novel molecular diagnostic model obtained by saliva protein fingerprinting for distinguishing gastric carcinoma from chronic gastritis is sensitive and noninvasive.
Collapse
|
37
|
Mereiter S, Balmaña M, Gomes J, Magalhães A, Reis CA. Glycomic Approaches for the Discovery of Targets in Gastrointestinal Cancer. Front Oncol 2016; 6:55. [PMID: 27014630 PMCID: PMC4783390 DOI: 10.3389/fonc.2016.00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022] Open
Abstract
Gastrointestinal (GI) cancer is the most common group of malignancies and many of its types are among the most deadly. Various glycoconjugates have been used in clinical practice as serum biomarker for several GI tumors, however, with limited diagnose application. Despite the good accessibility by endoscopy of many GI organs, the lack of reliable serum biomarkers often leads to late diagnosis of malignancy and consequently low 5-year survival rates. Recent advances in analytical techniques have provided novel glycoproteomic and glycomic data and generated functional information and putative biomarker targets in oncology. Glycosylation alterations have been demonstrated in a series of glycoconjugates (glycoproteins, proteoglycans, and glycosphingolipids) that are involved in cancer cell adhesion, signaling, invasion, and metastasis formation. In this review, we present an overview on the major glycosylation alterations in GI cancer and the current serological biomarkers used in the clinical oncology setting. We further describe recent glycomic studies in GI cancer, namely gastric, colorectal, and pancreatic cancer. Moreover, we discuss the role of glycosylation as a modulator of the function of several key players in cancer cell biology. Finally, we address several state-of-the-art techniques currently applied in this field, such as glycomic and glycoproteomic analyses, the application of glycoengineered cell line models, microarray and proximity ligation assay, and imaging mass spectrometry, and provide an outlook to future perspectives and clinical applications.
Collapse
Affiliation(s)
- Stefan Mereiter
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona , Girona , Spain
| | - Joana Gomes
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Magalhães
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal
| |
Collapse
|
38
|
Lee CS, Taib NAM, Ashrafzadeh A, Fadzli F, Harun F, Rahmat K, Hoong SM, Abdul-Rahman PS, Hashim OH. Unmasking Heavily O-Glycosylated Serum Proteins Using Perchloric Acid: Identification of Serum Proteoglycan 4 and Protease C1 Inhibitor as Molecular Indicators for Screening of Breast Cancer. PLoS One 2016; 11:e0149551. [PMID: 26890881 PMCID: PMC4758733 DOI: 10.1371/journal.pone.0149551] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/02/2016] [Indexed: 12/29/2022] Open
Abstract
Heavily glycosylated mucin glycopeptides such as CA 27.29 and CA 15-3 are currently being used as biomarkers for detection and monitoring of breast cancer. However, they are not well detected at the early stages of the cancer. In the present study, perchloric acid (PCA) was used to enhance detection of mucin-type O-glycosylated proteins in the serum in an attempt to identify new biomarkers for early stage breast cancer. Sensitivity and specificity of an earlier developed sandwich enzyme-linked lectin assay were significantly improved with the use of serum PCA isolates. When a pilot case-control study was performed using the serum PCA isolates of normal participants (n = 105) and patients with stage 0 (n = 31) and stage I (n = 48) breast cancer, higher levels of total O-glycosylated proteins in sera of both groups of early stage breast cancer patients compared to the normal control women were demonstrated. Further analysis by gel-based proteomics detected significant inverse altered abundance of proteoglycan 4 and plasma protease C1 inhibitor in both the early stages of breast cancer patients compared to the controls. Our data suggests that the ratio of serum proteoglycan 4 to protease C1 inhibitor may be used for screening of early breast cancer although this requires further validation in clinically representative populations.
Collapse
Affiliation(s)
- Cheng-Siang Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ali Ashrafzadeh
- Medical Biotechnology Laboratory, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Farhana Fadzli
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Faizah Harun
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kartini Rahmat
- Department of Biomedical Imaging, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - See Mee Hoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Puteri Shafinaz Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Onn Haji Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| |
Collapse
|
39
|
Coghlin C, Murray GI. Progress in the development of protein biomarkers of oesophageal and gastric cancers. Proteomics Clin Appl 2016; 10:532-45. [DOI: 10.1002/prca.201500079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/10/2015] [Accepted: 11/12/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Caroline Coghlin
- Department of Cellular Pathology; Craigavon Area Hospital; Portadown UK
| | - Graeme I. Murray
- Pathology, Division of Applied Medicine, School of Medicine and Dentistry; University of Aberdeen; Aberdeen UK
| |
Collapse
|
40
|
Ferreira JA, Peixoto A, Neves M, Gaiteiro C, Reis CA, Assaraf YG, Santos LL. Mechanisms of cisplatin resistance and targeting of cancer stem cells: Adding glycosylation to the equation. Drug Resist Updat 2016; 24:34-54. [DOI: 10.1016/j.drup.2015.11.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/09/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
|
41
|
Hoffmann M, Marx K, Reichl U, Wuhrer M, Rapp E. Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins. Mol Cell Proteomics 2015; 15:624-41. [PMID: 26598643 PMCID: PMC4739677 DOI: 10.1074/mcp.m115.053546] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/04/2022] Open
Abstract
Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from low-energy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono- and disialylated core-1 mucin-type O-glycans (T-antigen). The developed workflow allows the identification and characterization of the major population of the human blood plasma O-glycoproteome and our results provide new insights, which can help to unravel structure-function relationships. The data were deposited to ProteomeXchange PXD003270.
Collapse
Affiliation(s)
- Marcus Hoffmann
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | | | - Udo Reichl
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany; ¶Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Manfred Wuhrer
- ‖Center for Proteomics and Metabolomics, Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Erdmann Rapp
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany; **glyXera GmbH, Leipziger Strasse 44 (Zenit), 39120 Magdeburg, Germany
| |
Collapse
|
42
|
Kalniņa Z, Meistere I, Kikuste I, Tolmanis I, Zayakin P, Linē A. Emerging blood-based biomarkers for detection of gastric cancer. World J Gastroenterol 2015; 21:11636-11653. [PMID: 26556992 PMCID: PMC4631966 DOI: 10.3748/wjg.v21.i41.11636] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/08/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality, and for improving the management of patients with gastric cancer (GC). Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for population-wide or risk group-based screening programs, while circulating biomarkers that reflect the genetic make-up and dynamics of the tumor would allow monitoring of treatment efficacy, predict recurrences and assess the genetic heterogeneity of the tumor. Recent research to identify blood-based biomarkers of GC has resulted in the identification of a wide variety of cancer-associated molecules, including various proteins, autoantibodies against tumor associated antigens, cell-free DNA fragments, mRNAs and various non-coding RNAs, circulating tumor cells and cancer-derived extracellular vesicles. Each type of these biomarkers provides different information on the disease status, has different advantages and disadvantages, and distinct clinical usefulness. In the current review, we summarize the recent developments in blood-based GC biomarker discovery, discuss the origin of various types of biomarkers and their clinical usefulness and the technological challenges in the development of biomarker assays for clinical use.
Collapse
|
43
|
Azevedo CC, Guzmán-Guillén R, Martins JC, Osório H, Vasconcelos V, da Fonseca RR, Campos A. Proteomic profiling of gill GSTs in Mytilus galloprovincialis from the North of Portugal and Galicia evidences variations at protein isoform level with a possible relation with water quality. MARINE ENVIRONMENTAL RESEARCH 2015; 110:152-161. [PMID: 26364681 DOI: 10.1016/j.marenvres.2015.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 08/20/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Glutathione transferases (GSTs) are key for xenobiotic detoxification at the molecular level across phyla. These enzymes are therefore likely to be part of the defence mechanisms used by marine organisms, such as mussels, that thrive in highly polluted environments. Taking this hypothesis into account, we used proteomics to characterize the profile of GSTs from the gills of marine mussel Mytilus galloprovincialis in order to discriminate natural mussel populations exposed to different levels of pollution. Samples were collected between Cabo Home (Spain) and Matosinhos (Portugal) covering a north-south transect of approximately 122 Km of the Atlantic Ocean along the Western Coast of the Iberian Peninsula. GSTs from mussel gills were extracted and purified by affinity chromatography with glutathione as the binding substrate to the solid medium. We studied the abundance of GST isoforms by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight mass spectrometry and assessed total activity. Eleven putative individual GSTs from classes Mu, Pi and Sigma were identified by proteomics. Few variations were observed in total GST activity of post-mitochondrial samples between sampling sites, with animals from Matosinhos (polluted site) showing highest GST activity and Cabo Home (clean site) showing lowest. This contrasts with the increased number of differences in the individual GST isoforms. Each mussel population showed unique GST proteomic profiles. Based on the results we conclude that proteomics surpasses the conventional GST enzymatic activity method to discriminate natural mussel populations and has potential application in environmental monitoring. It is reasonable to suggest that the GST proteomic profiles observed may reflect differences in contamination levels.
Collapse
Affiliation(s)
- Catarina C Azevedo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Porto, Portugal
| | | | - José C Martins
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Porto, Portugal
| | - Hugo Osório
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Porto, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Rute R da Fonseca
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alexandre Campos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR/CIMAR, Porto, Portugal.
| |
Collapse
|
44
|
Abstract
Despite recent progress in understanding the cancer genome, there is still a relative delay in understanding the full aspects of the glycome and glycoproteome of cancer. Glycobiology has been instrumental in relevant discoveries in various biological and medical fields, and has contributed to the deciphering of several human diseases. Glycans are involved in fundamental molecular and cell biology processes occurring in cancer, such as cell signalling and communication, tumour cell dissociation and invasion, cell-matrix interactions, tumour angiogenesis, immune modulation and metastasis formation. The roles of glycans in cancer have been highlighted by the fact that alterations in glycosylation regulate the development and progression of cancer, serving as important biomarkers and providing a set of specific targets for therapeutic intervention. This Review discusses the role of glycans in fundamental mechanisms controlling cancer development and progression, and their applications in oncology.
Collapse
Affiliation(s)
- Salomé S Pinho
- Instituto de Investigação e Inovação em Saúde (Institute for Research and Innovation in Health), University of Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira n.228, 4050-313 Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde (Institute for Research and Innovation in Health), University of Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira n.228, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| |
Collapse
|
45
|
Campos D, Freitas D, Gomes J, Reis CA. Glycoengineered cell models for the characterization of cancer O-glycoproteome: an innovative strategy for biomarker discovery. Expert Rev Proteomics 2015; 12:337-42. [DOI: 10.1586/14789450.2015.1059758] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
46
|
Campos D, Freitas D, Gomes J, Magalhães A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA. Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery. Mol Cell Proteomics 2015; 14:1616-29. [PMID: 25813380 PMCID: PMC4458724 DOI: 10.1074/mcp.m114.046862] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Circulating O-glycoproteins shed from cancer cells represent important serum biomarkers for diagnostic and prognostic purposes. We have recently shown that selective detection of cancer-associated aberrant glycoforms of circulating O-glycoprotein biomarkers can increase specificity of cancer biomarker assays. However, the current knowledge of secreted and circulating O-glycoproteins is limited. Here, we used the COSMC KO "SimpleCell" (SC) strategy to characterize the O-glycoproteome of two gastric cancer SimpleCell lines (AGS, MKN45) as well as a gastric cell line (KATO III) which naturally expresses at least partially truncated O-glycans. Overall, we identified 499 O-glycoproteins and 1236 O-glycosites in gastric cancer SimpleCells, and a total 47 O-glycoproteins and 73 O-glycosites in the KATO III cell line. We next modified the glycoproteomic strategy to apply it to pools of sera from gastric cancer and healthy individuals to identify circulating O-glycoproteins with the STn glycoform. We identified 37 O-glycoproteins in the pool of cancer sera, and only nine of these were also found in sera from healthy individuals. Two identified candidate O-glycoprotein biomarkers (CD44 and GalNAc-T5) circulating with the STn glycoform were further validated as being expressed in gastric cancer tissue. A proximity ligation assay was used to show that CD44 was expressed with the STn glycoform in gastric cancer tissues. The study provides a discovery strategy for aberrantly glycosylated O-glycoproteins and a set of O-glycoprotein candidates with biomarker potential in gastric cancer.
Collapse
Affiliation(s)
- Diana Campos
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Daniela Freitas
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Joana Gomes
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Ana Magalhães
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Catharina Steentoft
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catarina Gomes
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Malene B Vester-Christensen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - José Alexandre Ferreira
- ¶Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal; ‖QOPNA, Department of Chemistry of the University of Aveiro, Campus Universitário de Santiago 3810-193 Aveiro, Portugal
| | - Luis P Afonso
- **Department of Pathology, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal
| | - Lúcio L Santos
- ¶Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida 4200-072 Porto, Portugal
| | - João Pinto de Sousa
- ‡‡Faculty of Medicine of the University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ulla Mandel
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark;
| | - Celso A Reis
- §IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal; ‡‡Faculty of Medicine of the University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; §§Institute of Biomedical Sciences Abel Salazar, ICBAS, Rua de Jorge Viterbo Ferreira n.228, 4050-313 Porto, Portugal
| |
Collapse
|
47
|
Liu H, Zhang N, Wan D, Cui M, Liu Z, Liu S. Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery. Clin Proteomics 2014; 11:14. [PMID: 24722010 PMCID: PMC3984494 DOI: 10.1186/1559-0275-11-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/19/2014] [Indexed: 02/08/2023] Open
Abstract
Glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for glycoprotein analysis. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.
Collapse
Affiliation(s)
| | | | | | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P, R, China.
| | | | | |
Collapse
|
48
|
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.
Collapse
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
| | | | | | | |
Collapse
|
49
|
Rodrigo MAM, Zitka O, Krizkova S, Moulick A, Adam V, Kizek R. MALDI-TOF MS as evolving cancer diagnostic tool: a review. J Pharm Biomed Anal 2014; 95:245-55. [PMID: 24699369 DOI: 10.1016/j.jpba.2014.03.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 02/09/2023]
Abstract
Recent developments in mass spectrometry have introduced clinical proteomics to the forefront of diseases diagnosis, offering reliable, robust and efficient analytical method for biomarker discovery and monitoring. MALDI-TOF is a powerful tool for surveying proteins and peptides comprising the realm for clinical analysis. MALDI-TOF has the potential to revolutionize cancer diagnostics by facilitating biomarker discovery, enabling tissue imaging and quantifying biomarker levels. Healthy (control) and cancerous tissues can be analyzed on the basis of mass spectrometry (MALDI-TOF) imaging to identify cancer-specific changes that may prove to be clinically useful. We review MALDI-TOF profiling techniques as tools for detection of cancer biomarkers in various cancers. We mainly discuss recent advances including period from 2011 to 2013.
Collapse
Affiliation(s)
- Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic.
| |
Collapse
|
50
|
Azevedo CC, Azevedo J, Osório H, Vasconcelos V, Campos A. Early physiological and biochemical responses of rice seedlings to low concentration of microcystin-LR. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:107-121. [PMID: 24323250 DOI: 10.1007/s10646-013-1156-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/30/2013] [Indexed: 06/03/2023]
Abstract
Microcystin-leucine and arginine (microcystin-LR) is a cyanotoxin produced by cyanobacteria like Microcystis aeruginosa, and it's considered a threat to water quality, agriculture, and human health. Rice (Oryza sativa) is a plant of great importance in human food consumption and economy, with extensive use around the world. It is therefore important to assess the possible effects of using water contaminated with microcystin-LR to irrigate rice crops, in order to ensure a safe, high quality product to consumers. In this study, 12 and 20-day-old plants were exposed during 2 or 7 days to a M. aeruginosa extract containing environmentally relevant microcystin-LR concentrations, 0.26-78 μg/L. Fresh and dry weight of roots and leaves, chlorophyll fluorescence, glutathione S-transferase and glutathione peroxidase activities, and protein identification by mass spectrometry through two-dimensional gel electrophoresis from root and leaf tissues, were evaluated in order to gauge the plant's physiological condition and biochemical response after toxin exposure. Results obtained from plant biomass, chlorophyll fluorescence, and enzyme activity assays showed no significant differences between control and treatment groups. However, proteomics data indicates that plants respond to M. aeruginosa extract containing environmentally relevant microcystin-LR concentrations by changing their metabolism, responding differently to different toxin concentrations. Biological processes most affected were related to protein folding and stress response, protein biosynthesis, cell signalling and gene expression regulation, and energy and carbohydrate metabolism which may denote a toxic effect induced by M. aeruginosa extract and microcystin-LR. The implications of the metabolic alterations in plant physiology and growth require further elucidation.
Collapse
Affiliation(s)
- Catarina C Azevedo
- Centro Interdisciplinar de Investigação Marinha e Ambiental, CIIMAR/CIMAR, Rua dos Bragas 289, 4050-123, Porto, Portugal
| | | | | | | | | |
Collapse
|