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Lu X, Chen W, Tian G, Ge F. THEM6 is a prognostic biomarker for breast cancer and is associated with immune infiltration. Sci Rep 2023; 13:21974. [PMID: 38081884 PMCID: PMC10713618 DOI: 10.1038/s41598-023-49379-5] [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: 08/24/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
To characterize the implications of lipid metabolism-related gene thioesterase superfamily member 6 (THEM6) in breast cancer. Several databases including The Cancer Genome Atlas (TCGA) were utilized for our meticulous bioinformatics analysis. We further performed qRT-PCR, immunoblotting and IHC assays to validate the expression of THEM6 in various breast cancer cells and tissues. In addition, we have carried out relevant functional experiments to explore the regulatory role of THEM6 in vitro. Lipid metabolism-related genes are independent factors for overall survival. According to several databases, THEM6 was significantly more expressed in cancerous tissues of breast invasive carcinoma (BRCA) compared to its paracancerous tissues. Furthermore, THEM6 overexpression was correlated with poorer overall survival of BRCA patients, serving as a separate prognostic factor for BRCA. Biological functional analyses revealed that THEM6 was associated with tumor progression and pathogenesis. Finally, we discovered that in BRCA, THEM6 expression was linked to multiple immune cell types. qRT-PCR and Western blotting experiments demonstrated a general upregulation of THEM6 expression in breast carcinoma cells. IHC showed that THEM6 was expressed in both breast cancer tissues and para-cancer tissues, but its expression level was significantly higher in carcinoma tissues. In vitro studies indicated that THEM6 increased proliferation, invasion, and inhibited apoptosis of breast carcinoma cells, while also affecting the cell cycle and promoting cancer progression. Furthermore, THEM6 may influence macrophage recruitment and polarization in the tumor microenvironment by regulating CCL2 secretion, which in turn affects macrophage recruitment in the tumor microenvironment. Our findings indicate that the overexpression of THEM6, which is linked to the development of breast cancer, is a predictor of a poor prognosis and has an impact on the degree of immune cell infiltration. Therefore, THEM6 has the potential to be a valuable target for BRCA.
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Affiliation(s)
- Xingjia Lu
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, 650223, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, 650223, China
- Key Laboratory of Animal Models and Human, Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Yunnan, 650223, China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650223, China
| | - Gengzhou Tian
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, 650223, China
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, 650223, China.
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Li J, Wang J, Liu Z, Guo H, Wei X, Wei Q, Zheng S, Xu X. Tumor-suppressive role of microfibrillar associated protein 4 and its clinical significance as prognostic factor and diagnostic biomarker in hepatocellular carcinoma. J Cancer Res Ther 2022; 18:1919-1925. [PMID: 36647950 DOI: 10.4103/jcrt.jcrt_693_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Objective Revealing microfibrillar-associated protein 4 (MFAP4)'s function and its clinical significance in hepatocellular carcinoma (HCC). Methods Quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting were used to evaluate MFAP4 mRNA and protein expression in paired HCC and paracarcinoma tissues, respectively. MFAP4 serum concentration was detected using enzyme-linked immunosorbent assays in healthy people (n = 30), cirrhosis (n = 15) and HCC patients (n = 80). MFAP4 protein expression was detected in two tissue microarrays (n = 60 and n = 90). Plasmids were transfected into human HCC cell line Bel-7402, and MFAP4 function was determined in vitro in cell experiments. Furthermore, tumorigenicity studies in nude mice served to assess the function of MFAP4 for HCC. Results Both MFAP4 mRNA and protein expression were significantly downregulated in HCC tissue compared with paracarcinoma tissue (P < 0.05). Decreased MFAP4 expression in paracarcinoma tissue was associated with poor postoperative survival in HCC patients (P = 0.027). MFAP4 was also downregulated in HCC sera compared with healthy people (P < 0.05). In vitro, MFAP4 upregulation in Bel-7402 cells induced S phase arrest, promoted apoptosis, and inhibited migration and invasion. Western blotting indicated MFAP4 overexpression increased CDK4, CDK6, pRB, P27, and BCL-XS expression. Tumorigenicity study showed that the upregulation of MFAP4 inhibited the proliferation of Bel-7402 cells in nude mice. Conclusions MFAP4 expression was significantly lower both in sera and tissue of HCC patients. MFAP4 can serve as molecular marker for HCC diagnosis and prognosis. Additionally, MFAP4 acted as an important HCC tumor suppressor by inducing S phase arrest, and promoting apoptosis, cell migration, and invasion.
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Affiliation(s)
- Jie Li
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianguo Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhikun Liu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haijun Guo
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuyong Wei
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Wei
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Xu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine; NHC Key Laboratory of Combined Multi-Organ Transplantation; Institute of Organ Transplantation, Zhejiang University, Hangzhou, China
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Mohammadi A, Sorensen GL, Pilecki B. MFAP4-Mediated Effects in Elastic Fiber Homeostasis, Integrin Signaling and Cancer, and Its Role in Teleost Fish. Cells 2022; 11:cells11132115. [PMID: 35805199 PMCID: PMC9265350 DOI: 10.3390/cells11132115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix (ECM) protein belonging to the fibrinogen-related domain superfamily. MFAP4 is highly expressed in elastin-rich tissues such as lung, blood vessels and skin. MFAP4 is involved in organization of the ECM, regulating proper elastic fiber assembly. On the other hand, during pathology MFAP4 actively contributes to disease development and progression due to its interactions with RGD-dependent integrin receptors. Both tissue expression and circulating MFAP4 levels are associated with various disorders, including liver fibrosis and cancer. In other experimental models, such as teleost fish, MFAP4 appears to participate in host defense as a macrophage-specific innate immune molecule. The aim of this review is to summarize the accumulating evidence that indicates the importance of MFAP4 in homeostasis as well as pathological conditions, discuss its known biological functions with special focus on elastic fiber assembly, integrin signaling and cancer, as well as describe the reported functions of non-mammalian MFAP4 in fish. Overall, our work provides a comprehensive overview on the role of MFAP4 in health and disease.
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Zhang X, Tang J, Kou X, Huang W, Zhu Y, Jiang Y, Yang K, Li C, Hao M, Qu Y, Ma L, Chen C, Shi S, Zhou Y. Proteomic analysis of MSC-derived apoptotic vesicles identifies Fas inheritance to ameliorate haemophilia a via activating platelet functions. J Extracell Vesicles 2022; 11:e12240. [PMID: 36856683 PMCID: PMC9927920 DOI: 10.1002/jev2.12240] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/12/2022] Open
Abstract
Apoptotic vesicles (apoVs) are apoptotic cell-derived nanosized vesicles that play a crucial role in multiple pathophysiological settings. However, their detailed characteristics, specific surface markers, and biological properties are not fully elucidated. In this study, we compared mesenchymal stem cell (MSC)-derived apoVs and exosomes from three different types of MSCs including human bone marrow MSCs (hBMSCs), human adipose MSCs (hASCs), and mouse bone marrow MSCs (mBMSCs). We established a unique protein map of MSC-derived apoVs and identified the differences between apoVs and exosomes in terms of functional protein cargo and surface markers. Furthermore, we identified 13 proteins specifically enriched in apoVs compared to exosomes, which can be used as apoV-specific biomarkers. In addition, we showed that apoVs inherited apoptotic imprints such as Fas to ameliorate haemophilia A in factor VIII knockout mice via binding to the platelets' FasL to activate platelet functions, and therefore rescuing the blood clotting disorder. In summary, we systemically characterized MSC-derived apoVs and identified their therapeutic role in haemophilia A treatment through a previously unknown Fas/FasL linkage mechanism.
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Affiliation(s)
- Xiao Zhang
- Department of ProsthodonticsPeking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental MaterialsBeijing100081China
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Jianxia Tang
- Hunan Key Laboratory of Oral Health Research & Hunan Clinical Research Center of Oral Major Diseases and Oral HealthXiangya School of Stomatology, Xiangya Stomatological Hospital, Central South UniversityChangsha410000China
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Xiaoxing Kou
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat‐Sen University)Ministry of EducationGuangzhou510080China
| | - Weiying Huang
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Yuan Zhu
- Department of ProsthodonticsPeking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental MaterialsBeijing100081China
| | - Yuhe Jiang
- Department of ProsthodonticsPeking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental MaterialsBeijing100081China
| | - Kunkun Yang
- Department of ProsthodonticsPeking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental MaterialsBeijing100081China
| | - Can Li
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Meng Hao
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Yan Qu
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Lan Ma
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
| | - Chider Chen
- Department of Oral and Maxillofacial Surgery and PharmacologyUniversity of Pennsylvania, School of Dental MedicinePhiladelphiaPA 19104USA
| | - Songtao Shi
- South China Center of Craniofacial Stem Cell ResearchHospital of Stomatology, Guanghua School of Stomatology, Sun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat‐Sen University)Ministry of EducationGuangzhou510080China
| | - Yongsheng Zhou
- Department of ProsthodonticsPeking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental MaterialsBeijing100081China
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Tan M, Wang S, Li F, Xu H, Gao J, Zhu L. A methylation-driven genes prognostic signature and the immune microenvironment in epithelial ovarian cancer. Carcinogenesis 2022; 43:635-646. [PMID: 35639961 DOI: 10.1093/carcin/bgac048] [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: 02/15/2022] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant gene methylation has been implicated in the development and progression of tumors. In this study, we aimed to identity methylation driven genes involved in epithelial ovarian cancer (EOC) to establish a prognostic signature for patients with EOC. We identified and verified 6 MDGs that are closely related to the prognosis of ovarian cancer. A prognostic risk score model and nomogram for predicting the prognosis of ovarian cancer were constructed based on the six MDGs. It can also effectively reflect the immune environment and immunotherapy response of ovarian cancer. These MDGs have great significance to the implementation of individualized treatment and disease monitoring of ovarian cancer patients.
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Affiliation(s)
- Mingzi Tan
- Department of Gynecology, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang 110042, Liaoning Province, P R China.,Department of Gynecology, Liaoning Cancer Hospital & Institute, No.44 Xiaoheyan Road, Dadong District, Shenyang 110042, Liaoning Province, P R China
| | - Shengtan Wang
- Department of Gynecology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570011, P.R. China
| | - Feifei Li
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Haoya Xu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P.R. China
| | - Jian Gao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P.R. China
| | - Liancheng Zhu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Shenyang, 110004, P.R. China
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Guo H, Wang L, Deng Y, Ye J. Novel perspectives of environmental proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147588. [PMID: 34023612 DOI: 10.1016/j.scitotenv.2021.147588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/08/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.
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Affiliation(s)
- Huiying Guo
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Institute of Orthopedic Diseases, Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Lili Wang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ying Deng
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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Hara Y, Zhang B, Suzuki A, Yamaguchi S, Adachi J, Tomonaga T, Yasunaga S, Saku K, Aoyama T, Hirano KI. Effect of Tricaprin on Cardiac Proteome in a Mouse Model for Triglyceride Deposit Cardiomyovasculopathy. J Oleo Sci 2020; 69:1569-1577. [PMID: 33177279 DOI: 10.5650/jos.ess20185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Triglyceride deposit cardiomyovasculopathy (TGCV), a rare cardiovascular disorder caused by genetic or acquired dysfunction of adipose triglyceride lipase (ATGL), is marked by defective intracellular lipolysis that results in excessive accumulation of triglycerides (TGs) in the myocardium and coronary arteries, leading to intractable heart failure (HF). We have developed a specific treatment for TGCV using tricaprin, a medium chain TG, as part of a governmental rare disease project in Japan. We recently reported that tricaprin diet improved cardiac TG metabolism and left ventricular function in an ATGL-knockout (KO) mouse, a mouse model for TGCV. Here, we report the effect of tricaprin on the myocardial proteome of KO mice to elucidate the mechanisms of action of tricaprin at protein expression levels. We compared proteomic changes in the hearts of KO mice fed control or tricaprin diet. Tandem mass tag-based shotgun proteomics identified 1832 proteins common to all sample groups. Whole proteomic distribution in the heart was largely up-regulated in KO mice fed control diet. When using cut-off values (>1.5 or <0.67, FDR-adjusted p value<0.01), in fact, 65 proteins were up-regulated whereas only 2 proteins were down-regulated in the hearts of KO mice fed control diet. The former included proteins assigned to "Cardiac Arrhythmia", and "Cardiac Damage" reflecting HF by a toxicity function analysis. One of the latter was Ces1d, which is known to regulate intracellular TG metabolism. These proteomic changes observed in KO mice were dramatically rescued by the tricaprin diet. These results indicated that tricaprin diet ameliorated HF in a TGCV mouse model at protein expression levels and also provided important clues to understand mechanisms for the beneficial effect of tricaprin.
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Affiliation(s)
- Yasuhiro Hara
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Bo Zhang
- Department of Biochemistry, Fukuoka University Medical School
| | - Akira Suzuki
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Satoshi Yamaguchi
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition
| | | | - Keijiro Saku
- General Medical Research Center, Fukuoka University Medical School
| | - Toshiaki Aoyama
- Food Biotechnology Platform Promoting Project, New industry Creation Hatchery Center (NICHe) at Tohoku University
| | - Ken-Ichi Hirano
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
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Guerrero PE, Duran A, Ortiz MR, Castro E, Garcia-Velasco A, Llop E, Peracaula R. Microfibril associated protein 4 (MFAP4) is a carrier of the tumor associated carbohydrate sialyl-Lewis x (sLe x) in pancreatic adenocarcinoma. J Proteomics 2020; 231:104004. [PMID: 33038510 DOI: 10.1016/j.jprot.2020.104004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/04/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Late diagnosis of pancreatic ductal adenocarcinoma (PDA) is one of the reasons of its low 5-year survival rate and it is due to its unspecific symptoms during the first stages of the disease and the lack of reliable serological markers. Since PDA shows an altered glycan expression, here we have focused on finding novel potential biomarkers, namely glycoproteins that express the tumor associated carbohydrate structure sialyl-Lewis x (sLex), which is described in PDA. Through a glycoproteomic approach, we have analyzed target proteins containing sLex from PDA tissues by 2DE and immunodetection techniques, and have identified by mass spectrometry the protein MFAP4 as a carrier of sLex in PDA. MFAP4 showed a higher expression in PDA tissues compared with pancreatic control tissues. In addition, the colocalization of sLex over MFAP4 was found only in PDA and not in control pancreatic tissues. The analysis of MFAP4 expression in PDA cell lines and their secretome, in combination with immunohistochemistry of pancreatic tissues, revealed that MFAP4 was not produced by PDA cells, but it was found in the pancreatic extracellular matrix. The specificity of MFAP4 glycoform containing sLex in PDA tissues shows its relevance as a potential PDA biomarker. SIGNIFICANCE: Despite advances in the field of cancer research, pancreatic ductal adenocarcinoma (PDA) lacks of a specific and sensitive biomarker for its early detection, when curative resection is still possible before metastases arise. Thus, efforts to discover new PDA biomarkers represent the first line in the fight against the increase of its incidence reported in recent years. Glycan alterations on glycoconjugates, such as glycoproteins have emerged as a rich source for the identification of novel cancer markers. In the present work, we aimed to shed light on novel biomarkers based on altered glycosylation in PDA, in particular those glycoproteins of PDA tissues carrying the tumor carbohydrate antigen sialyl-Lewis x (sLex). Through a glycoproteomic approach, we have shown that the glycoprotein MFAP4 carries sLex in PDA tissues and not in control pancreatic tissues. MFAP4 is found in the extracellular matrix in PDA and although its role in cancer progression is unclear, its sLex glycoform could be a potential biomarker in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Pedro Enrique Guerrero
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, 17003 Girona, Spain
| | - Adrià Duran
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, 17003 Girona, Spain
| | - Maria Rosa Ortiz
- Pathology Department, Josep Trueta University Hospital, 17007 Girona, Spain
| | - Ernesto Castro
- Hepato-biliary and Pancreatic Surgery Unit, Josep Trueta University Hospital, 17007 Girona, Spain
| | | | - Esther Llop
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, 17003 Girona, Spain..
| | - Rosa Peracaula
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, 17003 Girona, Spain..
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Hama N, Nishimura K, Hasegawa A, Yuki A, Kume H, Adachi J, Kinoshita M, Ogawa Y, Nakajima S, Nomura T, Watanabe H, Mizukawa Y, Tomonaga T, Shimizu H, Abe R. Galectin-7 as a potential biomarker of Stevens-Johnson syndrome/toxic epidermal necrolysis: identification by targeted proteomics using causative drug-exposed peripheral blood cells. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2019; 7:2894-2897.e7. [PMID: 31100551 DOI: 10.1016/j.jaip.2019.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/22/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Natsumi Hama
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiko Nishimura
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Akito Hasegawa
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akihiko Yuki
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideaki Kume
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Manao Kinoshita
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Youichi Ogawa
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Saeko Nakajima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Nomura
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideaki Watanabe
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Yoshiko Mizukawa
- Department of Dermatology, Kyorin University, School of Medicine, Tokyo, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Riichiro Abe
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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Yang J, Song H, Chen L, Cao K, Zhang Y, Li Y, Hao X. Integrated analysis of microfibrillar-associated proteins reveals MFAP4 as a novel biomarker in human cancers. Epigenomics 2019; 11:1635-1651. [DOI: 10.2217/epi-2018-0080] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: The potential functions and underlying mechanism of microfibrillar-associated proteins (MFAPs) are explored in human cancers. Materials & methods: Here, we examined the expression profiles, prognostic values, epigenetic and genetic alterations of MFAPs in human cancers from public omics repository. Results: Among MFAPs family, MFAP4 was frequently downregulated in the most human cancers and high mRNA expression of MFAP4 significantly correlated with better overall survival in breast cancer. DNA hypermethylation in the promoter of MFAP4 decreased its mRNA expression. MFAP4 strongly associated with pathway in impairment and alteration of the elastic fibers. Conclusion: This integrated analysis provides new insights into MFAPs in human cancers and indicates that MFAP4 could be used as novel biomarker for developing therapies against human cancers.
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Affiliation(s)
- Jue Yang
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
| | - Hui Song
- The Key Laboratory of Endemic & Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang 550004, PR China
- The Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guizhou Province, Guiyang 550004, PR China
| | - Li Chen
- Guiyang University of Chinese Medicine, School of Pharmaceutical Sciences, Guiyang 550025, PR China
| | - Kun Cao
- Department of General Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, PR China
| | - Yongqiang Zhang
- Guizhou University, School of Pharmaceutical Sciences, Guiyang, 550025, PR China
| | - Yanmei Li
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
| | - Xiaojiang Hao
- The State Key Laboratory of Functions & Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province & Chinese Academic of Sciences, Guiyang 550014, PR China
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11
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Yang J, Xie Q, Zhou H, Chang L, Wei W, Wang Y, Li H, Deng Z, Xiao Y, Wu J, Xu P, Hong X. Proteomic Analysis and NIR-II Imaging of MCM2 Protein in Hepatocellular Carcinoma. J Proteome Res 2018; 17:2428-2439. [DOI: 10.1021/acs.jproteome.8b00181] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing Yang
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Qi Xie
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Center for Experimental Basic Medical Education, School of Basic Medical Sciences, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan 430071, China
| | - Hui Zhou
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yin Wang
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hong Li
- Pathology Department, Binzhou Medical University Hospital, Binzhou 256600, China
| | - Zixin Deng
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yuling Xiao
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Junzhu Wu
- Center for Experimental Basic Medical Education, School of Basic Medical Sciences, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan 430071, China
| | - Ping Xu
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Anhui Medical University, Hefei 230032, China
| | - Xuechuan Hong
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Medical College, Tibet University, Lasa 850000, China
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12
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Wang K, Wang Y, Wang X, Ren Q, Han S, Ding L, Li Z, Zhou X, Li W, Zhang L. Comparative salivary proteomics analysis of children with and without dental caries using the iTRAQ/MRM approach. J Transl Med 2018; 16:11. [PMID: 29351798 PMCID: PMC5775567 DOI: 10.1186/s12967-018-1388-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/15/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Dental caries is a major worldwide oral disease afflicting a large proportion of children. As an important host factor of caries susceptibility, saliva plays a significant role in the occurrence and development of caries. The aim of the present study was to characterize the healthy and cariogenic salivary proteome and determine the changes in salivary protein expression of children with varying degrees of active caries, also to establish salivary proteome profiles with a potential therapeutic use against dental caries. METHODS In this study, unstimulated saliva samples were collected from 30 children (age 10-12 years) with no dental caries (NDC, n = 10), low dental caries (LDC, n = 10), and high dental caries (HDC, n = 10). Salivary proteins were extracted, reduced, alkylated, trypsin digested and labeled with isobaric tags for relative and absolute quantitation, and then they were analyzed with GO annotation, biological pathway analysis, hierarchical clustering analysis, and protein-protein interaction analysis. Targeted verifications were then performed using multiple reaction monitoring mass spectrometry. RESULTS A total of 244 differentially expressed proteins annotated with GO annotation in biological processes, cellular component and molecular function were identified in comparisons among children with varying degrees of active caries. A number of caries-related proteins as well as pathways were identified in this study. As compared with caries-free children, the most significantly enriched pathways involved by the up-regulated proteins in LDC and HDC were the ubiquitin mediated proteolysis pathway and African trypanosomiasis pathway, respectively. Subsequently, we selected 53 target proteins with differential expression in different comparisons, including mucin 7, mucin 5B, histatin 1, cystatin S and cystatin SN, basic salivary proline rich protein 2, for further verification using MRM assays. Protein-protein interaction analysis of these proteins revealed complex protein interaction networks, indicating synergistic action of salivary proteins in caries resistance or cariogenicity. CONCLUSIONS Overall, our results afford new insight into the salivary proteome of children with dental caries. These findings might have bright prospect in future in developing novel biomimetic peptides with preventive and therapeutic benefits for childhood caries.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Yufei Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Xiuqing Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Qian Ren
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Sili Han
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Longjiang Ding
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Zhongcheng Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Wei Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
| | - Linglin Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
- Department of Cariology and Endodontics West China Hospital of Stomatology, Sichuan University, No. 14, Section 3 of Renmin South Road, Chengdu, Sichuan China
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13
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Zhao T, Wu J, Liu X, Zhang L, Chen G, Lu H. Diagnosis of thymic epithelial tumor subtypes by a quantitative proteomic approach. Analyst 2018; 143:2491-2500. [PMID: 29645059 DOI: 10.1039/c8an00218e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This study shows the first depth proteomic profiling of all TET subtypes and six candidate biomarkers were identified and validated.
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Affiliation(s)
- Ting Zhao
- Institutes of Biomedical Sciences and Department of Chemistry
- Fudan University
- Shanghai 200032
- P.R. China
| | - Jie Wu
- Department of Pathology
- Zhongshan Hospital
- Fudan University
- Shanghai 200032
- P.R. China
| | - Xiaohui Liu
- Institutes of Biomedical Sciences and Department of Chemistry
- Fudan University
- Shanghai 200032
- P.R. China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Department of Chemistry
- Fudan University
- Shanghai 200032
- P.R. China
| | - Gang Chen
- Department of Pathology
- Zhongshan Hospital
- Fudan University
- Shanghai 200032
- P.R. China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Department of Chemistry
- Fudan University
- Shanghai 200032
- P.R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
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14
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Quantitation of putative colorectal cancer biomarker candidates in serum extracellular vesicles by targeted proteomics. Sci Rep 2017; 7:12782. [PMID: 28986585 PMCID: PMC5630664 DOI: 10.1038/s41598-017-13092-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/19/2017] [Indexed: 02/07/2023] Open
Abstract
At the moment, there is no sensitive clinical test for detecting early-stage colorectal cancer (CRC). Target proteomics has enabled high-throughput verification of hundreds of biomarker candidate proteins. Using this technology, we verified 725 previously reported CRC biomarker candidate proteins that are functionally correlated with CRC in extracellular vesicles (EVs) from patients. Of these, 356 proteins were quantified, and 34 peptides (22 proteins) showed significant differences in the serum EVs between healthy controls and CRC patients of two independent cohorts (n = 77 and 84). These peptides were evaluated as single or multiple markers, and four single peptides in annexin family proteins and eight combinations of peptides showed area under the curve > 0.9 for discriminating between healthy controls and CRC patients. The sensitivities of annexins A3, A4, and A11 peptides for detecting early-stage CRC greatly exceed those of carcinoembryonic antigen. These peptides are promising biomarkers for early detection of CRC.
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15
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Functional proteomics outlines the complexity of breast cancer molecular subtypes. Sci Rep 2017; 7:10100. [PMID: 28855612 PMCID: PMC5577137 DOI: 10.1038/s41598-017-10493-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/10/2017] [Indexed: 12/30/2022] Open
Abstract
Breast cancer is a heterogeneous disease comprising a variety of entities with various genetic backgrounds. Estrogen receptor-positive, human epidermal growth factor receptor 2-negative tumors typically have a favorable outcome; however, some patients eventually relapse, which suggests some heterogeneity within this category. In the present study, we used proteomics and miRNA profiling techniques to characterize a set of 102 either estrogen receptor-positive (ER+)/progesterone receptor-positive (PR+) or triple-negative formalin-fixed, paraffin-embedded breast tumors. Protein expression-based probabilistic graphical models and flux balance analyses revealed that some ER+/PR+ samples had a protein expression profile similar to that of triple-negative samples and had a clinical outcome similar to those with triple-negative disease. This probabilistic graphical model-based classification had prognostic value in patients with luminal A breast cancer. This prognostic information was independent of that provided by standard genomic tests for breast cancer, such as MammaPrint, OncoType Dx and the 8-gene Score.
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16
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Gajbhiye A, Dabhi R, Taunk K, Jagadeeshaprasad MG, RoyChoudhury S, Mane A, Bayatigeri S, Chaudhury K, Santra MK, Rapole S. Multipronged quantitative proteomics reveals serum proteome alterations in breast cancer intrinsic subtypes. J Proteomics 2017; 163:1-13. [DOI: 10.1016/j.jprot.2017.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/29/2022]
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17
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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18
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Nie CH, Wan SM, Tomljanovic T, Treer T, Hsiao CD, Wang WM, Gao ZX. Comparative proteomics analysis of teleost intermuscular bones and ribs provides insight into their development. BMC Genomics 2017; 18:147. [PMID: 28183283 PMCID: PMC5301324 DOI: 10.1186/s12864-017-3530-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/31/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Intermuscular bones (IBs) and ribs both are a part of skeletal system in teleosts, but with different developing process. The chemical composition of fish IBs and ribs as well as the underlying mechanism about their development have not been investigated. In the present study, histological structures showed that one bone cavity containing osteoclasts were existed in ribs, but not in IBs of Megalobrama amblycephala. We constructed the first proteomics map for fish bones including IBs and ribs, and identified the differentially expressed proteins between IBs and ribs through iTRAQ LC-MS/MS proteomic analysis. RESULTS The proteins extracted from IBs and ribs at 1- to 2-year old M. amblycephala were quantified 2,342 proteins, with 1,451 proteins annotated with GO annotation in biological processes, molecular function and cellular component. A number of bone related proteins as well as pathways were identified in the study. A total of 93 and 154 differently expressed proteins were identified in comparison groups of 1-IB-vs-1-Rib and 2-IB-vs-2-Rib, which indicated the obvious differences of chemical composition between these two bone tissues. The two proteins (vitronectin b precursor and matrix metalloproteinase-2) related to osteoclasts differentiation were significantly up-regulated in ribs compared with IBs (P < 0.05), which was in accordance with the results from histological structures. In comparison groups of 1-IB-vs-2-IB and 1-Rib-vs-2-Rib, 33 and 51 differently expressed proteins were identified and the function annotation results showed that these proteins were involved in regulating bone development and differentiation. Subsequently, 11 and 13 candidate proteins in comparison group of 1-IB-vs-1-Rib and 1-IB-vs-2-IB related to bone development were validated by MRM assays. CONCLUSIONS Our present study suggested the different key proteins involved in the composition of fish ribs and IBs as well as their growth development. These findings could provide important clues towards further understanding of fish skeletal system and the roles of proteins playing in regulating diverse biological processes in fish.
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Affiliation(s)
- Chun-Hong Nie
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
| | - Shi-Ming Wan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
| | - Tea Tomljanovic
- Department for Fisheries, Beekeeping, Game management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Tomislav Treer
- Department for Fisheries, Beekeeping, Game management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070 Hubei China
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Uzozie AC, Selevsek N, Wahlander A, Nanni P, Grossmann J, Weber A, Buffoli F, Marra G. Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis. Mol Cell Proteomics 2017; 16:407-427. [PMID: 28062797 DOI: 10.1074/mcp.m116.062273] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
Targeted proteomic methods can accelerate the verification of multiple tumor marker candidates in large series of patient samples. We utilized the targeted approach known as selected/multiple reaction monitoring (S/MRM) to verify potential protein markers of colorectal adenoma identified by our group in previous transcriptomic and quantitative shotgun proteomic studies of a large cohort of precancerous colorectal lesions. We developed SRM assays to reproducibly detect and quantify 25 (62.5%) of the 40 selected proteins in an independent series of precancerous and cancerous tissue samples (19 adenoma/normal mucosa pairs; 17 adenocarcinoma/normal mucosa pairs). Twenty-three proteins were significantly up-regulated (n = 17) or downregulated (n = 6) in adenomas and/or adenocarcinomas, as compared with normal mucosa (linear fold changes ≥ ±1.3, adjusted p value <0.05). Most changes were observed in both tumor types (up-regulation of ANP32A, ANXA3, SORD, LDHA, LCN2, NCL, S100A11, SERPINB5, CDV3, OLFM4, and REG4; downregulation of ARF6 and PGM5), and a five-protein biomarker signature distinguished neoplastic tissue from normal mucosa with a maximum area under the receiver operating curve greater than 0.83. Other changes were specific for adenomas (PPA1 and PPA2 up-regulation; KCTD12 downregulation) or adenocarcinoma (ANP32B, G6PD, RCN1, and SET up-regulation; downregulated AKR1B1, APEX1, and PPA1). Some changes significantly correlated with a few patient- or tumor-related phenotypes. Twenty-two (96%) of the 23 proteins have a potential to be released from the tumors into the bloodstream, and their detectability in plasma has been previously reported. The proteins identified in this study expand the pool of biomarker candidates that can be used to develop a standardized precolonoscopy blood test for the early detection of colorectal tumors.
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Affiliation(s)
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Asa Wahlander
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Paolo Nanni
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, University/ETH Zurich, Zurich, Switzerland
| | - Achim Weber
- ¶Institute of Surgical Pathology, University of Zurich, Switzerland
| | - Federico Buffoli
- ‖ Gastroenterology and Endoscopy Unit, Hospital of Cremona, Italy
| | - Giancarlo Marra
- From the ‡Institute of Molecular Cancer Research, University of Zurich, Switzerland;
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Guerin M, Gonçalves A, Toiron Y, Baudelet E, Audebert S, Boyer JB, Borg JP, Camoin L. How may targeted proteomics complement genomic data in breast cancer? Expert Rev Proteomics 2016; 14:43-54. [PMID: 27813428 DOI: 10.1080/14789450.2017.1256776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Breast cancer (BC) is the most common female cancer in the world and was recently deconstructed in different molecular entities. Although most of the recent assays to characterize tumors at the molecular level are genomic-based, proteins are the actual executors of cellular functions and represent the vast majority of targets for anticancer drugs. Accumulated data has demonstrated an important level of quantitative and qualitative discrepancies between genomic/transcriptomic alterations and their protein counterparts, mostly related to the large number of post-translational modifications. Areas covered: This review will present novel proteomics technologies such as Reverse Phase Protein Array (RPPA) or mass-spectrometry (MS) based approaches that have emerged and that could progressively replace old-fashioned methods (e.g. immunohistochemistry, ELISA, etc.) to validate proteins as diagnostic, prognostic or predictive biomarkers, and eventually monitor them in the routine practice. Expert commentary: These different targeted proteomic approaches, able to complement genomic data in BC and characterize tumors more precisely, will permit to go through a more personalized treatment for each patient and tumor.
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Affiliation(s)
- Mathilde Guerin
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France.,b Department of Medical Oncology , Institut Paoli-Calmettes , Marseille , France
| | - Anthony Gonçalves
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France.,b Department of Medical Oncology , Institut Paoli-Calmettes , Marseille , France
| | - Yves Toiron
- b Department of Medical Oncology , Institut Paoli-Calmettes , Marseille , France
| | - Emilie Baudelet
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France
| | - Stéphane Audebert
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France
| | - Jean-Baptiste Boyer
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France
| | - Jean-Paul Borg
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France
| | - Luc Camoin
- a Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique , Marseille , France
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21
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Su Y, Xu L, Wang Z, Peng Q, Yang Y, Chen Y, Que Y. Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane. BMC Genomics 2016; 17:800. [PMID: 27733120 PMCID: PMC5062822 DOI: 10.1186/s12864-016-3146-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 10/05/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the development of genome-assisted resistance breeding programs. Furthermore, the molecular basis of sugarcane response to S. scitamineum infection at the proteome level was incomplete and combining proteomic and transcriptional analysis has not yet been conducted. RESULTS We identified 273 and 341 differentially expressed proteins in sugarcane smut-resistant (Yacheng05-179) and susceptible (ROC22) genotypes at 48 h after inoculation with S. scitamineum by employing an isobaric tag for relative and absolute quantification (iTRAQ). The proteome quantitative data were then validated by multiple reaction monitoring (MRM). The integrative analysis showed that the correlations between the quantitative proteins and the corresponding genes that was obtained in our previous transcriptome study were poor, which were 0.1502 and 0.2466 in Yacheng05-179 and ROC22, respectively, thereby revealing a post-transcriptional event during Yacheng05-179-S. scitamineum incompatible interaction and ROC22-S. scitamineum compatible interaction. Most differentially expressed proteins were closely related to sugarcane smut resistance such as beta-1,3-glucanase, peroxidase, pathogenesis-related protein 1 (PR1), endo-1,4-beta-xylanase, heat shock protein, and lectin. Ethylene and gibberellic acid pathways, phenylpropanoid metabolism and PRs, such as PR1, PR2, PR5 and PR14, were more active in Yacheng05-179, which suggested of their possible roles in sugarcane smut resistance. However, calcium signaling, reactive oxygen species, nitric oxide, and abscisic acid pathways in Yacheng05-179 were repressed by S. scitamineum and might not be crucial for defense against this particular pathogen. CONCLUSIONS These results indicated complex resistance-related events in sugarcane-S. scitamineum interaction, and provided novel insights into the molecular mechanism underlying the response of sugarcane to S. scitamineum infection.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuqing Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qiong Peng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuting Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yun Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Collaborative Innovation Center of Sugarcane Industry, Guangxi University, Nanning, 530005 China
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22
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Gajbhiye A, Dabhi R, Taunk K, Vannuruswamy G, RoyChoudhury S, Adhav R, Seal S, Mane A, Bayatigeri S, Santra MK, Chaudhury K, Rapole S. Urinary proteome alterations in HER2 enriched breast cancer revealed by multipronged quantitative proteomics. Proteomics 2016; 16:2403-18. [DOI: 10.1002/pmic.201600015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/27/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Akshada Gajbhiye
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
- Savitribai Phule Pune University; Ganeshkhind Pune Maharashtra India
| | - Raju Dabhi
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Khushman Taunk
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Sourav RoyChoudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Ragini Adhav
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | | | - Anupama Mane
- Grant Medical Foundation; Ruby Hall Clinic; Pune Maharashtra India
| | | | - Manas K. Santra
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
| | - Koel Chaudhury
- School of Medical Science and Technology; Indian Institute of Technology; Kharagpur West Bengal India
| | - Srikanth Rapole
- Proteomics Lab; National Centre for Cell Science; Ganeshkhind Pune Maharashtra India
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23
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Zhang L, Jiang H, Xu G, Chu N, Xu N, Wen H, Gu B, Liu J, Mao S, Na R, Jing Y, Ding Q, Zhang Y, Wang L. iTRAQ-based quantitative proteomic analysis reveals potential early diagnostic markers of clear-cell Renal cell carcinoma. Biosci Trends 2016; 10:210-9. [PMID: 27319973 DOI: 10.5582/bst.2016.01055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Early detection is the key to improve the prognosis of kidney cancer. This study profiled and identified differentially expressed serum proteins in stage T1a renal cell carcinoma (RCC) using isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. A total amount of 99 serum samples including 29 patients with ccRCC, 24 patients with a benign kidney mass, 28 patients with another type of urological tumor (20 cases of transitional cell carcinoma and 8 cases of prostate cancer or a male genital tumor), and 18 healthy controls were subjected to iTRAQ-based mass spectrometry. ProteinPilot software was used to identify the differentially expressed serum proteins in RCC compared to the other three populations. Hierarchical clustering analysis according to The Cancer Genome Atlas (TCGA) RCC database was then performed as the cross-platform validation. Immunohistochemistry was performed to verify the expression of selected proteins in tissue samples from these subjects. iTRAQ identified 27 differentially expressed serum proteins in the RCC patients, and 11 of these proteins were cross validated in RCC tissues from the TCGA database. The expression of C1QC, C1QB, S100A8, S100A9, ceruplasmin, and lumican was verified and associated with the tumor stage and/or grade. There were 27 differentially expressed proteins in early-stage RCC identified by iTRAQ; among them, the expression of C1QC, C1QB, S100A8, S100A9, ceruplasmin, and lumican were associated with the tumor stage and/or grade. Further studies are needed to confirm these data for their use as biomarkers for the early detection of RCC.
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Affiliation(s)
- Limin Zhang
- Department of Urology, Huashan Hospital, Fudan University
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24
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Large-scale proteome analysis of abscisic acid and ABSCISIC ACID INSENSITIVE3-dependent proteins related to desiccation tolerance in Physcomitrella patens. Biochem Biophys Res Commun 2016; 471:589-95. [PMID: 26869511 DOI: 10.1016/j.bbrc.2016.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 01/30/2023]
Abstract
Desiccation tolerance is an ancestral feature of land plants and is still retained in non-vascular plants such as bryophytes and some vascular plants. However, except for seeds and spores, this trait is absent in vegetative tissues of vascular plants. Although many studies have focused on understanding the molecular basis underlying desiccation tolerance using transcriptome and proteome approaches, the critical molecular differences between desiccation tolerant plants and non-desiccation plants are still not clear. The moss Physcomitrella patens cannot survive rapid desiccation under laboratory conditions, but if cells of the protonemata are treated by the phytohormone abscisic acid (ABA) prior to desiccation, it can survive 24 h exposure to desiccation and regrow after rehydration. The desiccation tolerance induced by ABA (AiDT) is specific to this hormone, but also depends on a plant transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3). Here we report the comparative proteomic analysis of AiDT between wild type and ABI3 deleted mutant (Δabi3) of P. patens using iTRAQ (Isobaric Tags for Relative and Absolute Quantification). From a total of 1980 unique proteins that we identified, only 16 proteins are significantly altered in Δabi3 compared to wild type after desiccation following ABA treatment. Among this group, three of the four proteins that were severely affected in Δabi3 tissue were Arabidopsis orthologous genes, which were expressed in maturing seeds under the regulation of ABI3. These included a Group 1 late embryogenesis abundant (LEA) protein, a short-chain dehydrogenase, and a desiccation-related protein. Our results suggest that at least three of these proteins expressed in desiccation tolerant cells of both Arabidopsis and the moss are very likely to play important roles in acquisition of desiccation tolerance in land plants. Furthermore, our results suggest that the regulatory machinery of ABA- and ABI3-mediated gene expression for desiccation tolerance might have evolved in ancestral land plants before the separation of bryophytes and vascular plants.
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25
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Narumi R, Tomonaga T. Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM). Methods Mol Biol 2016; 1355:85-101. [PMID: 26584920 DOI: 10.1007/978-1-4939-3049-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mass spectrometry-based phosphoproteomics is an indispensible technique used in the discovery and quantification of phosphorylation events on proteins in biological samples. The application of this technique to tissue samples is especially useful for the discovery of biomarkers as well as biological studies. We herein describe the application of a large-scale phosphoproteome analysis and SRM/MRM-based quantitation to develop a strategy for the systematic discovery and validation of biomarkers using tissue samples.
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Affiliation(s)
- Ryohei Narumi
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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26
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Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG. The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Rev Proteomics 2015; 13:99-114. [PMID: 26581546 DOI: 10.1586/14789450.2016.1122529] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) -based proteomics has become an indispensable tool with broad applications in systems biology and biomedical research. With recent advances in liquid chromatography (LC) and MS instrumentation, LC-MS is making increasingly significant contributions to clinical applications, especially in the area of cancer biomarker discovery and verification. To overcome challenges associated with analyses of clinical samples (for example, a wide dynamic range of protein concentrations in bodily fluids and the need to perform high throughput and accurate quantification of candidate biomarker proteins), significant efforts have been devoted to improve the overall performance of LC-MS-based clinical proteomics platforms. Reviewed here are the recent advances in LC-MS and its applications in cancer biomarker discovery and quantification, along with the potentials, limitations and future perspectives.
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Affiliation(s)
- Hui Wang
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tujin Shi
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tao Liu
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Jacob Kagan
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Sudhir Srivastava
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Richard D Smith
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Karin D Rodland
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - David G Camp
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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27
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Pendharkar N, Gajbhiye A, Taunk K, RoyChoudhury S, Dhali S, Seal S, Mane A, Abhang S, Santra MK, Chaudhury K, Rapole S. Quantitative tissue proteomic investigation of invasive ductal carcinoma of breast with luminal B HER2 positive and HER2 enriched subtypes towards potential diagnostic and therapeutic biomarkers. J Proteomics 2015; 132:112-30. [PMID: 26642762 DOI: 10.1016/j.jprot.2015.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/16/2015] [Accepted: 11/26/2015] [Indexed: 02/09/2023]
Abstract
Worldwide, breast cancer is one of the frequently diagnosed cancers in women with high mortality if not diagnosed at early stage. Although biomarker discoveries through various proteomic approaches have been studied in breast cancer, a limited number of studies have explored the invasive ductal carcinoma with Luminal B HER2 positive (LB) and HER2 enriched (HE) subtypes. The present study employed the complementary quantitative proteomic approaches to find a panel of markers that could discriminate LB and HE subtypes as well as early (ES) and late stages (LS) of these subtypes. A total of 67 and 68 differentially expressed proteins were identified by DIGE for the subtype and stage wise categories, respectively. Multivariate statistical analysis was employed to identify the set of most significant proteins, which could discriminate between these two subtypes and also early and late stages under study. Immunoblotting and MRM based validation in a separate cohort of samples confirmed that panel of biosignatures for LB are APOA1, GELS, HS90B, EF1A1, NHRF1 and PRDX3 and for HE are PRDX1, CATD, CALR, ATPB and CH60. For the diagnosis of early and late stages the potential markers are TPM4, CATD, PRDX3, ANXA3, HSPB1 and CALR, TRFE, GELS, CH60, CAPG, NHRF1, 1433G, GRP78 respectively.
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Affiliation(s)
- Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; B. J. Medical College, Sassoon Hospital, Pune 411001, MH, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Sourav RoyChoudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | - Anupama Mane
- Grant Medical Foundation, Ruby Hall Clinic, Pune 411001, MH, India
| | | | - Manas K Santra
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
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28
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Dimayacyac-Esleta BRT, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ. Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. Anal Chem 2015; 87:12016-23. [PMID: 26554430 DOI: 10.1021/acs.analchem.5b03639] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Toward comprehensive membrane proteomic profiling for small amounts of samples (10 μg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (∼15 min.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides encompassing transmembrane helix (TMH) domain, as compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. Almost 5000 proteins (∼60% membrane proteins) can be identified in only 10 μg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The method allowed up to 9- and 6-fold increase in the identification of unique hydrophobic and hydrophilic peptides, respectively. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane subproteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several up-regulated membrane proteins with key roles in lung cancer progression.
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Affiliation(s)
- Baby Rorielyn T Dimayacyac-Esleta
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines.,Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Chia-Feng Tsai
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wai-Kok Choong
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Tai-Du Lin
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Biochemical Sciences, National Taiwan University , Taipei 10617, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University , Taipei 10617, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital , Taipei 10617, Taiwan.,National Taiwan University College of Medicine , Taipei 10051, Taiwan.,Institute of Biomedical Science, Academia Sinica , Taipei 115, Taiwan
| | - Susan D Arco
- Institute of Chemistry, University of the Philippines , Diliman Quezon City 1101, Philippines
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica , Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30013, Taiwan.,Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan
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29
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Wang Y, Shan Q, Hou G, Zhang J, Bai J, Lv X, Xie Y, Zhu H, Su S, Li Y, Zi J, Lin L, Han W, Zhao X, Wang H, Xu N, Wu L, Lou X, Liu S. Discovery of potential colorectal cancer serum biomarkers through quantitative proteomics on the colonic tissue interstitial fluids from the AOM-DSS mouse model. J Proteomics 2015; 132:31-40. [PMID: 26581642 DOI: 10.1016/j.jprot.2015.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/25/2015] [Accepted: 11/10/2015] [Indexed: 01/29/2023]
Abstract
UNLABELLED Quantitative proteomic analysis was performed using iTRAQ to discover colorectal cancer (CRC)-related proteins in tissue interstitial fluids (TIFs). A typical inflammation-related CRC mouse model was generated using azoxymethane-dextran sodium sulfate (AOM-DSS), and TIFs were collected from these mice in four stages during CRC development. Using stringent criteria, a total of 144 proteins displayed changes in their abundances during tumor growth, including 45 that consecutively increased, 17 that consecutively decreased and 82 that changed irregularly. Of these 144 proteins, 24 of the consecutively changed proteins were measured using MRM in individual TIF samples, and 18 were verified. Twelve proteins verified to be consecutively increased in TIFs were examined using MRM to evaluate changes in their abundance in individual mouse serum samples. The abundances of leucine-rich alpha-2-glycoprotein 1 (LRG1), tubulin beta-5 chain (TUBB5) and immunoglobulin J chain (IGJ) were significantly higher in CRC mice than in control mice. Using clinical samples and MRM, we further verified that LRG1 and TUBB5 are potential CRC serum biomarkers. These data demonstrate that coupling dynamic TIF proteomics with targeted serum proteomics in an animal model is a promising avenue for pursuing the discovery of tumor serum biomarkers. BIOLOGICAL SIGNIFICANCE Colorectal cancer (CRC) is one of the most dangerous diseases worldwide. However, few of CRC biomarkers possess satisfied specificity and sensitivity in clinical practices. Exploration of more CRC biomarkers, especially in serum, is an urgent and also a time-consuming campaign in the CRC study. Our study demonstrates that quantitatively evaluating the phase-dependent proteins in colonic tissue interstitial fluids from AOM-DSS mice is a feasible and effective way for exploration of the CRC-related proteins and the potential serum biomarkers. We identified two proteins, LRG1 and TUBB5, which may be practicable in human clinical samples as CRC serum biomarkers. To sum up, this study provides a novel angle to explore the critical factors in tumorigenesis and a new pipeline for potential serum biomarker discovery and verification.
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Affiliation(s)
- Yang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guixue Hou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolei Lv
- Beijing Protein Innovation, Beijing 101318, China
| | - Yingying Xie
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huishan Zhu
- Beijing Protein Innovation, Beijing 101318, China
| | - Siyuan Su
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Beijing Protein Innovation, Beijing 101318, China
| | - Jin Zi
- Proteomics Division, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wenxiao Han
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xinhua Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Lin Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Proteomics Division, BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
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30
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Liu L, Li G, Sun P, Lei C, Huang Q. Experimental verification and molecular basis of active immunization against fungal pathogens in termites. Sci Rep 2015; 5:15106. [PMID: 26458743 PMCID: PMC4602225 DOI: 10.1038/srep15106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/15/2015] [Indexed: 01/30/2023] Open
Abstract
Termites are constantly exposed to many pathogens when they nest and forage in the field, so they employ various immune strategies to defend against pathogenic infections. Here, we demonstrate that the subterranean termite Reticulitermes chinensis employs active immunization to defend against the entomopathogen Metarhizium anisopliae. Our results showed that allogrooming frequency increased significantly between fungus-treated termites and their nestmates. Through active social contact, previously healthy nestmates only received small numbers of conidia from fungus-treated individuals. These nestmates experienced low-level fungal infections, resulting in low mortality and apparently improved antifungal defences. Moreover, infected nestmates promoted the activity of two antioxidant enzymes (SOD and CAT) and upregulated the expression of three immune genes (phenoloxidase, transferrin, and termicin). We found 20 differentially expressed proteins associated with active immunization in R. chinensis through iTRAQ proteomics, including 12 stress response proteins, six immune signalling proteins, and two immune effector molecules. Subsequently, two significantly upregulated (60S ribosomal protein L23 and isocitrate dehydrogenase) and three significantly downregulated (glutathione S-transferase D1, cuticle protein 19, and ubiquitin conjugating enzyme) candidate immune proteins were validated by MRM assays. These findings suggest that active immunization in termites may be regulated by different immune proteins.
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Affiliation(s)
- Long Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ganghua Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Pengdong Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Chaoliang Lei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiuying Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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31
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Pernikářová V, Bouchal P. Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps. Expert Rev Proteomics 2015; 12:651-67. [PMID: 26456120 DOI: 10.1586/14789450.2015.1094381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics - based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps - now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.
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Affiliation(s)
- Vendula Pernikářová
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic
| | - Pavel Bouchal
- a Masaryk University , Faculty of Science, Department of Biochemistry , Kotlářská 2, 61137 Brno , Czech Republic.,b Masaryk Memorial Cancer Institute , Regional Centre for Applied Molecular Oncology , Žlutý kopec 7, 65653 Brno , Czech Republic
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32
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res 2015; 14:2807-18. [DOI: 10.1021/acs.jproteome.5b00315] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Ruedi Aebersold
- Department
of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, 8092 Zurich, Switzerland
| | | | - Emma Niméus
- Division
of Surgery, Skåne University Hospital, 221 85 Lund, Sweden
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Sato M, Matsubara T, Adachi J, Hashimoto Y, Fukamizu K, Kishida M, Yang YA, Wakefield LM, Tomonaga T. Differential Proteome Analysis Identifies TGF-β-Related Pro-Metastatic Proteins in a 4T1 Murine Breast Cancer Model. PLoS One 2015; 10:e0126483. [PMID: 25993439 PMCID: PMC4436378 DOI: 10.1371/journal.pone.0126483] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/03/2015] [Indexed: 01/04/2023] Open
Abstract
Transforming growth factor-β (TGF-β) has a dual role in tumorigenesis, acting as either a tumor suppressor or as a pro-oncogenic factor in a context-dependent manner. Although TGF-β antagonists have been proposed as anti-metastatic therapies for patients with advanced stage cancer, how TGF-β mediates metastasis-promoting effects is poorly understood. Establishment of TGF-β-related protein expression signatures at the metastatic site could provide new mechanistic information and potentially allow identification of novel biomarkers for clinical intervention to discriminate TGF-β oncogenic effects from tumor suppressive effects. In the present study, we found that systemic administration of the TGF-β receptor kinase inhibitor, SB-431542, significantly inhibited lung metastasis from transplanted 4T1 mammary tumors in Balb/c mice. The differentially expressed proteins in the comparison of lung metastases from SB-431542 treated and control vehicle-treated groups were analyzed by a quantitative LTQ Orbitrap Velos system coupled with stable isotope dimethyl labeling. A total of 36,239 peptides from 6,694 proteins were identified, out of which 4,531 proteins were characterized as differentially expressed. A subset of upregulated proteins in the control group was validated by western blotting and immunohistochemistry. The eukaryotic initiation factor (eIF) family members constituted the most enriched protein pathway in vehicle-treated compared with SB-43512-treated lung metastases, suggesting that increased protein expression of specific eIF family members, especially eIF4A1 and eEF2, is related to the metastatic phenotype of advanced breast cancer and can be down-regulated by TGF-β pathway inhibitors. Thus our proteomic approach identified eIF pathway proteins as novel potential mediators of TGF-β tumor-promoting activity.
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Affiliation(s)
- Misako Sato
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan; Department of Hepatology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Tsutomu Matsubara
- Department of Anatomy and Regenerative Biology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan
| | - Yuuki Hashimoto
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan
| | - Kazuna Fukamizu
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan
| | - Marina Kishida
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan
| | - Yu-An Yang
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, Proteome Research Center, National Institute of Biomedical Innovation, Saito, Osaka, Japan
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35
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Kurono S, Kaneko Y, Matsuura S, Niwayama S. Quantification of proteins using (13)C7-labeled and unlabeled iodoacetanilide by nano liquid chromatography/nanoelectrospray ionization and by selected reaction monitoring mass spectrometry. Bioorg Med Chem Lett 2015; 25:1110-6. [PMID: 25619637 DOI: 10.1016/j.bmcl.2014.12.090] [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: 11/01/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022]
Abstract
The combination of cysteine-specific modifiers, iodoacetanilide (IAA) and (13)C7-labeled iodoacetanilide ((13)C7-IAA), has been applied to absolute quantification of proteins. The selected reaction monitoring (SRM) with the use of nano liquid chromatography/nanoelectrospray ionization ion trap mass spectrometry (nano LC/nano-ESI-IT-MS) analysis was applied to precise quantification of three commercial proteins. Good correlation was observed between the theoretical ratios and observed ratios for all these proteins both in a simple buffer solution and in a complex protein environment. Due to efficient tagging, this method does not require separate synthesis of isotope-labeled peptides for the SRM studies. Therefore, this method is expected to be a useful tool for proteomics research.
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Affiliation(s)
- Sadamu Kurono
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory Chemicals Division, Wako Pure Chemical Industries, Ltd., 3-1-2 Doshomachi, Chuo-ku, Osaka, Osaka 540-8605, Japan
| | - Yuka Kaneko
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory Chemicals Division, Wako Pure Chemical Industries, Ltd., 3-1-2 Doshomachi, Chuo-ku, Osaka, Osaka 540-8605, Japan
| | - Shuji Matsuura
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satomi Niwayama
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA; Department of Ophthalmology and Visual Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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36
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Quantitative iTRAQ LC-MS/MS proteomics reveals the proteome profiles of DF-1 cells after infection with subgroup J Avian leukosis virus. BIOMED RESEARCH INTERNATIONAL 2015; 2015:395307. [PMID: 25632391 PMCID: PMC4302370 DOI: 10.1155/2015/395307] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/09/2014] [Accepted: 12/17/2014] [Indexed: 12/18/2022]
Abstract
Avian leukosis virus subgroup J (ALV-J) is an avian oncogenic retrovirus that can induce various clinical tumors and has caused severe economic losses in China. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of ALV-J infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect the protein changes in DF-1 cells infected and mock-infected with ALV-J. A total of 75 cellular proteins were significantly changed, including 33 upregulated proteins and 42 downregulated proteins. The reliability of iTRAQ-LC MS/MS was confirmed via real-time PCR. Most of these proteins were related to the physiological functions of metabolic processes, biosynthetic processes, responses to stimuli, protein binding, signal transduction, cell cytoskeleton, and so forth. We also found some proteins that play important roles in apoptosis and oncogenicity. The differentially expressed proteins identified may provide valuable information to elucidate the pathogenesis of virus infection and virus-host interactions.
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Trapp J, Armengaud J, Salvador A, Chaumot A, Geffard O. Next-generation proteomics: toward customized biomarkers for environmental biomonitoring. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13560-13572. [PMID: 25345346 DOI: 10.1021/es501673s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
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38
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Deutsch DR, Fröhlich T, Otte KA, Beck A, Habermann FA, Wolf E, Arnold GJ. Stage-Specific Proteome Signatures in Early Bovine Embryo Development. J Proteome Res 2014; 13:4363-76. [DOI: 10.1021/pr500550t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniela R. Deutsch
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Kathrin A. Otte
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Andrea Beck
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Felix A. Habermann
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Georg J. Arnold
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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40
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Mermelekas G, Zoidakis J. Mass spectrometry-based membrane proteomics in cancer biomarker discovery. Expert Rev Mol Diagn 2014; 14:549-63. [DOI: 10.1586/14737159.2014.917965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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41
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Kume H, Muraoka S, Kuga T, Adachi J, Narumi R, Watanabe S, Kuwano M, Kodera Y, Matsushita K, Fukuoka J, Masuda T, Ishihama Y, Matsubara H, Nomura F, Tomonaga T. Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis. Mol Cell Proteomics 2014; 13:1471-84. [PMID: 24687888 DOI: 10.1074/mcp.m113.037093] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.
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Affiliation(s)
- Hideaki Kume
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Satoshi Muraoka
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Takahisa Kuga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Jun Adachi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Ryohei Narumi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Shio Watanabe
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Masayoshi Kuwano
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Yoshio Kodera
- §Laboratory of Biomolecular Dynamics, Department of Physics, Kitasato University School of Science, Kanagawa, Japan
| | - Kazuyuki Matsushita
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Junya Fukuoka
- **Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Masuda
- ‡‡Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Yasushi Ishihama
- §§Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hisahiro Matsubara
- ¶¶Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Takeshi Tomonaga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
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42
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Huang S, Chen L, Te R, Qiao J, Wang J, Zhang W. Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803. MOLECULAR BIOSYSTEMS 2014; 9:2565-74. [PMID: 23942477 DOI: 10.1039/c3mb70188c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequential adaptation to environmental stress needs complex regulation at different cellular levels in cyanobacteria. To uncover the regulatory mechanism in response to nitrogen starvation, we investigated the genome-wide correlation between protein abundance and gene expression in a model cyanobacterium Synechocystis sp. PCC 6803 using complementary quantitative iTRAQ proteomics and RNA-seq transcriptomics. Consistent with the cell growth inhibition, proteomic analysis indicated phase-dependent down-regulation of proteins related to nitrogen metabolism, ribosome complexes, glycolysis pathway and tricarboxylic acid (TCA) cycles by nitrogen starvation. Transcriptomic analysis also showed that genes related to "Photosynthesis", "Protein synthesis" and "Energy metabolism" were significantly down-regulated by nitrogen starvation. Interestingly, the concordance between protein abundances and their corresponding mRNAs exhibited a functional categories-dependent pattern, with some categories, such as "Protein synthesis" and "Energy metabolism", having a relatively high correlation, while others even with numerous discordant changes in protein-mRNA pairs, indicated divergent regulation of transcriptional and post-transcriptional processes. In particular, an increased abundance of proteins related to "Photosynthesis" upon nitrogen starvation was found to be reversely correlated with the down-regulation of their corresponding mRNAs. In addition, two metabolic modules highly correlated with nitrogen starvation were identified by a co-expression network analysis, and were found to contain mostly photosynthetic proteins and hypothetical proteins, respectively. We further confirmed the involvement of the photosynthetic genes in nitrogen starvation tolerance by constructing and analyzing the psbV gene deletion mutant.
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Affiliation(s)
- Siqiang Huang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China.
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43
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Chen C, Liu X, Zheng W, Zhang L, Yao J, Yang P. Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics. J Proteome Res 2014; 13:1969-78. [PMID: 24597967 DOI: 10.1021/pr4010986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
To completely annotate the human genome, the task of identifying and characterizing proteins that currently lack mass spectrometry (MS) evidence is inevitable and urgent. In this study, as the first effort to screen missing proteins in large scale, we developed an approach based on SDS-PAGE followed by liquid chromatography-multiple reaction monitoring (LC-MRM), for screening of those missing proteins with only a single peptide hit in the previous liver proteome data set. Proteins extracted from normal human liver were separated in SDS-PAGE and digested in split gel slice, and the resulting digests were then subjected to LC-schedule MRM analysis. The MRM assays were developed through synthesized crude peptides for target peptides. In total, the expressions of 57 target proteins were confirmed from 185 MRM assays in normal human liver tissues. Among the proved 57 one-hit wonders, 50 proteins are of the minimally redundant set in the PeptideAtlas database, 7 proteins even have none MS-based information previously in various biological processes. We conclude that our SDS-PAGE-MRM workflow can be a powerful approach to screen missing or poorly characterized proteins in different samples and to provide their quantity if detected. The MRM raw data have been uploaded to ISB/SRM Atlas/PASSEL (PXD000648).
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Affiliation(s)
- Chen Chen
- Department of Chemistry, Fudan University , Shanghai 200032, P. R. China
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44
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Gromov P, Moreira JMA, Gromova I. Proteomic analysis of tissue samples in translational breast cancer research. Expert Rev Proteomics 2014; 11:285-302. [DOI: 10.1586/14789450.2014.899469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Goh WWB, Wong L. Computational proteomics: designing a comprehensive analytical strategy. Drug Discov Today 2014; 19:266-74. [DOI: 10.1016/j.drudis.2013.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/28/2013] [Accepted: 07/11/2013] [Indexed: 02/02/2023]
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46
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Beretov J, Wasinger VC, Graham PH, Millar EK, Kearsley JH, Li Y. Proteomics for breast cancer urine biomarkers. Adv Clin Chem 2014; 63:123-67. [PMID: 24783353 DOI: 10.1016/b978-0-12-800094-6.00004-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although the survival of breast cancer (BC) patients has increased over the last two decades due to improved screening programs and postoperative adjuvant systemic therapies, many patients die from metastatic relapse. Current biomarkers used in the clinic are not useful for the early detection of BC, or monitoring its progression, and have limited value in predicting response to treatment. The development of proteomic techniques has sparked new searches for novel protein markers for many diseases including BC. Proteomic techniques allow for a high-throughput analysis of samples with the visualization and quantification of thousands of potential protein and peptide markers. Human urine is one of the most interesting and useful biofluids for routine testing and provides an excellent resource for the discovery of novel biomarkers, with the advantage over tissue biopsy samples due to the ease and less invasive nature of collection. In this review, we summarize the results from studies where urine was used as a source for BC biomarker research and discuss urine sample preparation, its advantage, challenges, and limitation. We focus on the gel-based proteomic approaches as well as the recent development of quantitative techniques in BC urine biomarker detection. Finally, the future use of modern proteomic techniques in BC biomarker identification will be discussed.
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47
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Serada S, Naka T. Screening for novel serum biomarker for monitoring disease activity in rheumatoid arthritis using iTRAQ technology-based quantitative proteomic approach. Methods Mol Biol 2014; 1142:99-110. [PMID: 24706280 DOI: 10.1007/978-1-4939-0404-4_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Useful biomarkers, which enable the prediction of drug susceptibility, identification of side effects, and/or evaluation of disease activity during drug treatment, are urgently needed to select adequate drugs for patients. Gene mutation status, protein expression levels in a biopsy, and serum proteins are often used as biomarkers. One of the methods to screen for protein biomarkers involves quantitative proteomic approaches using mass spectrometry. Owing to the development of quantitative proteomic approaches, the efficiency of identifying novel biomarkers from clinical samples has improved. In particular, isobaric tag for relative and absolute quantitation technology, which enables relative comparative analysis of up to eight samples, enables high-throughput analysis of screening for biomarkers at the protein level. Here, we describe the identification of a novel biomarker, which is useful for the evaluation of disease activity in patients with rheumatoid arthritis who were treated with anti-TNF-α therapy.
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Affiliation(s)
- Satoshi Serada
- Laboratory for Immune Signal, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
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Sano S, Tagami S, Hashimoto Y, Yoshizawa-Kumagaye K, Tsunemi M, Okochi M, Tomonaga T. Absolute quantitation of low abundance plasma APL1β peptides at sub-fmol/mL Level by SRM/MRM without immunoaffinity enrichment. J Proteome Res 2013; 13:1012-20. [PMID: 24354742 DOI: 10.1021/pr4010103] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selected/multiple reaction monitoring (SRM/MRM) has been widely used for the quantification of specific proteins/peptides, although it is still challenging to quantitate low abundant proteins/peptides in complex samples such as plasma/serum. To overcome this problem, enrichment of target proteins/peptides is needed, such as immunoprecipitation; however, this is labor-intense and generation of antibodies is highly expensive. In this study, we attempted to quantify plasma low abundant APLP1-derived Aβ-like peptides (APL1β), a surrogate marker for Alzheimer's disease, by SRM/MRM using stable isotope-labeled reference peptides without immunoaffinity enrichment. A combination of Cibacron Blue dye mediated albumin removal and acetonitrile extraction followed by C18-strong cation exchange multi-StageTip purification was used to deplete plasma proteins and unnecessary peptides. Optimal and validated precursor ions to fragment ion transitions of APL1β were developed on a triple quadruple mass spectrometer, and the nanoliquid chromatography gradient for peptide separation was optimized to minimize the biological interference of plasma. Using the stable isotope-labeled (SI) peptide as an internal control, absolute concentrations of plasma APL1β peptide could be quantified as several hundred amol/mL. To our knowledge, this is the lowest detection level of endogenous plasma peptide quantified by SRM/MRM.
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Affiliation(s)
- Shozo Sano
- Laboratory of Proteome Research, National Institute of Biomedical Innovation , Osaka 567-0085, Japan
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Hara Y, Kawasaki N, Hirano KI, Hashimoto Y, Adachi J, Watanabe S, Tomonaga T. Quantitative proteomic analysis of cultured skin fibroblast cells derived from patients with triglyceride deposit cardiomyovasculopathy. Orphanet J Rare Dis 2013; 8:197. [PMID: 24360150 PMCID: PMC3891998 DOI: 10.1186/1750-1172-8-197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/12/2013] [Indexed: 11/17/2022] Open
Abstract
Background Triglyceride deposit cardiomyovasculopathy (TGCV) is a rare disease, characterized by the massive accumulation of triglyceride (TG) in multiple tissues, especially skeletal muscle, heart muscle and the coronary artery. TGCV is caused by mutation of adipose triglyceride lipase, which is an essential molecule for the hydrolysis of TG. TGCV is at high risk for skeletal myopathy and heart dysfunction, and therefore premature death. Development of therapeutic methods for TGCV is highly desirable. This study aims to discover specific molecules responsible for TGCV pathogenesis. Methods To identify differentially expressed proteins in TGCV patient cells, the stable isotope labeling with amino acids in cell culture (SILAC) method coupled with LC-MS/MS was performed using skin fibroblast cells derived from two TGCV patients and three healthy volunteers. Altered protein expression in TGCV cells was confirmed using the selected reaction monitoring (SRM) method. Microarray-based transcriptome analysis was simultaneously performed to identify changes in gene expression in TGCV cells. Results Using SILAC proteomics, 4033 proteins were quantified, 53 of which showed significantly altered expression in both TGCV patient cells. Twenty altered proteins were chosen and confirmed using SRM. SRM analysis successfully quantified 14 proteins, 13 of which showed the same trend as SILAC proteomics. The altered protein expression data set was used in Ingenuity Pathway Analysis (IPA), and significant networks were identified. Several of these proteins have been previously implicated in lipid metabolism, while others represent new therapeutic targets or markers for TGCV. Microarray analysis quantified 20743 transcripts, and 252 genes showed significantly altered expression in both TGCV patient cells. Ten altered genes were chosen, 9 of which were successfully confirmed using quantitative RT-PCR. Biological networks of altered genes were analyzed using an IPA search. Conclusions We performed the SILAC- and SRM-based identification-through-confirmation study using skin fibroblast cells derived from TGCV patients, and first identified altered proteins specific for TGCV. Microarray analysis also identified changes in gene expression. The functional networks of the altered proteins and genes are discussed. Our findings will be exploited to elucidate the pathogenesis of TGCV and discover clinically relevant molecules for TGCV in the near future.
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Affiliation(s)
| | | | | | | | | | | | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation 7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan.
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Contemporary network proteomics and its requirements. BIOLOGY 2013; 3:22-38. [PMID: 24833333 PMCID: PMC4009760 DOI: 10.3390/biology3010022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 01/10/2023]
Abstract
The integration of networks with genomics (network genomics) is a familiar field. Conventional network analysis takes advantage of the larger coverage and relative stability of gene expression measurements. Network proteomics on the other hand has to develop further on two critical factors: (1) expanded data coverage and consistency, and (2) suitable reference network libraries, and data mining from them. Concerning (1) we discuss several contemporary themes that can improve data quality, which in turn will boost the outcome of downstream network analysis. For (2), we focus on network analysis developments, specifically, the need for context-specific networks and essential considerations for localized network analysis.
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