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Xie X, Kong S, Cao W. Targeting protein glycosylation to regulate inflammation in the respiratory tract: novel diagnostic and therapeutic candidates for chronic respiratory diseases. Front Immunol 2023; 14:1168023. [PMID: 37256139 PMCID: PMC10225578 DOI: 10.3389/fimmu.2023.1168023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
Protein glycosylation is a widespread posttranslational modification that can impact the function of proteins. Dysregulated protein glycosylation has been linked to several diseases, including chronic respiratory diseases (CRDs). CRDs pose a significant public health threat globally, affecting the airways and other lung structures. Emerging researches suggest that glycosylation plays a significant role in regulating inflammation associated with CRDs. This review offers an overview of the abnormal glycoenzyme activity and corresponding glycosylation changes involved in various CRDs, including chronic obstructive pulmonary disease, asthma, cystic fibrosis, idiopathic pulmonary fibrosis, pulmonary arterial hypertension, non-cystic fibrosis bronchiectasis, and lung cancer. Additionally, this review summarizes recent advances in glycomics and glycoproteomics-based protein glycosylation analysis of CRDs. The potential of glycoenzymes and glycoproteins for clinical use in the diagnosis and treatment of CRDs is also discussed.
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Affiliation(s)
- Xiaofeng Xie
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weiqian Cao
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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2
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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3
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Activities against Lung Cancer of Biosynthesized Silver Nanoparticles: A Review. Biomedicines 2023; 11:biomedicines11020389. [PMID: 36830926 PMCID: PMC9953519 DOI: 10.3390/biomedicines11020389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Nanomedicine is an interdisciplinary field where nanostructured objects are applied to treat or diagnose disease. Nanoparticles (NPs) are a special class of materials at nanometric scale that can be prepared from lipids, polymers, or noble metals through bottom-up approaches. Biological synthesis is a reliable, sustainable, and non-toxic bottom-up method that uses phytochemicals, microorganisms, and enzymes to induce the reduction of metal ions into NPs. Silver (Ag) NPs exhibit potent therapeutic properties that can be exploited to overcome the limitations of current treatment modalities for human health issues such as lung cancer (LC). Here, we review the preparation of AgNPs using biological synthesis and their application against LC using in vitro and in vivo models. An overview of the staging, diagnosis, genetic mutations, and treatment of LC, as well as its main subtypes, is presented. A summary of the reaction mechanisms of AgNPs using microbial cell cultures, plant extracts, phytochemicals, and amino acids is included. The use of capping agents in the biosynthesis of AgNPs with anticancer activity is also detailed. The history and biological activities of metal-based nanostructures synthesized with gold, copper, palladium, and platinum are considered. The possible anticancer mechanisms of AgNPs against LC models are covered. Our perspective about the future of AgNPs in LC treatment and nanomedicine is added.
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4
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Role of Prosaposin and Extracellular Sulfatase Sulf-1 Detection in Pleural Effusions as Diagnostic Biomarkers of Malignant Mesothelioma. Biomedicines 2022; 10:biomedicines10112803. [PMID: 36359323 PMCID: PMC9687327 DOI: 10.3390/biomedicines10112803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
Malignant pleural mesothelioma is an aggressive malignancy with poor prognosis. Unilateral pleural effusion is frequently the initial clinical sign requiring therapeutic thoracentesis, which also offers a diagnostic opportunity. Detection of soluble biomarkers can support diagnosis, but few show good diagnostic accuracy. Here, we studied the expression levels and discriminative power of two putative biomarkers, prosaposin and extracellular sulfatase SULF-1, identified by proteomic and transcriptomic analysis, respectively. Pleural effusions from a total of 44 patients (23 with mesothelioma, 8 with lung cancer, and 13 with non-malignant disease) were analyzed for prosaposin and SULF-1 by enzyme-linked immunosorbent assay. Pleural effusions from mesothelioma patients had significantly higher levels of prosaposin and SULF-1 than those from non-malignant disease patients. Receiver-operating characteristic (ROC) analysis showed that both biomarkers have good discriminating power as pointed out by an AUC value of 0.853 (p = 0.0005) and 0.898 (p < 0.0001) for prosaposin and SULF-1, respectively. Combining data ensued a model predicting improvement of the diagnostic performance (AUC = 0.916, p < 0.0001). In contrast, prosaposin couldn’t discriminate mesothelioma patients from lung cancer patients while ROC analysis of SULF-1 data produced an AUC value of 0.821 (p = 0.0077) but with low sensitivity. In conclusion, prosaposin and SULF-1 levels determined in pleural effusion may be promising biomarkers for differential diagnosis between mesothelioma and non-malignant pleural disease. Instead, more patients need to be enrolled before granting the possible usefulness of these soluble proteins in differentiating mesothelioma pleural effusions from those linked to lung cancer.
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5
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Donadieu J, Bou Mitri F, Beaupain B, Alajidi N, Viallard JF, Paih JPL, Yacoub M, Leblanc T, Quero L, Rouland A, Labbe L, Deback C, Bellanne-Chantelot C, Emile JF. ELANE neutropenia and solid tumors: Four cases from the French severe chronic neutropenia registry. Pediatr Blood Cancer 2022; 69:e29923. [PMID: 35969146 DOI: 10.1002/pbc.29923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/10/2022]
Abstract
Neutropenia related to ELANE gene mutations predisposes patients to infection and leukemia/myelodysplasia, but little is known about the predisposition to cancer. Among a cohort of 147 patients, we identified four with malignant solid tumors (papillary thyroid cancer, anal squamous cell cancer, papillary renal cell carcinoma, and adrenocortical carcinoma), all aged 25-50 years. Three occurred with cyclic neutropenia, and one occurred with severe chronic neutropenia. Previous radiotherapy was identified as a risk factor in one patient. No genetic predisposition was identified in the three other patients.
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Affiliation(s)
- Jean Donadieu
- French Registry for Severe Chronic Neutropenia, Armand-Trousseau Hospital, APHP, Paris, France
| | - Fares Bou Mitri
- French Registry for Severe Chronic Neutropenia, Armand-Trousseau Hospital, APHP, Paris, France
| | - Blandine Beaupain
- French Registry for Severe Chronic Neutropenia, Armand-Trousseau Hospital, APHP, Paris, France
| | - Nathalie Alajidi
- Onco-hematology Unit, Pediatic Department, Children Hospital, Groupe Hospitalier Pellegrin, Bordeaux, France
| | - Jean Francois Viallard
- Internal Medicine and Infectious Disease Department, Haut-Lévêque Hospital, University of Bordeaux, Bordeaux, France
| | | | - Mokrane Yacoub
- Pathology Department, Bordeaux University Hospital, Bordeaux, France
| | | | - Laurent Quero
- Oncology and Radiotherapy Department, Hopital Saint Louis, APHP, Paris, France
| | - Alexia Rouland
- Endocrinology Department, Dijon University Hospital, Dijon, France
| | - Louis Labbe
- Endocrinology Department, Hotel Dieu, Le Creusot, France
| | - Claire Deback
- Virology Department, Paul Brousse Hospital, Villejuif, France
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6
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Shi X, Dong A, Jia X, Zheng G, Wang N, Wang Y, Yang C, Lu J, Yang Y. Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on T-cell marker genes to predict prognosis and therapeutic response in lung squamous cell carcinoma. Front Immunol 2022; 13:992990. [PMID: 36311764 PMCID: PMC9614104 DOI: 10.3389/fimmu.2022.992990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer immunotherapy is an increasingly successful strategy for treating patients with advanced or conventionally drug-resistant cancers. T cells have been proved to play important roles in anti-tumor and tumor microenvironment shaping, while these roles have not been explained in lung squamous cell carcinoma (LUSC). In this study, we first performed a comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data from the gene expression omnibus (GEO) database to identify 72 T-cell marker genes. Subsequently, we constructed a 5-gene prognostic signature in the training cohort based on the T-cell marker genes from the cancer genome atlas (TCGA) database, which was further validated in the testing cohort and GEO cohort. The areas under the receiver operating characteristic curve at 1-, 3-, and 5-years were 0.614, 0.713 and 0.702 in the training cohort, 0.669, 0.603 and 0.645 in the testing cohort, 0.661, 0.628 and 0.590 in the GEO cohort, respectively. Furthermore, we created a highly reliable nomogram to facilitate clinical application. Gene set enrichment analysis showed that immune-related pathways were mainly enriched in the high-risk group. Tumor immune microenvironment indicated that high-risk group exhibited higher immune score, stromal score, and immune cell infiltration levels. Moreover, genes of the immune checkpoints and human leukocyte antigen family were all overexpressed in high-risk group. Drug sensitivity revealed that low-risk group was sensitive to 8 chemotherapeutic drugs and high-risk group to 4 chemotherapeutic drugs. In short, our study reveals a novel prognostic signature based on T-cell marker genes, which provides a new target and theoretical support for LUSC patients.
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7
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Paudel KR, Mehta M, Yin GHS, Yen LL, Malyla V, Patel VK, Panneerselvam J, Madheswaran T, MacLoughlin R, Jha NK, Gupta PK, Singh SK, Gupta G, Kumar P, Oliver BG, Hansbro PM, Chellappan DK, Dua K. Berberine-loaded liquid crystalline nanoparticles inhibit non-small cell lung cancer proliferation and migration in vitro. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:46830-46847. [PMID: 35171422 PMCID: PMC9232428 DOI: 10.1007/s11356-022-19158-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/06/2022] [Indexed: 05/02/2023]
Abstract
Non-small cell lung cancer (NSCLC) is reported to have a high incidence rate and is one of the most prevalent types of cancer contributing towards 85% of all incidences of lung cancer. Berberine is an isoquinoline alkaloid which offers a broad range of therapeutical and pharmacological actions against cancer. However, extremely low water solubility and poor oral bioavailability have largely restricted its therapeutic applications. To overcome these limitations, we formulated berberine-loaded liquid crystalline nanoparticles (LCNs) and investigated their in vitro antiproliferative and antimigratory activity in human lung epithelial cancer cell line (A549). 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), trypan blue staining, and colony forming assays were used to evaluate the anti-proliferative activity, while scratch wound healing assay and a modified Boyden chamber assay were carried out to determine the anti-migratory activity. We also investigated major proteins associated with lung cancer progression. The developed nanoparticles were found to have an average particle size of 181.3 nm with spherical shape, high entrapment efficiency (75.35%) and have shown sustained release behaviour. The most remarkable findings reported with berberine-loaded LCNs were significant suppression of proliferation, inhibition of colony formation, inhibition of invasion or migration via epithelial mesenchymal transition, and proliferation related proteins associated with cancer progression. Our findings suggest that anti-cancer compounds with the problem of poor solubility and bioavailability can be overcome by formulating them into nanotechnology-based delivery systems for better efficacy. Further in-depth investigations into anti-cancer mechanistic research will expand and strengthen the current findings of berberine-LCNs as a potential NSCLC treatment option.
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Affiliation(s)
- Keshav R Paudel
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia
| | - Meenu Mehta
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Geena Hew Suet Yin
- School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Lee Li Yen
- School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Vamshikrishna Malyla
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Vyoma K Patel
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia
| | - Jithendra Panneerselvam
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Thiagarajan Madheswaran
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Ronan MacLoughlin
- IDA Business Park, Dangan, H91 HE94, Galway, Ireland
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, D02 YN77, Ireland
- School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, D02 PN40, Ireland
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Piyush Kumar Gupta
- Department of Life Sciences, School of Basic Sciences and Research (SBSR), Sharda University, Knowledge Park III, Greater Noida-201310, Uttar Pradesh, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Pradeep Kumar
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Brian G Oliver
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, 2006, Australia
| | - Philip M Hansbro
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia.
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia.
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia.
| | - Kamal Dua
- Centre for Inflammation, Centenary Institute, Sydney, NSW, 2050, Australia.
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia.
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, 2006, Australia.
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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Proteomic Analysis of Lung Cancer Types—A Pilot Study. Cancers (Basel) 2022; 14:cancers14112629. [PMID: 35681609 PMCID: PMC9179298 DOI: 10.3390/cancers14112629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the leading cause of tumor-related mortality, therefore significant effort is directed towards understanding molecular alterations occurring at the origin of the disease to improve current treatment options. The aim of our pilot-scale study was to carry out a detailed proteomic analysis of formalin-fixed paraffin-embedded tissue sections from patients with small cell or non-small cell lung cancer (adenocarcinoma, squamous cell carcinoma, and large cell carcinoma). Tissue surface digestion was performed on relatively small cancerous and tumor-adjacent normal regions and differentially expressed proteins were identified using label-free quantitative mass spectrometry and subsequent statistical analysis. Principal component analysis clearly distinguished cancerous and cancer adjacent normal samples, while the four lung cancer types investigated had distinct molecular profiles and gene set enrichment analysis revealed specific dysregulated biological processes as well. Furthermore, proteins with altered expression unique to a specific lung cancer type were identified and could be the targets of future studies.
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He Y, Zang X, Kuang J, Yang H, Gu T, Yang J, Li Z, Zheng E, Xu Z, Cai G, Wu Z, Hong L. iTRAQ-based quantitative proteomic analysis of porcine uterine fluid during pre-implantation period of pregnancy. J Proteomics 2022; 261:104570. [DOI: 10.1016/j.jprot.2022.104570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/28/2022] [Accepted: 03/19/2022] [Indexed: 10/18/2022]
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10
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Yang S, Xia J, Yang Z, Xu M, Li S. Lung cancer molecular mutations and abnormal glycosylation as biomarkers for early diagnosis. Cancer Treat Res Commun 2021; 27:100311. [PMID: 33465560 DOI: 10.1016/j.ctarc.2021.100311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Lung cancer is the leading cause of mortality and morbidity in tumor-related deaths in the world. Early detection of tumors can greatly improve the survival rate of patients. However, the lack of reliable blood biomarkers remains a major challenge for early diagnosis. The blood proteins secreted by the lung bronchi and bronchial arteries may have characteristic glycosylation patterns associated with tumors, which are different from normal physiological and pathological conditions. In this review, we outline the oncogenic drivers, signaling pathways related to KRAS, gene and protein mutations, and oncogenic regulation of protein glycosylation. Based on to the TCGA transcriptomics and antibody-based proteomics data, we discussed oncogene and glycoproteins detected in the blood as tumor biomarkers. We hypothesize that glycoproteins whose glycosylation can be reversed by targeted drugs may serve as potential tumor biomarkers.
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Affiliation(s)
- Shuang Yang
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, China
| | - Zeren Yang
- Applied Biomimetic, Gaithersburg, Maryland 20878, United States
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China
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11
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Lacerenza S, Ciregia F, Giusti L, Bonotti A, Greco V, Giannaccini G, D'Antongiovanni V, Fallahi P, Pieroni L, Cristaudo A, Lucacchini A, Mazzoni MR, Foddis R. Putative Biomarkers for Malignant Pleural Mesothelioma Suggested by Proteomic Analysis of Cell Secretome. Cancer Genomics Proteomics 2020; 17:225-236. [PMID: 32345664 DOI: 10.21873/cgp.20183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/24/2020] [Accepted: 02/28/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) a rare neoplasm linked to asbestos exposure is characterized by a poor prognosis. Soluble mesothelin is currently considered the most specific diagnostic biomarker. The aim of the study was to identify novel biomarkers by proteomic analysis of two MPM cell lines secretome. MATERIALS AND METHODS The protein patterns of MPM cells secretome were examined and compared to a non-malignant mesothelial cell line using two-dimensional gel electrophoresis coupled to mass spectrometry. Serum levels of candidate biomarkers were determined in MPM patients and control subjects. RESULTS Two up-regulated proteins involved in cancer biology, prosaposin and quiescin Q6 sulfhydryl oxidase 1, were considered candidate biomarkers. Serum levels of both proteins were significantly higher in MPM patients than control subjects. Combining the data of each receiver-operating characteristic analysis predicted a good diagnostic accuracy. CONCLUSION A panel of the putative biomarkers represents a promising tool for MPM diagnosis.
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Affiliation(s)
| | - Federica Ciregia
- Department of Pharmacy, University of Pisa, Pisa, Italy.,Department of Rheumatology, GIGA Research, Centre Hospitalier Universitaire (CHU) de Liège, Liège, Belgium
| | - Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessandra Bonotti
- Department of Translational Research and New Medical and Surgical Technologies, Occupational Medicine Unit, University-Hospital of Pisa, Pisa, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Chemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | - Poupak Fallahi
- Department of Translational Research and New Medical and Surgical Technologies, Occupational Medicine Unit, University-Hospital of Pisa, Pisa, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS-Fondazione Santa Lucia, Rome, Italy
| | - Alfonso Cristaudo
- Department of Translational Research and New Medical and Surgical Technologies, Occupational Medicine Unit, University-Hospital of Pisa, Pisa, Italy
| | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Rudy Foddis
- Department of Translational Research and New Medical and Surgical Technologies, Occupational Medicine Unit, University-Hospital of Pisa, Pisa, Italy
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12
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Lathwal A, Kumar R, Arora C, Raghava GPS. Identification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical data. J Cancer Res Clin Oncol 2020; 146:2743-2752. [PMID: 32661603 DOI: 10.1007/s00432-020-03318-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Intra-tumor heterogeneity and high mortality among patients with non-small-cell lung carcinoma (NSCLC) emphasize the need to identify reliable prognostic markers unique to each subtype. METHODS In this study, univariate cox regression and prognostic index (PI)-based approaches were used to develop models for predicting NSCLC patients' subtype-specific survival. RESULTS Prognostic analysis of TCGA dataset identified 1334 and 2129 survival-specific genes for LUSC (488 samples) and LUAD (497 samples), respectively. Individually, 32 and 271 prognostic genes were found and validated in GSE study exclusively for LUSC and LUAD. Nearly, 9-10% of the validated genes in each subtype were already reported in multiple studies thus highlighting their importance as prognostic biomarkers. Strong literature evidence against these prognostic genes like "ELANE" (LUSC) and "AHSG" (LUAD) instigates further investigation for their therapeutic and diagnostic roles in the corresponding cohorts. Prognostic models built on five and four genes were validated for LUSC [HR = 2.10, p value = 1.86 × 10-5] and LUAD [HR = 2.70, p value = 3.31 × 10-7], respectively. The model based on the combination of age and tumor stage performed well in both NSCLC subtypes, suggesting that despite having distinctive histological features and treatment paradigms, some clinical features can be good prognostic predictors in both. CONCLUSION This study advocates that investigating the survival-specific biomarkers restricted to respective cohorts can advance subtype-specific prognosis, diagnosis, and treatment for NSCLC patients. Prognostic models and markers described for each subtype may provide insight into the heterogeneity of disease etiology and help in the development of new therapeutic approaches for the treatment of NSCLC patients.
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Affiliation(s)
- Anjali Lathwal
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India
| | - Rajesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chakit Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India
| | - Gajendra Pal Singh Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi, Okhla Industrial Estate, Phase III (Near Govind Puri Metro Station), A-302 (R&D Block), New Delhi, 110020, India.
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13
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Zhou Y, Yang W, Ao M, Höti N, Gabrielson E, Chan DW, Zhang H, Li QK. Proteomic Analysis of the Air-Way Fluid in Lung Cancer. Detection of Periostin in Bronchoalveolar Lavage (BAL). Front Oncol 2020; 10:1072. [PMID: 32719746 PMCID: PMC7350406 DOI: 10.3389/fonc.2020.01072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Bronchoalveolar lavage (BAL) is a specific type of air-way fluid. It is a commonly used clinical specimen for the diagnosis of benign diseases and cancers of the lung. Although previous studies have identified several disease-associated proteins in the BAL, the potential utility of BAL in lung cancer is still not well-studied. Based upon the fact that the majority of secreted proteins are glycoproteins, we have profiled N-glycoproteins in BAL collected from lung cancers, and investigated the expression of glycoproteins such as the matrix N-glycoprotein, periostin, in lung cancers. Methods: BAL specimens (n = 16) were collected from lung cancer patients, and analyzed using mass spectrometry-based quantitative N-glycoproteomic technique. Additional BAL specimens (n = 39) were independently collected to further evaluate the expression of periostin by using an enzyme-linked immunosorbent assay (ELISA). Results: A total of 462 glycoproteins were identified in BAL samples using N-glycoproteomic technique, including 290 in lung adenocarcinoma (ADC, n = 5), 376 in squamous cell carcinoma (SQCC, n = 4), 309 in small cell lung carcinoma (SCLC, n = 4), and 316 in benign lung disease (n = 3). The expressions of several glycoproteins were elevated, including 8 in ADC, 12 in SQCC, and 17 in SCLC, compared to benign BALs. The expression of periostin was detected in all subtypes of lung cancers. To further investigate the expression of periostin, an ELISA assay was performed using additional independently collected BALs (n = 39) The normalized levels of periostin in benign disease, ADC, SQCC, and SCLC were 255 ± 104 (mean ± SE) and 4,002 ± 2,181, 3,496 ± 1,765, and 1,772 ± 1,119 ng/mg of total BAL proteins. Conclusion: Our findings demonstrate that proteomic analysis of BAL can be used for the study of cancer-associated extracellular proteins in air-way fluid from lung cancer patients.
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Affiliation(s)
- Yangying Zhou
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Weiming Yang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Minghui Ao
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, United States.,Department of Oncology, Sidney Kimmel Cancer Center at Johns Hopkins Medical Institutions, Baltimore, MD, United States
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14
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Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteomics 2020; 17:17. [PMID: 32489335 PMCID: PMC7247207 DOI: 10.1186/s12014-020-09283-w] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
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Affiliation(s)
- Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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15
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Ding Y, Qi N, Wang K, Huang Y, Liao J, Wang H, Tan A, Liu L, Zhang Z, Li J, Kong J, Qin S, Jiang Y. FTO Facilitates Lung Adenocarcinoma Cell Progression by Activating Cell Migration Through mRNA Demethylation. Onco Targets Ther 2020; 13:1461-1470. [PMID: 32110044 PMCID: PMC7035887 DOI: 10.2147/ott.s231914] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/24/2019] [Indexed: 12/24/2022] Open
Abstract
Background The fat mass and obesity-associated protein (FTO) was identified as a critical demethylase involved in regulating cellular mRNA stability by removing N6-methyladenosine (m6A) residues from mRNA. Emerging evidence has revealed that FTO is deeply implicated in lung cancer. However, knowledge of the function of FTO in lung adenocarcinoma (LUAC) is limited. Methods FTO and FTO R96Q (R96Q), an FTO missense mutant lacking demethylase activity, were ectopically overexpressed, and FTO was knocked down via siRNA in A549 and H1299 cells. The relationships between FTO with cell characteristics and mRNA m6A levels were explored. Furthermore, RNA sequencing was performed on A549 cells. Results FTO overexpression enhanced the proliferation, migration, and invasion ability of A549 and H1299 cells, decreased mRNA m6A levels. Interestingly, overexpression of R96Q, blunted the effects of FTO overexpression on cell proliferation and invasion. Through RNA sequencing analysis of A549 cells overexpressing FTO or R96Q and control A594 cells, 45 genes were identified as affected by m6A mRNA demethylation. Most of these genes were related to lung cancer, such as laminin γ2, thrombospondin 1, nerve growth factor inducible, integrin alpha11, and proprotein convertase subtilisin/kexin type 9. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggested that these genes are fundamental to cancer development processes, such as cell migration and extracellular matrix organization. Conclusion Our research shows that FTO facilitates LUAC cell progression by activating cell migration through m6A demethylation; however, further research on the mechanism underlying FTO activity in LUAC is necessary.
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Affiliation(s)
- Yudi Ding
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Nana Qi
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Ke Wang
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yiming Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Jinling Liao
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Hongxue Wang
- Department of Chemotherapy, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Aihua Tan
- Department of Chemotherapy, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Lihua Liu
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Zhenqiang Zhang
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Jinlong Li
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Jinliang Kong
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Shouming Qin
- Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yonghua Jiang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Key Laboratory of Genomic and Personalized Medicine, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, Guangxi 530021, People's Republic of China
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16
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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17
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Zhang W, Peng P, Ou X, Shen K, Wu X. Ovarian cancer circulating extracelluar vesicles promote coagulation and have a potential in diagnosis: an iTRAQ based proteomic analysis. BMC Cancer 2019; 19:1095. [PMID: 31718609 PMCID: PMC6852975 DOI: 10.1186/s12885-019-6176-1] [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: 02/21/2019] [Accepted: 09/20/2019] [Indexed: 02/08/2023] Open
Abstract
Background Circulating extracelluar vesicles (EVs) in epithelial ovarian cancer (EOC) patients emanate from multiple cells. These EVs are emerging as a new type of biomarker as they can be obtained by non-invasive approaches. The aim of this study was to investigate circulating EVs from EOC patients and healthy women to evaluate their biological function and potential as diagnostic biomarkers. Methods A quantitative proteomic analysis (iTRAQ) was applied and performed on 10 EOC patients with advanced stage (stage III–IV) and 10 controls. Twenty EOC patients and 20 controls were applied for validation. The candidate proteins were further validated in another 40-paired cohort to investigate their biomarker potential. Coagulation cascades activation was accessed by determining Factor X activity. Results Compared with controls, 200 proteins were upregulated and 208 proteins were downregulated in the EOC group. The most significantly involved pathway is complement and coagulation cascades. ApoE multiplexed with EpCAM, plg, serpinC1 and C1q provide optimal diagnostic information for EOC with AUC = 0.913 (95% confidence interval (CI) =0.848–0.957, p < 0.0001). Level of activated Factor X was significantly higher in EOC group than control (5.35 ± 0.14 vs. 3.69 ± 0.29, p < 0.0001). Conclusions Our study supports the concept of circulating EVs as a tool for non-invasive diagnosis of ovarian cancer. EVs also play pivotal roles in coagulation process, implying the inherent mechanism of generation of thrombus which often occurred in ovarian cancer patients at late stages.
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Affiliation(s)
- Wei Zhang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-an Road, Shanghai, 200032, People's Republic of China
| | - Peng Peng
- Department of Obstetrics and Gynecology Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoxuan Ou
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-an Road, Shanghai, 200032, People's Republic of China
| | - Keng Shen
- Department of Obstetrics and Gynecology Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, 270 Dong-an Road, Shanghai, 200032, People's Republic of China.
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18
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Wang Q, Zhi Y, Ren W, Li S, Dou Z, Xing X, Quan X, Wang Y, Jiang C, Liang X, Gao L, Zhi K. Suppression of OSCC malignancy by oral glands derived-PIP identified by iTRAQ combined with 2D LC-MS/MS. J Cell Physiol 2019; 234:15330-15341. [PMID: 30693510 PMCID: PMC6590427 DOI: 10.1002/jcp.28180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignancy in head and neck cancer and a global cause of cancer-related death. Due to the poor survival rates associated with OSCC, there is a growing need to develop novel technologies and predictive biomarkers to improve disease diagnosis. The identification of new cellular targets in OSCC tumors will benefit such developments. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics analysis combined with 2-dimensional liquid chromatography and tandem mass spectrometry (2D LC-MS/MS) were used to identify differentially expressed proteins (DEPs) between tumor and normal tissues. Of the DEPs detected, the most significantly downregulated protein in OSCC tissue was prolactin-inducible protein (PIP). Clonogenic and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) experiments showed that the proliferation capacity of OSCC cells overexpressing PIP decreased due to cell cycle arrest at the G0/G1 checkpoint. Wound-healing and transwell assay further showed that PIP overexpression also reduced the migration and invasion of OSCC cells. Immunohistochemistry (IHC) was used to analyze the expression in OSCC, indicating that PIP may be secreted by glandular cells and have an inhibitory effect on OSCC cells to produce. In western blot analysis, silencing studies confirmed that PIP mediates these effects through the AKT/mitogen-activated protein kinase (MAPK) signaling axis in OSCC cells. Taken together, this study reveals PIP as a key mediator of OSCC cell growth, migration, and invasion through its effect on AKT/MAPK signaling.
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Affiliation(s)
- Qibo Wang
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina,School of Stomatology, Qingdao UniversityQingdaoShandongChina
| | - Yuan Zhi
- Xiangya School of Stomatology, Central South UniversityChangshaHunanChina
| | - Wenhao Ren
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Shaoming Li
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Zhichao Dou
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Xiaoming Xing
- Department of ResearchThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Xinyu Quan
- School of Stomatology, Qingdao UniversityQingdaoShandongChina
| | - Yuting Wang
- School of Stomatology, Qingdao UniversityQingdaoShandongChina
| | - Chunmiao Jiang
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina,School of Stomatology, Qingdao UniversityQingdaoShandongChina
| | - Xiao Liang
- Department of NeurologyHaukeland University HospitalBergenNorway
| | - Ling Gao
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Keqian Zhi
- Department of Oral Maxillofacial SurgeryKey Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
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19
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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20
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Matsuda-Lennikov M, Biancalana M, Zou J, Ravell JC, Zheng L, Kanellopoulou C, Jiang P, Notarangelo G, Jing H, Masutani E, Oler AJ, Olano LR, Schulz BL, Lenardo MJ. Magnesium transporter 1 (MAGT1) deficiency causes selective defects in N-linked glycosylation and expression of immune-response genes. J Biol Chem 2019; 294:13638-13656. [PMID: 31337704 DOI: 10.1074/jbc.ra119.008903] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/08/2019] [Indexed: 12/22/2022] Open
Abstract
Magnesium transporter 1 (MAGT1) critically mediates magnesium homeostasis in eukaryotes and is highly-conserved across different evolutionary branches. In humans, loss-of-function mutations in the MAGT1 gene cause X-linked magnesium deficiency with Epstein-Barr virus (EBV) infection and neoplasia (XMEN), a disease that has a broad range of clinical and immunological consequences. We have previously shown that EBV susceptibility in XMEN is associated with defective expression of the antiviral natural-killer group 2 member D (NKG2D) protein and abnormal Mg2+ transport. New evidence suggests that MAGT1 is the human homolog of the yeast OST3/OST6 proteins that form an integral part of the N-linked glycosylation complex, although the exact contributions of these perturbations in the glycosylation pathway to disease pathogenesis are still unknown. Using MS-based glycoproteomics, along with CRISPR/Cas9-KO cell lines, natural killer cell-killing assays, and RNA-Seq experiments, we now demonstrate that humans lacking functional MAGT1 have a selective deficiency in both immune and nonimmune glycoproteins, and we identified several critical glycosylation defects in important immune-response proteins and in the expression of genes involved in immunity, particularly CD28. We show that MAGT1 function is partly interchangeable with that of the paralog protein tumor-suppressor candidate 3 (TUSC3) but that each protein has a different tissue distribution in humans. We observed that MAGT1-dependent glycosylation is sensitive to Mg2+ levels and that reduced Mg2+ impairs immune-cell function via the loss of specific glycoproteins. Our findings reveal that defects in protein glycosylation and gene expression underlie immune defects in an inherited disease due to MAGT1 deficiency.
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Affiliation(s)
- Mami Matsuda-Lennikov
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew Biancalana
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan Zou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan C Ravell
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Chrysi Kanellopoulou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Giulia Notarangelo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Huie Jing
- Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Evan Masutani
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lisa Renee Olano
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Benjamin L Schulz
- University of Queensland, School of Chemistry and Molecular Biology, Brisbane, St. Lucia, Queensland 4072, Australia
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892 .,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
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21
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Dang L, Jia L, Zhi Y, Li P, Zhao T, Zhu B, Lan R, Hu Y, Zhang H, Sun S. Mapping human N-linked glycoproteins and glycosylation sites using mass spectrometry. Trends Analyt Chem 2019; 114:143-150. [PMID: 31831916 PMCID: PMC6907083 DOI: 10.1016/j.trac.2019.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. Over the last decade, large-scale profiling of N-linked glycoproteins and glycosylation sites from biological and clinical samples has been achieved through mass spectrometry-based glycoproteomic approaches. In this paper, we reviewed the human glycoproteomic profiles that have been reported in more than 80 individual studies, and mainly focused on the N-glycoproteins and glycosylation sites identified through their deglycosylated forms of glycosite-containing peptides. According to our analyses, more than 30,000 glycosite-containing peptides and 7,000 human glycoproteins have been identified from five different body fluids, twelve human tissues (or related cell lines), and four special cell types. As the glycoproteomic data is still missing for many organs and tissues, a systematical glycoproteomic analysis of various human tissues and body fluids using a uniform platform is still needed for an integrated map of human N-glycoproteomes.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yuan Zhi
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Pengfei Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Ting Zhao
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Rongxia Lan
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
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22
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Preferential Localization of MUC1 Glycoprotein in Exosomes Secreted by Non-Small Cell Lung Carcinoma Cells. Int J Mol Sci 2019; 20:ijms20020323. [PMID: 30646616 PMCID: PMC6358839 DOI: 10.3390/ijms20020323] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/14/2022] Open
Abstract
Lung cancer remains to be the leading cause of cancer-related mortality worldwide. Finding new noninvasive biomarkers for lung cancer is still a significant clinical challenge. Exosomes are membrane-bound, nano-sized vesicles that are released by various living cells. Studies on exosomal proteomics may provide clues for developing clinical assays. In this study, we performed semi-quantitative proteomic analysis of proteins that were purified from exosomes of NCI-H838 non-small cell lung cancer cell line, with total cellular membrane proteins as control. In the exosomes, LC-MS/MS by data-independent analysis mode identified 3235 proteins. THBS1, ANXA6, HIST1H4A, COL18A1, MDK, SRGN, ENO1, TUBA4A, SLC3A2, GPI, MIF, MUC1, TALDO1, SLC7A5, ICAM1, HSP90AA1, G6PD, and LRP1 were found to be expressed in exosomes at more than 5-fold higher level as compared to total cellular membrane proteins. A well-known cancer biomarker, MUC1, is expressed at 8.98-fold higher in exosomes than total cellular membrane proteins. Subsequent analysis of plasma exosomes from non-small cell lung cancer (NSCLC) patients by a commercial electrochemiluminescence immunoassay showed that exosomal MUC1 level is 1.5-fold higher than healthy individuals (mean value 1.55 ± 0.16 versus mean value 1.05 ± 0.06, p = 0.0213). In contrast, no significant difference of MUC1 level was found between NSCLC patients and healthy individuals' plasma (mean value 5.48 ± 0.65 versus mean value 4.16 ± 0.49). These results suggest that certain proteins, such as MUC1, are selectively enriched in the exosome compartment. The mechanisms for their preferential localization and their biological roles remain to be studied.
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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A new metabolic gene signature in prostate cancer regulated by JMJD3 and EZH2. Oncotarget 2018; 9:23413-23425. [PMID: 29805743 PMCID: PMC5955128 DOI: 10.18632/oncotarget.25182] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Histone methylation is essential for gene expression control. Trimethylated lysine 27 of histone 3 (H3K27me3) is controlled by the balance between the activities of JMJD3 demethylase and EZH2 methyltransferase. This epigenetic mark has been shown to be deregulated in prostate cancer, and evidence shows H3K27me3 enrichment on gene promoters in prostate cancer. To study the impact of this enrichment, a transcriptomic analysis with TaqMan Low Density Array (TLDA) of several genes was studied on prostate biopsies divided into three clinical grades: normal (n = 23) and two tumor groups that differed in their aggressiveness (Gleason score ≤ 7 (n = 20) and >7 (n = 19)). ANOVA demonstrated that expression of the gene set was upregulated in tumors and correlated with Gleason score, thus discriminating between the three clinical groups. Six genes involved in key cellular processes stood out: JMJD3, EZH2, MGMT, TRA2A, U2AF1 and RPS6KA2. Chromatin immunoprecipitation demonstrated collocation of EZH2 and JMJD3 on gene promoters that was dependent on disease stage. Gene set expression was also evaluated on prostate cancer cell lines (DU 145, PC-3 and LNCaP) treated with an inhibitor of JMJD3 (GSK-J4) or EZH2 (DZNeP) to study their involvement in gene regulation. Results showed a difference in GSK-J4 sensitivity under PTEN status of cell lines and an opposite gene expression profile according to androgen status of cells. In summary, our data describe the impacts of JMJD3 and EZH2 on a new gene signature involved in prostate cancer that may help identify diagnostic and therapeutic targets in prostate cancer.
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Yang L, Che Y, Guo L, Zheng B, Wang B, Yang Z, Zhu Y, Li J. Correlation analysis of mesenchymal-epithelial transition factor protein and human epidermal growth receptor 2 protein expression in 1479 cases of lung adenocarcinoma in China. Thorac Cancer 2018; 9:439-444. [PMID: 29400000 PMCID: PMC5879060 DOI: 10.1111/1759-7714.12595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND To investigate the correlation between mesenchymal-epithelial transition factor (C-Met) and human epidermal growth receptor 2 (HER2) protein expression in primary lung adenocarcinoma tissues. METHOD A total of 1479 resected primary lung adenocarcinoma patients were enrolled in the present study for detecting of C-Met and HER2 protein by immunohistochemistry, and correlation analysis was made between the above two biomarkers and related clinicopathological features. RESULT Both C-Met and HER2 proteins were found to stain highly positive in lung adenocarcinomas, and a positive correlation was found between them (χ2 = 118.5, P = 2.707 × 10-21 ). In addition, HER2 protein expression was correlated with sex, pathological stage, lymph node metastasis, and major subtypes; and C-Met was correlated with sex (P < 0.05). CONCLUSION The expression of C-Met and HER2 protein in lung adenocarcinoma is highly correlated, and whether it is synergistic in the targeted therapy of lung adenocarcinoma deserves further study.
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Affiliation(s)
- Lin Yang
- Department of PathologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yiqun Che
- Department of Clinical LaboratoryNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lei Guo
- Department of PathologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Bo Zheng
- Department of PathologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Bingning Wang
- Department of PathologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenxi Yang
- Department of Clinical LaboratoryNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yixiang Zhu
- Department of Medical OncologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Junling Li
- Department of Medical OncologyNational Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Zarogoulidis P, Papadopoulos V, Maragouli E, Papatsibas G, Karapantzos I, Bai C, Huang H. Tumor heterogenicity: multiple needle biopsies from different lesion sites-key to successful targeted therapy and immunotherapy. Transl Lung Cancer Res 2018. [PMID: 29531904 DOI: 10.21037/tlcr.2018.01.07] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Paul Zarogoulidis
- Pulmonary Department-Oncology Unit, "Theageneio" Cancer Hospital, Thessaloniki, Greece
| | | | - Elena Maragouli
- Oncology Department, University of Thessaly, Larissa, Greece
| | | | - Ilias Karapantzos
- Ear, Nose and Throat Department, "Saint Luke" Private Hospital, Panorama, Thessaloniki, Greece
| | - Chong Bai
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Second Military Medical University, Shanghai 200000, China
| | - Haidong Huang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Second Military Medical University, Shanghai 200000, China
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