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Selvaraj C, Panwar U, Ramalingam KR, Vijayakumar R, Singh SK. Exploring the macromolecules for secretory pathway in cancer disease. Adv Protein Chem Struct Biol 2023; 133:55-83. [PMID: 36707206 DOI: 10.1016/bs.apcsb.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Secretory proteins play an important role in the tumor microenvironment and are widely distributed throughout tumor tissues. Tumor cells secrete a protein that mediates communication between tumor cells and stromal cells, thereby controlling tumor growth and affecting the success of cancer treatments in the clinic. The cancer secretome is produced by various secretory pathways and has a wide range of applications in oncoproteomics. Secretory proteins are involved in cancer development and tumor cell migration, and thus serve as biomarkers or effective therapeutic targets for a variety of cancers. Several proteomic strategies have recently been used for the analysis of cancer secretomes in order to gain a better understanding and elaborate interpretation. For instance, the development of exosome proteomics, degradomics, and tumor-host cell interaction provide clear information regarding the mechanism of cancer pathobiology. In this chapter, we emphasize the recent advances in secretory protein and the challenges in the field of secretome analysis and their clinical applications.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Karthik Raja Ramalingam
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Gianazza E, Brioschi M, Eligini S, Banfi C. Mass spectrometry for the study of adipocyte cell secretome in cardiovascular diseases. Mass Spectrom Rev 2022:e21812. [PMID: 36161723 DOI: 10.1002/mas.21812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/04/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023]
Abstract
Adipose tissue is classically considered the primary site of lipid storage, but in recent years has garnered appreciation for its broad role as an endocrine organ, capable of remotely signaling to other tissues to alter their metabolic program. The adipose tissue is now recognized as a crucial regulator of cardiovascular health, mediated by the secretion of several bioactive products, with a wide range of endocrine and paracrine effects on the cardiovascular system. Thanks to the development and improvement of high-throughput mass spectrometry, the size and components of the human secretome have been characterized. In this review, we summarized the recent advances in mass spectrometry-based studies of the cell and tissue secretome for the understanding of adipose tissue biology, which may help to decipher the complex molecular mechanisms controlling the crosstalk between the adipose tissue and the cardiovascular system, and their possible clinical translation.
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Affiliation(s)
- Erica Gianazza
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Maura Brioschi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Sonia Eligini
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino IRCCS, Unit of Functional Proteomics, Metabolomics and Network Analysis, Milan, Italy
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Zhang J, Wang K, Hainisayimu T, Li H, Altieri F. Pan-Cancer Analysis of PDIA3: Identifying It as a Potential Biomarker for Tumor Prognosis and Immunotherapy. Oxidative Medicine and Cellular Longevity 2022; 2022:1-42. [PMID: 36046686 PMCID: PMC9423987 DOI: 10.1155/2022/9614819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022]
Abstract
Protein disulfide isomerase A3 (PDIA3) is a kind of thiol oxidoreductase with a wide range of functions, and its expression is elevated in a variety of tumors, which is closely related to the invasion and metastasis of tumor cells, and has a significant impact on the immunogenicity of tumor cells. Although more and more studies have shown that PDIA3 plays an important role in the occurrence and development of many tumors, there is no systematic pan-cancer study on PDIA3. Therefore, in this study, the differential expression of PDIA3 in 33 kinds of tumors was analyzed to explore its ability to regulate tumor immunity as a biomarker and evaluate its role in different cancer onset stages or clinical prognosis. In this paper, by analyzing the multilevel data including 33 kinds of cancers in the databases of Cancer Genome Atlas (TCGA), UCSC Xena, Cancer Cell Encyclopedia (CCLE), Genotypic Tissue Expression (GTEx), Human Protein Atlas (HPA), cBioPortal, and GDC; the differential expression level of PDIA3 in different types of malignant tumors and its relationship with prognosis and the potential correlation between PDIA3 expression and microsatellite instability (MSI), tumor mutation load (TMB), mismatch repair gene (MMR), DNA methylation level, and immune infiltration level were analyzed with bioinformatics. The results showed that PDIA3 was highly expressed in 19 types of cancers, but downregulated only in THCA. Next, PDIA3 in different tumors was positively or negatively correlated with patient outcome, Kaplan-Meier survival analysis showed that PDIA3 plays an important role in the prognosis of patients with KIRP, KICH, and CESC and may be used as a prognostic biomarker, and the methylation level of PDIA3 promoter region was closely related to patient outcome in eight tumors. The expression level of PDIA3 was correlated with TMB in 13 tumors and MSI in 9 tumors. Among them, the expression level of PDIA3 in THYM has the strongest correlation with TMB, and the expression level of PDIA3 in READ has the strongest correlation with MSI. In addition, the expression of PDIA3 in eight kinds of tumors, including BRCA, HNSC, THYM, LGG, LUAD, LUSC, PRAD, and THCA, had the highest correlation with the infiltration degree of immune cells, and the expression of PDIA3 had the highest correlation with the infiltration degree of 11 kinds of immune cells, including regulatory T cell and macrophages. And LGG is the tumor most likely to be affected by the tumor microenvironment to affect its development and prognosis. To sum up, this study suggests that PDIA3 plays an important role in the occurrence and development of KIRP, KICH, and CESC and in the immunotherapeutic response of THYM, READ, and LGG and can be used as a prognostic biomarker for these tumors.
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Wu Y, Yang D, Chen GY. Targeted disruption of Gdi2 causes early embryonic lethality. Placenta 2022; 126:17-25. [PMID: 35689892 DOI: 10.1016/j.placenta.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/10/2022] [Indexed: 01/16/2023]
Abstract
INTRODUCTION GDI2 regulates the GDP/GTP exchange reaction of Rab proteins by inhibiting the dissociation of GDP and the subsequent binding of GTP, dysregulation of GDI2 has been reported in many different cancers. Recently, we found that GDI2 bound to the ITIM domain of Siglec-G under normal homeostasis, whereas Rab1a was recruited to the ITIM domain during bacterial infection. Therefore, GDI2 and Rab1a may regulate the immune response through interaction with the ITIM domain during bacterial infection. However, the regulation of the inflammatory response by GDI2 in vivo and its regulatory mechanism remain unknown. METHODS We generated a Gdi2 null mutant mouse with a trapped Gdi2 gene and examined the expression by X-gal and immunohistochemistry staining. TUNEL staining was used to determine the apoptosis cells. RESULTS Here we show that Gdi2 is essential for embryonic development. One functional Gdi2 allele is sufficient for murine embryo development, but complete loss of Gdi2 leads to embryonic lethality. Developmental retardation of Gdi2-/- mice is apparent at E10.5 to E14.5, with no viable Gdi2-/- embryos detected after E14.5. Histological analysis revealed extensive cell death and cell loss in Gdi2-/- embryos. Apoptosis was confirmed by staining with cleaved caspase-3, suggesting that Gdi2 maintain homeostasis by regulating the apoptosis of the cells. There was no significant difference in cytokine production and survival between wild-type and Gdi2+/- mice after LPS challenge. DISCUSSION These findings suggest that one Gdi2 allele is sufficient to maintain function. However, the detailed molecular mechanism underlying Gdi2 in regulating the embryonic development needs further identification.
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Affiliation(s)
- Yin Wu
- Children's Foundation Research Institute at Le Bonheur Children's Hospital, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38103, USA
| | - Darong Yang
- Children's Foundation Research Institute at Le Bonheur Children's Hospital, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38103, USA
| | - Guo-Yun Chen
- Children's Foundation Research Institute at Le Bonheur Children's Hospital, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38103, USA.
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Udhaya Kumar S, Balasundaram A, Anu Preethi V, Chatterjee S, Kameshwari Gollakota GV, Kashyap MK, George Priya Doss C, Zayed H. Integrative ontology and pathway-based approach identifies distinct molecular signatures in transcriptomes of esophageal squamous cell carcinoma. Adv Protein Chem Struct Biol 2022; 131:177-206. [PMID: 35871890 DOI: 10.1016/bs.apcsb.2022.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) remains a serious concern globally due to many factors that including late diagnosis, lack of an ideal biomarker for diagnosis and prognosis, and high rate of mortality. In this study, we aimed to identify the essential dysregulated genes and molecular signatures associated with the progression and development of ESCC. The dataset with 15 ESCCs and the 15 adjacent normal tissue samples from the surrounding histopathologically tumor-free mucosa was selected. We applied bioinformatics pipelines including various topological parameters from MCODE, CytoNCA, and cytoHubba to prioritize the most significantly associated DEGs with ESCC. We performed functional enrichment annotation for the identified DEGs using DAVID and MetaCore™ GeneGo platforms. Furthermore, we validated the essential core genes in TCGA and GTEx datasets between the normal mucosa and ESCC for their expression levels. These DEGs were primarily enriched in positive regulation of transferase activity, negative regulation of organelle organization, cell cycle mitosis/S-phase transition, spindle organization/assembly, development, and regulation of angiogenesis. Subsequently, the DEGs were associated with the pathways such as oocyte meiosis, cell cycle, and DNA replication. Our study identified the eight-core genes (AURKA, AURKB, MCM2, CDC20, TPX2, PLK1, FOXM1, and MCM7) that are highly expressed among the ESCC, and TCGA dataset. The multigene comparison and principal component analysis resulted in elevated signals for the AURKA, MCM2, CDC20, TPX2, PLK1, and FOXM1. Overall, our study reported GO profiles and molecular signatures that might help researchers to grasp the pathological mechanisms underlying ESCC development and eventually provide novel therapeutic and diagnostic strategies.
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Affiliation(s)
- S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - V Anu Preethi
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - Sayoni Chatterjee
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - G V Kameshwari Gollakota
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Gurugram, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar.
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Zhang W, Liu Z, Xia S, Yao L, Li L, Gan Z, Tang H, Guo Q, Yan X, Sun Z. GDI2 is a novel diagnostic and prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2021; 13:25304-25324. [PMID: 34894398 PMCID: PMC8714169 DOI: 10.18632/aging.203748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022]
Abstract
Background: GDP Dissociation inhibitor 2 (GDI2) gene has been correlated with some important biological processes in a variety of cancers, whereas the role of GDI2 in hepatocellular carcinoma (HCC) is ill-defined. We aimed to demonstrate the relationship between GDI2 and HCC based on The Cancer Genome Atlas (TCGA) data mining. Methods: The expression of GDI2 was compared between cancer and normal tissues of 371 HCC patients collected from TCGA-LIHC, and verified in HCC cell lines. Gene set enrichment analysis (GSEA) was applied to annotate biological function of GDI2. Furthermore, Wilcoxon rank sum test, Logistics regression, as well as Cox regression and Kaplan-Meier survival analysis, were employed to evaluate the association of GDI2 expression with clinicopathological characteristics, and survival status of HCC patients, respectively. Results: It showed that the expression of GDI2 was much higher in tumor tissues than in normal tissues (P < 0.001) of HCC patients. And the elevated expression of GDI2 was correlated with more aggressive HCC tumor status, including severe primary tumor extent, advanced pathological stage, serious histologic grade, and mutated TP53 status (P < 0.05). Moreover, high GDI2 expression was strongly associated with a poor survival rate (P < 0.001). Both enrichment and immune infiltration analyses implied that GDI2-associated signaling mainly involve lipid metabolism and extracellular matrix (ECM) constructing pathways related to tumor microenvironment (TME) (P < 0.05). Conclusions: The elevated expression of GDI2 predicts poor prognosis in HCC patients, indicating that GDI2 could be applied as a predictive biomarker for diagnosis and prognosis of HCC.
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Affiliation(s)
- Wen Zhang
- School of Medicine, Kunming University of Science and Technology, Affiliated by The First People's Hospital of Yunnan Province, Kunming 650504, Yunnan, China.,Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Zhongjian Liu
- Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Shilin Xia
- Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Lei Yao
- General Surgery Department, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Lan Li
- Ophthalmology Department, Jiangxi Provincial People's Hospital, Nanchang 330006, Jiangxi, China
| | - Ziying Gan
- Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Hui Tang
- Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Qiang Guo
- Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Xinmin Yan
- Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
| | - Zhiwei Sun
- School of Medicine, Kunming University of Science and Technology, Affiliated by The First People's Hospital of Yunnan Province, Kunming 650504, Yunnan, China.,Yunnan Digestive Endoscopy Clinical Medical Center, Gastroenterology Department, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan, China
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Heffner KM, Wang Q, Hizal DB, Can Ö, Betenbaugh MJ. Glycoengineering of Mammalian Expression Systems on a Cellular Level. Adv Biochem Eng Biotechnol 2021. [PMID: 29532110 DOI: 10.1007/10_2017_57] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammalian expression systems such as Chinese hamster ovary (CHO), mouse myeloma (NS0), and human embryonic kidney (HEK) cells serve a critical role in the biotechnology industry as the production host of choice for recombinant protein therapeutics. Most of the recombinant biologics are glycoproteins that contain complex oligosaccharide or glycan attachments representing a principal component of product quality. Both N-glycans and O-glycans are present in these mammalian cells, but the engineering of N-linked glycosylation is of critical interest in industry and many efforts have been directed to improve this pathway. This is because altering the N-glycan composition can change the product quality of recombinant biotherapeutics in mammalian hosts. In addition, sialylation and fucosylation represent components of the glycosylation pathway that affect circulatory half-life and antibody-dependent cellular cytotoxicity, respectively. In this chapter, we first offer an overview of the glycosylation, sialylation, and fucosylation networks in mammalian cells, specifically CHO cells, which are extensively used in antibody production. Next, genetic engineering technologies used in CHO cells to modulate glycosylation pathways are described. We provide examples of their use in CHO cell engineering approaches to highlight these technologies further. Specifically, we describe efforts to overexpress glycosyltransferases and sialyltransfereases, and efforts to decrease sialidase cleavage and fucosylation. Finally, this chapter covers new strategies and future directions of CHO cell glycoengineering, such as the application of glycoproteomics, glycomics, and the integration of 'omics' approaches to identify, quantify, and characterize the glycosylated proteins in CHO cells. Graphical Abstract.
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Affiliation(s)
- Kelley M Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Qiong Wang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Özge Can
- Department of Medical Engineering, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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Coppens V, De Wachter O, Goossens J, Hendrix J, Maudsley S, Azmi A, van Gastel J, Van Saet A, Lauwers T, Morrens M. Profiling of the Peripheral Blood Mononuclear Cell Proteome in Schizophrenia and Mood Disorders for the Discovery of Discriminatory Biomarkers: A Proof-of-Concept Study. Neuropsychobiology 2021; 79:324-334. [PMID: 32392557 DOI: 10.1159/000507631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 03/29/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Current diagnoses in psychiatry are solely based on the evaluation of clinical presentation by the treating psychiatrist. This results in a high percentage of misdiagnosis and consequential inefficient treatment; especially regarding major depressive disorder (MDD), depression in the context of bipolar disorder (BD-D), bipolar disorder with manic symptoms (BD-M), and psychosis in the context of schizophrenia (SZ). Objective biomarkers allowing for accurate discriminatory diagnostics are therefore urgently needed. METHODS Peripheral blood mononuclear cell (PBMC) proteomes of patients with MDD (n = 5) , BD-D (n = 3), BD-M (n = 4), and SZ (n = 4), and also of healthy controls (HC; n = 6) were analyzed by state-of-the-art mass spectrometry. Proteins with a differential expression of a >2 standard deviation (SD) expression fold change from that of the HC and between either MDD versus BD-D or BD-M versus SZ were subsequently identified as potential discriminatory biomarkers. RESULTS In total, 4,271 individual proteins were retrieved from the HC. Of these, about 2,800 were detected in all patient and HC samples. For objective discrimination between MDD and BD-D, 66 candidate biomarkers were found. In parallel, 72 proteins might harbor a biomarker capacity for differential diagnostics of BD-M and SZ. A single biomarker was contraregulated versus HC in each pair of comparisons. DISCUSSION With this work, we provide a register of candidate biomarkers with the potential to objectively discriminate MDD from BD-D, and BD-M from SZ. Although concerning a proof-of-concept study with limited sample size, these data provide a stepping-stone for follow-up research on the validation of the true discriminatory potential and feasibility of clinical implementation of the discovered biomarker candidates.
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Affiliation(s)
- Violette Coppens
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium, .,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium,
| | - Oskar De Wachter
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium.,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium
| | - Jobbe Goossens
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium.,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium
| | - Jolien Hendrix
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Abdelkrim Azmi
- Center for Molecular Neurology, VIB, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jaana van Gastel
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Alysia Van Saet
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium.,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium
| | - Tina Lauwers
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium.,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium
| | - Manuel Morrens
- Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), Collaborative Antwerp Psychiatric Research Institute (CAPRI), University of Antwerp, Antwerp, Belgium.,Scientific Initiative for Neuropsychiatric and Psychopharmacological Studies (SINAPS), University Psychiatric Center Duffel, Duffel, Belgium
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Dagamajalu S, Vijayakumar M, Shetty R, Rex DAB, Narayana Kotimoole C, Prasad TSK. Proteogenomic examination of esophageal squamous cell carcinoma (ESCC): new lines of inquiry. Expert Rev Proteomics 2020; 17:649-662. [PMID: 33151123 DOI: 10.1080/14789450.2020.1845146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Esophageal squamous cell carcinoma (ESCC), a histopathologic subtype of esophageal cancer is a major cause of cancer-related morbidity and mortality worldwide. This is primarily because patients are diagnosed at an advanced stage by the time symptoms appear. The genomics and mass spectrometry-based proteomics continue to provide important leads toward biomarker discovery for ESCC. However, such leads are yet to be translated into clinical utilities. Areas covered: We gathered information pertaining to proteomics and proteogenomics efforts in ESCC from the literature search until 2020. An overview of omics approaches to discover the candidate biomarkers for ESCC were highlighted. We present a summary of recent investigations of alterations in the level of gene and protein expression observed in biological samples including body fluids, tissue/biopsy and in vitro-based models. Expert opinion: A large number of protein-based biomarkers and therapeutic targets are being used in cancer therapy. Several candidates are being developed as diagnostics and prognostics for the management of cancers. High-resolution proteomic and proteogenomic approaches offer an efficient way to identify additional candidate biomarkers for diagnosis, monitoring of disease progression, prediction of response to chemo and radiotherapy. Some of these biomarkers can also be developed as therapeutic targets.
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Affiliation(s)
- Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Manavalan Vijayakumar
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Rohan Shetty
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University) , Mangalore, India
| | - D A B Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University) , Mangalore, India
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Zou J, Qian J, Fu H, Yin F, Zhao W, Xu L. MicroRNA‑15b‑5p exerts its tumor repressive role via targeting GDI2: A novel insight into the pathogenesis of thyroid carcinoma. Mol Med Rep 2020; 22:2723-2732. [PMID: 32945458 PMCID: PMC7453593 DOI: 10.3892/mmr.2020.11343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022] Open
Abstract
Thyroid carcinoma (THCA) is a malignant tumor of the endocrine system. Previous studies have revealed the vital roles of microRNAs (miRNAs/miRs) in THCA procession. The present study aimed to explore the effects of miR-15b-5p on the progression of THCA and its targeting mechanism. The data of THCA and healthy samples were firstly collected from starbase2.0 and used to analyze the relationship of miR-15b-5p with THCA. Dual-luciferase assay was performed to detect the direct interaction between miR-15b-5p and the predicted target gene GDP dissociation inhibitor 2 (GDI2). The effects of miR-15b-5p and GDI2 on the overall survival of patients with THCA were analyzed using Kaplan-Meier analysis with log rank test. Cell Counting Kit-8 and Transwell assays were conducted to assess the impacts of miR-15b-5p and GDI2 on the proliferation and invasion of THCA cells. Reverse transcription-quantitative PCR and western blot analyses were performed to analyze the expression levels of the related miRNAs and proteins, respectively. miR-15b-5p was found to be downregulated both in THCA tissues and cells, and the low expression of miR-15b-5p was associated with the short overall survival time of patients. Moreover, the upregulation or downregulation of miR-15b-5p could inhibit or enhance the proliferation and invasion of THCA cells, respectively. miR-15b-5p reduced the protein expression levels of matrix metalloproteinase (MMP)2 and MMP9, which were related to cell invasion. Furthermore, GDI2, which was enhanced in THCA and related to the poor prognosis of patients with THCA, was identified as the target gene of miR-15b-5p and negatively regulated by miR-15b-5p. Additional experiments demonstrated that GDI2 overexpression could significantly reduce the antitumor effect of miR-15b-5p and its inhibitory action on the expression levels of MMP2 and MMP9. Thus, the results indicated a potential tumor suppressive role of miR-15b-5p in THCA, which was mainly exerted by targeting GDI2 and modulating MMP2 and MMP9. These findings will increase the understanding on the pathogenesis of THCA and provide novel candidates for THCA therapy.
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Affiliation(s)
- Jidong Zou
- Thyroid Diseases Department, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250022, P.R. China
| | - Jiantong Qian
- Otolaryngology Department, Traditional Chinese Medicine Hospital of Juxian, Rizhao, Shandong 276599, P.R. China
| | - Haiyan Fu
- Pathology Department, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250022, P.R. China
| | - Fawen Yin
- Thyroid Diseases Department, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250022, P.R. China
| | - Wanjun Zhao
- Thyroid Diseases Department, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250022, P.R. China
| | - Liang Xu
- Thyroid Diseases Department, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250022, P.R. China
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11
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Jin L, Shen F, Weinfeld M, Sergi C. Insulin Growth Factor Binding Protein 7 (IGFBP7)-Related Cancer and IGFBP3 and IGFBP7 Crosstalk. Front Oncol 2020; 10:727. [PMID: 32500027 PMCID: PMC7242731 DOI: 10.3389/fonc.2020.00727] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/16/2020] [Indexed: 12/17/2022] Open
Abstract
The insulin/insulin-like growth factors (IGFs) have crucial tasks in the growth, differentiation, and proliferation of healthy and pernicious cells. They are involved in coordinated complexes, including receptors, ligands, binding proteins, and proteases. However, the systems can become dysregulated in tumorigenesis. Insulin-like growth factor-binding protein 7 (IGFBP7) is a protein belonging to the IGFBP superfamily (also termed GFBP-related proteins). Numerous studies have provided evidence that IGFBP3 and IGFBP7 are involved in a variety of cancers, including hepatocellular carcinoma (HCC), breast cancer, gastroesophageal cancer, colon cancer, prostate cancer, among many others. Still, very few suggest an interaction between these two molecules. In studying several cancer types in our laboratories, we found that both proteins share some crucial signaling pathways. The objective of this review is to present a comprehensive overview of the relationship between IGFBP7 and cancer, as well as highlighting IGFBP3 crosstalk with IGFBP7 reported in recent studies.
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Affiliation(s)
- Li Jin
- Department of Laboratory Medicine, Shiyan Taihe Hospital, College of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Fan Shen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Division of Experimental Oncology, Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Consolato Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.,Department of Orthopedics, Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, China.,Key Laboratory of Fermentation Engineering, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Stollery Children's Hospital, University Alberta Hospital, Edmonton, AB, Canada
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12
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Palumbo A Jr, Meireles Da Costa N, Pontes B, Leite de Oliveira F, Lohan Codeço M, Ribeiro Pinto LF, Nasciutti LE. Esophageal Cancer Development: Crucial Clues Arising from the Extracellular Matrix. Cells 2020; 9:E455. [PMID: 32079295 DOI: 10.3390/cells9020455] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
In the last years, the extracellular matrix (ECM) has been reported as playing a relevant role in esophageal cancer (EC) development, with this compartment being related to several aspects of EC genesis and progression. This sounds very interesting due to the complexity of this highly incident and lethal tumor, which takes the sixth position in mortality among all tumor types worldwide. The well-established increase in ECM stiffness, which is able to trigger mechanotransduction signaling, is capable of regulating several malignant behaviors by converting alteration in ECM mechanics into cytoplasmatic biochemical signals. In this sense, it has been shown that some molecules play a key role in these events, particularly the different collagen isoforms, as well as enzymes related to its turnover, such as lysyl oxidase (LOX) and matrix metalloproteinases (MMPs). In fact, MMPs are not only involved in ECM stiffness, but also in other events related to ECM homeostasis, which includes ECM remodeling. Therefore, the crucial role of distinct MMPs isoform has already been reported, especially MMP-2, -3, -7, and -9, along EC development, thus strongly associating these proteins with the control of important cellular events during tumor progression, particularly in the process of invasion during metastasis establishment. In addition, by distinct mechanisms, a vast diversity of glycoproteins and proteoglycans, such as laminin, fibronectin, tenascin C, galectin, dermatan sulfate, and hyaluronic acid exert remarkable effects in esophageal malignant cells due to the activation of oncogenic signaling pathways mainly involved in cytoskeleton alterations during adhesion and migration processes. Finally, the wide spectrum of interactions potentially mediated by ECM may represent a singular intervention scenario in esophageal carcinogenesis natural history and, due to the scarce knowledge on the cellular and molecular mechanisms involved in EC development, the growing body of evidence on ECM’s role along esophageal carcinogenesis might provide a solid base to improve its management in the future.
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13
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Wang C, Zhang S, Liu J, Tian Y, Ma B, Xu S, Fu Y, Luo Y. Secreted Pyruvate Kinase M2 Promotes Lung Cancer Metastasis through Activating the Integrin Beta1/FAK Signaling Pathway. Cell Rep 2020; 30:1780-1797.e6. [PMID: 32049010 DOI: 10.1016/j.celrep.2020.01.037] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/01/2019] [Accepted: 01/10/2020] [Indexed: 12/31/2022] Open
Abstract
Cancer cell-derived secretomes have been documented to play critical roles in cancer progression. Intriguingly, alternative extracellular roles of intracellular proteins are involved in various steps of tumor progression, which can offer strategies to fight cancer. Herein, we identify lung cancer progression-associated secretome signatures using mass spectrometry analysis. Among them, PKM2 is verified to be highly expressed and secreted in lung cancer cells and clinical samples. Functional analyses demonstrates that secreted PKM2 facilitates tumor metastasis. Furthermore, mass spectrometry analysis and functional validation identify integrin β1 as a receptor of secreted PKM2. Mechanistically, secreted PKM2 directly bound to integrin β1 and subsequently activated the FAK/SRC/ERK axis to promote tumor metastasis. Collectively, our findings suggest that PKM2 is a potential serum biomarker for diagnosing lung cancer and that targeting the secreted PKM2-integrin β1 axis can inhibit lung cancer development, which provides evidence of a potential therapeutic strategy in lung cancer.
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Affiliation(s)
- Caihong Wang
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Shaosen Zhang
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Jie Liu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yang Tian
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Boyuan Ma
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Siran Xu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yan Fu
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China
| | - Yongzhang Luo
- Cancer Biology Laboratory, School of Life Sciences, Tsinghua University, Beijing 100084, China; The National Engineering Laboratory for Anti-Tumor Protein Therapeutics, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Protein Therapeutics, Tsinghua University, Beijing 100084, China.
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14
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Abstract
Mass spectrometry-based proteomics analysis could categorize proteins and study their interactions in large scale in human cancers. By this method, many proteins are upregulated or downregulated in esophageal squamous cell carcinoma (ESCC) when compared to nonneoplastic esophageal mucosae. The method can also be used to identify novel, effective biomarkers for early diagnosis or predict prognosis of patients with ESCC. These changes are associated with different clinical and pathological parameters. Different biological matrices such as pathological tissue, body fluids, and cancer cell lines-based proteomics have widely been used. Herein, we described cell line-based label-free shotgun proteomics (in-solution tryptic digestion) to identify the protein biomarkers differently expressed in ESCC.
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15
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Patil S, Babu N, Subbannayya T, Mohan S, Sathe G, Solanki H, Rajagopalan P, Patel K, Advani J, Bhandi S, Sidransky D, Chatterjee A, Gowda H, Ferrari M. Secretome analysis of oral keratinocytes chronically exposed to shisha. Cancer Biomark 2019; 25:29-41. [DOI: 10.3233/cbm-182099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shankargouda Patil
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
| | - Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
| | | | - Sonali V. Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Hitendra S. Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Shilpa Bhandi
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - David Sidransky
- Department of Otolaryngology – Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Marco Ferrari
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
- Department of Restorative Dentistry, School of Dentistry, University of Leeds, Leeds, UK
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16
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Aftab Q, Mesnil M, Ojefua E, Poole A, Noordenbos J, Strale PO, Sitko C, Le C, Stoynov N, Foster LJ, Sin WC, Naus CC, Chen VC. Cx43-Associated Secretome and Interactome Reveal Synergistic Mechanisms for Glioma Migration and MMP3 Activation. Front Neurosci 2019; 13:143. [PMID: 30941001 PMCID: PMC6433981 DOI: 10.3389/fnins.2019.00143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/07/2019] [Indexed: 12/23/2022] Open
Abstract
Extracellular matrix (ECM) remodeling, degradation and glioma cell motility are critical aspects of glioblastoma multiforme (GBM). Despite being a rich source of potential biomarkers and targets for therapeutic advance, the dynamic changes occurring within the extracellular environment that are specific to GBM motility have yet to be fully resolved. The gap junction protein connexin43 (Cx43) increases glioma migration and invasion in a variety of in vitro and in vivo models. In this study, the upregulation of Cx43 in C6 glioma cells induced morphological changes and the secretion of proteins associated with cell motility. Demonstrating the selective engagement of ECM remodeling networks, secretome analysis revealed the near-binary increase of osteopontin and matrix metalloproteinase-3 (MMP3), with gelatinase and NFF-3 assays confirming the proteolytic activities. Informatic analysis of interactome and secretome downstream of Cx43 identifies networks of glioma motility that appear to be synergistically engaged. The data presented here implicate ECM remodeling and matrikine signals downstream of Cx43/MMP3/osteopontin and ARK1B10 inhibition as possible avenues to inhibit GBM.
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Affiliation(s)
- Qurratulain Aftab
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Marc Mesnil
- Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7003, University of Poitiers, Poitiers, France
| | - Emmanuel Ojefua
- Department of Chemistry, Brandon University, Brandon, MB, Canada
| | - Alisha Poole
- Department of Chemistry, Brandon University, Brandon, MB, Canada
| | - Jenna Noordenbos
- Department of Chemistry, Brandon University, Brandon, MB, Canada
| | - Pierre-Olivier Strale
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Chris Sitko
- Department of Chemistry, Brandon University, Brandon, MB, Canada
| | - Caitlin Le
- Department of Chemistry, Brandon University, Brandon, MB, Canada
| | - Nikolay Stoynov
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Wun-Chey Sin
- Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7003, University of Poitiers, Poitiers, France
| | - Christian C Naus
- Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7003, University of Poitiers, Poitiers, France
| | - Vincent C Chen
- Department of Chemistry, Brandon University, Brandon, MB, Canada
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17
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Bratlie SO, Wallenius V, Edebo A, Fändriks L, Casselbrant A. Proteomic Approach to the Potential Role of Angiotensin II in Barrett Dysplasia. Proteomics Clin Appl 2019; 13:e1800102. [DOI: 10.1002/prca.201800102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/02/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Svein Olav Bratlie
- Department of Gastrosurgical Research and EducationInstitute of Clinical SciencesSahlgrenska Academy at University of Gothenburg Gothenburg 41345 Sweden
| | - Ville Wallenius
- Department of Gastrosurgical Research and EducationInstitute of Clinical SciencesSahlgrenska Academy at University of Gothenburg Gothenburg 41345 Sweden
| | - Anders Edebo
- Department of Gastrosurgical Research and EducationInstitute of Clinical SciencesSahlgrenska Academy at University of Gothenburg Gothenburg 41345 Sweden
| | - Lars Fändriks
- Department of Gastrosurgical Research and EducationInstitute of Clinical SciencesSahlgrenska Academy at University of Gothenburg Gothenburg 41345 Sweden
| | - Anna Casselbrant
- Department of Gastrosurgical Research and EducationInstitute of Clinical SciencesSahlgrenska Academy at University of Gothenburg Gothenburg 41345 Sweden
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18
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Ma C, Liu Y, Zhu L, Ji H, Song X, Guo H, Yi T. Determination and regulation of hepatotoxic pyrrolizidine alkaloids in food: A critical review of recent research. Food Chem Toxicol 2018; 119:50-60. [DOI: 10.1016/j.fct.2018.05.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 11/26/2022]
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19
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018. [PMID: 30143675 DOI: 10.1038/s41598-018-30579-3,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India.,Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India.,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.,Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India.,Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India.,Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India.,Infosys Technologies Ltd, Bangalore, Karnataka, India.,Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India. .,Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India. .,Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India. .,School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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20
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Tungekar A, Mandarthi S, Mandaviya PR, Gadekar VP, Tantry A, Kotian S, Reddy J, Prabha D, Bhat S, Sahay S, Mascarenhas R, Badkillaya RR, Nagasampige MK, Yelnadu M, Pawar H, Hebbar P, Kashyap MK. ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. Sci Rep 2018; 8:12715. [PMID: 30143675 PMCID: PMC6109081 DOI: 10.1038/s41598-018-30579-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer (EC) is the eighth most aggressive malignancy and its treatment remains a challenge due to the lack of biomarkers that can facilitate early detection. EC is identified in two major histological forms namely - Adenocarcinoma (EAC) and Squamous cell carcinoma (ESCC), each showing differences in the incidence among populations that are geographically separated. Hence the detection of potential drug target and biomarkers demands a population-centric understanding of the molecular and cellular mechanisms of EC. To provide an adequate impetus to the biomarker discovery for ESCC, which is the most prevalent esophageal cancer worldwide, here we have developed ESCC ATLAS, a manually curated database that integrates genetic, epigenetic, transcriptomic, and proteomic ESCC-related genes from the published literature. It consists of 3475 genes associated to molecular signatures such as, altered transcription (2600), altered translation (560), contain copy number variation/structural variations (233), SNPs (102), altered DNA methylation (82), Histone modifications (16) and miRNA based regulation (261). We provide a user-friendly web interface ( http://www.esccatlas.org , freely accessible for academic, non-profit users) that facilitates the exploration and the analysis of genes among different populations. We anticipate it to be a valuable resource for the population specific investigation and biomarker discovery for ESCC.
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Affiliation(s)
- Asna Tungekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Sumana Mandarthi
- Mbiomics, Manipal, Karnataka, India
- Department of Biochemistry, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Pooja Rajendra Mandaviya
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Veerendra P Gadekar
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria
| | - Ananthajith Tantry
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
| | - Sowmya Kotian
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | - Jyotshna Reddy
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Sushma Bhat
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
| | | | - Roshan Mascarenhas
- Mbiomics, Manipal, Karnataka, India
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India
- Newcastle University Medicine Malaysia, Johor Bahru, 79200, Malaysia
| | - Raghavendra Rao Badkillaya
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Alva's college, Moodubidre, Karnataka, India
| | - Manoj Kumar Nagasampige
- Mbiomics, Manipal, Karnataka, India
- Department of Biotechnology, Sikkim Manipal University, Gangtok, Sikkim, 737102, India
| | - Mohan Yelnadu
- Mbiomics, Manipal, Karnataka, India
- Manipal Center for Information Sciences, Manipal University, Manipal, Karnataka, India
- Infosys Technologies Ltd, Bangalore, Karnataka, India
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Harsh Pawar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Prashantha Hebbar
- Mbiomics, Manipal, Karnataka, India.
- Manipal Life Sciences Center, Manipal University, Manipal, Karnataka, India.
| | - Manoj Kumar Kashyap
- Mbiomics, Manipal, Karnataka, India.
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India.
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, Uttar Pradesh, 247001, India.
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090, Vienna, Austria.
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21
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Wang X, He Y, Ye Y, Zhao X, Deng S, He G, Zhu H, Xu N, Liang S. SILAC-based quantitative MS approach for real-time recording protein-mediated cell-cell interactions. Sci Rep 2018; 8:8441. [PMID: 29855483 PMCID: PMC5981645 DOI: 10.1038/s41598-018-26262-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/04/2018] [Indexed: 02/05/2023] Open
Abstract
In tumor microenvironment, interactions among multiple cell types are critical for cancer progression. To understand the molecular mechanisms of these complex interplays, the secreted protein analysis between malignant cancer cells and the surrounding nonmalignant stroma is a good viewpoint to investigate cell-cell interactions. Here, we developed two stable isotope labeling of amino acids in cell culture (SILAC)-based mass spectrometry (MS)/MS approaches termed spike-in SILAC and triple-SILAC to quantify changes of protein secretion level in a cell co-cultured system. Within the co-culture system of CT26 and Ana-1 cells, the spike-in SILAC and triple-SILAC MS approaches are sensitive to quantitatively measure protein secretion changes. Three representative quantified proteins (Galectin-1, Cathepsin L1 and Thrombospondin-1) by two SILAC-based MS methods were further validated by Western blotting, and the coming result matched well with SILACs’. We further applied these two SILACs to human cell lines, NCM460 and HT29 co-culture system, for evaluating the feasibility, which confirmed the spike-in and triple SILAC were capable of monitoring the changed secreted proteins of human cell lines. Considering these two strategies in time consuming, sample complexity and proteome coverage, the triple-SILAC way shows more efficiency and economy for real-time recording secreted protein levels in tumor microenvironment.
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Affiliation(s)
- Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.,Chengdu Center for Disease Control and Prevention, Chengdu, 610041, P. R. China
| | - Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Yang Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Xinyu Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Shi Deng
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, P. R. China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100021, P. R. China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.,Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100021, P. R. China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and National Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China.
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22
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Fukamachi M, Kasamatsu A, Endo-Sakamoto Y, Fushimi K, Kasama H, Iyoda M, Minakawa Y, Shiiba M, Tanzawa H, Uzawa K. Multiple coagulation factor deficiency protein 2 as a crucial component in metastasis of human oral cancer. Exp Cell Res 2018; 368:119-25. [PMID: 29679592 DOI: 10.1016/j.yexcr.2018.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/29/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022]
Abstract
Multiple coagulation factor deficiency protein 2 (MCFD2), a binding partner of lectin mannose binding 1 (LMAN1), causes combined deficiencies of coagulation factors V and VIII. MCFD2 function in inherited hematologic disorders is well elucidated; however, little is known about its role in human tumorigenesis. The aim of the current study was to investigate the states of MCFD2 in oral squamous cell carcinoma (OSCC). The expression of MCFD2 was up-regulated significantly in all cell lines examined. Evaluation of the cellular functions associated with tumoral metastasis showed that MCFD2 knockdown (shMCFD2) cells exhibited significantly lower cellular invasiveness and migration and higher cellular adhesion compared with shControl cells. Of note, shMCFD2 cells also showed weak immunoreactivity of LMAN1 and a lower secretion level of galactoside-binding soluble 3 binding protein (LGALS3BP). In addition to in vitro validation, clinical data on 70 patients with OSCC indicated that state of MCFD2 expression level is associated with regional lymph node metastasis. Altogether, we have demonstrated that MCFD2 promotes cancer metastasis by regulating LMAN1 and LGALS3BP expression levels. Hence, MCFD2 may represent a promising candidate for a novel therapeutic target for patients with metastatic OSCCs.
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23
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Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget 2018; 9:18422-18434. [PMID: 29719615 PMCID: PMC5915082 DOI: 10.18632/oncotarget.24853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
The vast majority of esophageal cancers in China, India and Iran are esophageal squamous cell carcinomas (ESCC). A timely diagnosis provides surgical removal as the main therapeutic option for patients with ESCC. Currently, there are no targeted therapies available for ESCC. We carried out reverse phase protein array-based protein expression profiling of seven ESCC-derivedcell lines and a non-neoplastic esophageal epithelial cell line (Het-1A) to identify differentially expressed proteins in ESCC. SYK non-receptortyrosine kinase was overexpressed in six out of seven ESCC cell lines that were used in the study. We evaluated the role of SYK in ESCC using the pharmacological inhibitor entospletinib (GS-9973) and siRNA-based knock down studies. Entospletinib is a selective inhibitor of SYK, which is currently being evaluated in phase II clinical trials for hematological malignancies. Using in vivo subcutaneous tumor xenografts in mice, we demonstrate that treatment with entospletinib significantly inhibits tumor growth. Further clinical studies are needed to prove the efficacy of entospletinib as a targeted therapeutic agent for treating ESCC.
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Affiliation(s)
- Mustafa A. Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manoj K. Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, India
| | - Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
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24
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Barbhuiya MA, Kashyap MK, Puttamallesh VN, Kumar RV, Wu X, Pandey A, Gowda H. Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget 2018. [PMID: 29719615 DOI: 10.18632/oncotarget.24853,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The vast majority of esophageal cancers in China, India and Iran are esophageal squamous cell carcinomas (ESCC). A timely diagnosis provides surgical removal as the main therapeutic option for patients with ESCC. Currently, there are no targeted therapies available for ESCC. We carried out reverse phase protein array-based protein expression profiling of seven ESCC-derivedcell lines and a non-neoplastic esophageal epithelial cell line (Het-1A) to identify differentially expressed proteins in ESCC. SYK non-receptortyrosine kinase was overexpressed in six out of seven ESCC cell lines that were used in the study. We evaluated the role of SYK in ESCC using the pharmacological inhibitor entospletinib (GS-9973) and siRNA-based knock down studies. Entospletinib is a selective inhibitor of SYK, which is currently being evaluated in phase II clinical trials for hematological malignancies. Using in vivo subcutaneous tumor xenografts in mice, we demonstrate that treatment with entospletinib significantly inhibits tumor growth. Further clinical studies are needed to prove the efficacy of entospletinib as a targeted therapeutic agent for treating ESCC.
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Affiliation(s)
- Mustafa A Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Manoj K Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, India
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Xinyan Wu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sidney Kimmel Comprehensive Cancer Centre, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
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25
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Kashyap MK, Abdel-Rahman O. Expression, regulation and targeting of receptor tyrosine kinases in esophageal squamous cell carcinoma. Mol Cancer 2018. [PMID: 29455652 DOI: 10.1186/s12943-018-0790-4,] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Esophageal cancer is one of the most common types of cancer, which is a leading cause of cancer-related death worldwide. Based on histological behavior, it is mainly of two types (i) Esophageal squamous cell carcinoma (ESCC), and (ii) esophageal adenocarcinoma (EAD or EAC). In astronomically immense majority of malignancies, receptor tyrosine kinases (RTKs) have been kenned to play a consequential role in cellular proliferation, migration, and metastasis of the cells. The post-translational modifications (PTMs) including phosphorylation of tyrosine (pY) residue of the tyrosine kinase (TK) domain have been exploited for treatment in different malignancies. Lung cancer where pY residues of EGFR have been exploited for treatment purpose in lung adenocarcinoma patients, but we do not have such kind of felicitously studied and catalogued data in ESCC patients. Thus, the goal of this review is to summarize the studies carried out on ESCC to explore the role of RTKs, tyrosine kinase inhibitors, and their pertinence and consequentiality for the treatment of ESCC patients.
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Affiliation(s)
- Manoj Kumar Kashyap
- School of Life and Allied Health Sciences, Glocal University, Saharanpur, UP, 247121, India. .,Department of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.
| | - Omar Abdel-Rahman
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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26
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Kashyap MK, Abdel-Rahman O. Expression, regulation and targeting of receptor tyrosine kinases in esophageal squamous cell carcinoma. Mol Cancer 2018; 17:54. [PMID: 29455652 PMCID: PMC5817798 DOI: 10.1186/s12943-018-0790-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/01/2018] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer is one of the most common types of cancer, which is a leading cause of cancer-related death worldwide. Based on histological behavior, it is mainly of two types (i) Esophageal squamous cell carcinoma (ESCC), and (ii) esophageal adenocarcinoma (EAD or EAC). In astronomically immense majority of malignancies, receptor tyrosine kinases (RTKs) have been kenned to play a consequential role in cellular proliferation, migration, and metastasis of the cells. The post-translational modifications (PTMs) including phosphorylation of tyrosine (pY) residue of the tyrosine kinase (TK) domain have been exploited for treatment in different malignancies. Lung cancer where pY residues of EGFR have been exploited for treatment purpose in lung adenocarcinoma patients, but we do not have such kind of felicitously studied and catalogued data in ESCC patients. Thus, the goal of this review is to summarize the studies carried out on ESCC to explore the role of RTKs, tyrosine kinase inhibitors, and their pertinence and consequentiality for the treatment of ESCC patients.
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Affiliation(s)
- Manoj Kumar Kashyap
- grid.449790.7School of Life and Allied Health Sciences, Glocal University, Saharanpur, UP 247121 India
- grid.430140.2Department of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh India
| | - Omar Abdel-Rahman
- 0000 0004 0621 1570grid.7269.aClinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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27
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Brandi J, Manfredi M, Speziali G, Gosetti F, Marengo E, Cecconi D. Proteomic approaches to decipher cancer cell secretome. Semin Cell Dev Biol 2017; 78:93-101. [PMID: 28684183 DOI: 10.1016/j.semcdb.2017.06.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 01/17/2023]
Abstract
In this review, we give an overview of the actual proteomic approaches used in the study of cancer cells secretome. In particular, we describe the proteomic strategies to decipher cancer cell secretome initially focusing on the different aspects of sample preparation. We examine the issues related to the presence of low abundant proteins, the analysis of secreted proteins in the conditioned media with or without the removal of fetal bovine serum and strategies developed to reduce intracellular protein contamination. As regards the identification and quantification of secreted proteins, we described the different proteomic approaches used, i.e. gel-based, MS-based (label-based and label-free), and the antibody and array-based methods, together with some of the most recent applications in the field of cancer research. Moreover, we describe the bioinformatics tools developed for the in silico validation and characterization of cancer cells secretome. We also discuss the most important available tools for protein annotation and for prediction of classical and non-classical secreted proteins. In summary in this review advances, concerns and challenges in the field of cancer secretome analysis are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy; ISALIT S.r.l., Novara, Italy.
| | - Giulia Speziali
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Fabio Gosetti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Daniela Cecconi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
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28
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Wang X, Peng Y, Xie M, Gao Z, Yin L, Pu Y, Liu R. Identification of extracellular matrix protein 1 as a potential plasma biomarker of ESCC by proteomic analysis using iTRAQ and 2D-LC-MS/MS. Proteomics Clin Appl 2017; 11. [PMID: 28493612 DOI: 10.1002/prca.201600163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/30/2017] [Accepted: 05/08/2017] [Indexed: 12/22/2022]
Abstract
PURPOSE This study was aimed to conduct a proteomics profiling analysis on plasma obtained from ESCC patients with the goal of identifying appropriate plasma protein biomarkers in the progression of ESCC. EXPERIMENTAL DESIGN Plasma from 28 ESCC patients and 28 healthy controls (HC) were analyzed by iTRAQ combined with 2D-LC-MS/MS. ProteinPilot software was used to identify the differentially expressed plasma proteins in ESCC compared to HC. Western blot was performed to verify the expression of selected proteins in 37 independent ESCC patients and 37 HC. Transwell and MTT assays were used to detect the biological function of ECM1 protein in vitro. RESULTS Nineteen (four upregulated and fifteen downregulated) proteins were identified as differentially expressed between ESCC and HC (p <0.05). Biological functions of these proteins are involved in cell adhesion, cell apoptosis and metabolic processes, visual perception and immune response. Of these, extracellular matrix 1 (ECM1) and lumican (LUM) were selected further confirmation by Western blot (p <0.05), which were consistent with the iTRAQ results. Furthermore, the migration ability of EC9706 cell line after overexpressing ECM1 was increased significantly (p <0.05). The proliferation ability of HUVEC cell was enhanced when treated with the culture supernatants of EC9706 overexpressed ECM1(p <0.05). CONCLUSION AND CLINICAL RELEVANCE This proteome analysis indicate that ECM1 is a potential novel plasma protein biomarker for the detection of primary ESCC and evaluation of neoplasms progression.
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Affiliation(s)
- Xianghu Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yuan Peng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Ming Xie
- North China Petroleum Bureau General Hospital, Renqiu, China
| | - Zhikui Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
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Yu SB, Gao Q, Lin WW, Kang MQ. Proteomic analysis indicates the importance of TPM3 in esophageal squamous cell carcinoma invasion and metastasis. Mol Med Rep 2017; 15:1236-1242. [PMID: 28138712 PMCID: PMC5367371 DOI: 10.3892/mmr.2017.6145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 11/17/2016] [Indexed: 01/06/2023] Open
Abstract
Numerous esophageal squamous cell carcinoma (ESCC) patients exhibit tumor recurrence following radical resection. Invasion and metastasis are key factors in poor prognosis following esophagectomy. In the present study, two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used to define patterns of protein expression in ESCC tissues at different pathological stages. The expression levels of identified proteins were determined by immunohistochemistry and western blotting. A total of fifteen protein spots with >2-fold differences were observed when comparing results of 2-DE for stage III and stage I ESCC tissue sample. A total of 12 proteins were identified by mass spectrometry analysis and database searches. The results of immunohistochemistry and western blotting demonstrated expression levels of tropomyosin 3 (TPM3) were higher in stage III ESCC tissue compared with stage I (P<0.05). The findings of the present study identified twelve proteins, which are closely associated with ESCC invasion and metastasis, apoptosis and cell signal transduction. Furthermore, the overexpression of TPM3 may be important in ESCC invasion and metastasis.
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Affiliation(s)
- Shao-Bin Yu
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Qin Gao
- Department of General Surgery, Fuzhou General Hospital of Nanjing Military Area Command, Fuzhou, Fujian 350025, P.R. China
| | - Wen-Wei Lin
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Ming-Qiang Kang
- Second Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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Abstract
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.
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Affiliation(s)
- Somaditya Mukherjee
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
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31
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Harada K, Mizrak Kaya D, Shimodaira Y, Song S, Baba H, Ajani JA. Proteomics approach to identify biomarkers for upper gastrointestinal cancer. Expert Rev Proteomics 2016; 13:1041-1053. [PMID: 27718753 DOI: 10.1080/14789450.2016.1246189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The prognosis for patients with upper gastrointestinal cancers remains dismal despite the development of multimodality therapies that incorporate surgery, chemotherapy, and radiotherapy. Early diagnosis and personalized treatment should lead to better prognosis. Given the advances in proteomic technologies over the past decades, proteomics promises to be the most effective technique to identify novel diagnostics and therapeutic targets. Areas covered: For this review, keywords were searched in combination with 'proteomics' and 'gastric cancer' or 'esophageal cancer' in PubMed. Studies that evaluated proteomics associated with upper gastrointestinal cancer were identified through reading, with several studies quoted at second hand. We summarize the proteomics involved in upper gastrointestinal cancer and discuss potential biomarkers and therapeutic targets. Expert commentary: In particular, the development of mass spectrometry has enabled detection of multiple proteins and peptides in more biological samples over a shorter time period and at lower cost than was previously possible. In addition, more sophisticated protein databases have allowed a wider variety of proteins in samples to be quantified. Novel biomarkers that have been identified by new proteomic technologies should be applied in a clinical setting.
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Affiliation(s)
- Kazuto Harada
- a Department of Gastrointestinal Medical Oncology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA.,b Department of Gastroenterological Surgery, Graduate School of Medical Science , Kumamoto University , Kumamoto , Japan
| | - Dilsa Mizrak Kaya
- a Department of Gastrointestinal Medical Oncology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Yusuke Shimodaira
- a Department of Gastrointestinal Medical Oncology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Shumei Song
- a Department of Gastrointestinal Medical Oncology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Hideo Baba
- b Department of Gastroenterological Surgery, Graduate School of Medical Science , Kumamoto University , Kumamoto , Japan
| | - Jaffer A Ajani
- a Department of Gastrointestinal Medical Oncology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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Bennun SV, Hizal DB, Heffner K, Can O, Zhang H, Betenbaugh MJ. Systems Glycobiology: Integrating Glycogenomics, Glycoproteomics, Glycomics, and Other ‘Omics Data Sets to Characterize Cellular Glycosylation Processes. J Mol Biol 2016; 428:3337-3352. [DOI: 10.1016/j.jmb.2016.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022]
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33
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Caorsi C, Niccolai E, Capello M, Vallone R, Chattaragada MS, Alushi B, Castiglione A, Ciccone G, Mautino A, Cassoni P, De Monte L, Álvarez-Fernández SM, Amedei A, Alessio M, Novelli F. Protein disulfide isomerase A3-specific Th1 effector cells infiltrate colon cancer tissue of patients with circulating anti-protein disulfide isomerase A3 autoantibodies. Transl Res 2016; 171:17-28.e1-2. [PMID: 26772958 DOI: 10.1016/j.trsl.2015.12.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/27/2023]
Abstract
To investigate novel colorectal cancer (CRC)-associated antigens that could be targets of humoral or cellular responses, we analyzed the reactivity of serum from a long-surviving CRC patient (for more than 100 months of follow-up) in clinical remission, by serologic proteome analysis. Two-dimensional Western blotting (2D-WB) and mass spectrometry analysis revealed a strong reactivity of this serum against protein disulfide isomerase A3 (PDIA3). Anti-PDIA3 antibodies are not a diagnostic marker of CRC, 2D-WB and Luminex analysis revealed that they were equally present in about 10% of sera from healthy subjects and CRC patients. Kaplan-Meier analysis of survival in CRC patient cohort, after 48 months of follow-up, showed a trend of higher survival in patients with increased levels of autoantibodies to PDIA3. Therefore, the interplay between the presence of these antibodies and T-cell response was investigated. Peripheral blood T cells from CRC patients with high immunoglobulin G (IgG) reactivity to PDIA3 also secreted interferon gamma (IFN-γ) when stimulated in vitro with recombinant PDIA3, whereas those from CRC with low IgG reactivity to PDIA3 did not. PDIA3-pulsed dendritic cells efficiently induced proliferation and IFN-γ production of autologous CD4(+) and CD8(+) T cells. Finally, ex vivo analysis of tumor-infiltrating T lymphocytes from CRC patients with autoantibodies to PDIA3 revealed that PDIA3-specific Th1 effector cells accumulated in tumor tissue. These data indicate that the presence of autoantibodies to PDIA3 favors the development of an efficient and specific T-cell response against PDIA3 in CRC patients. These results may be relevant for the design of novel immunotherapeutic strategies in CRC patients.
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Brücher BLDM, Li Y, Schnabel P, Daumer M, Wallace TJ, Kube R, Zilberstein B, Steele S, Voskuil JLA, Jamall IS. Genomics, microRNA, epigenetics, and proteomics for future diagnosis, treatment and monitoring response in upper GI cancers. Clin Transl Med 2016; 5:13. [PMID: 27053248 PMCID: PMC4823224 DOI: 10.1186/s40169-016-0093-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 03/29/2016] [Indexed: 12/15/2022] Open
Abstract
One major objective for our evolving understanding in the treatment of cancers will be to address how a combination of diagnosis and treatment strategies can be used to integrate patient and tumor variables with an outcome-oriented approach. Such an approach, in a multimodal therapy setting, could identify those patients (1) who should undergo a defined treatment (personalized therapy) (2) in whom modifications of the multimodal therapy due to observed responses might lead to an improvement of the response and/or prognosis (individualized therapy), (3) who might not benefit from a particular toxic treatment regimen, and (4) who could be identified early on and thereby be spared the morbidity associated with such treatments. These strategies could lead in the direction of precision medicine and there is hope of integrating translational molecular data to improve cancer classifications. In order to achieve these goals, it is necessary to understand the key issues in different aspects of biotechnology to anticipate future directions of personalized and individualized diagnosis and multimodal treatment strategies. Providing an overview of translational data in cancers proved to be a challenge as different methods and techniques used to obtain molecular data are used and studies are based on different tumor entities with different tumor biology and prognoses as well as vastly different therapeutic approaches. The pros and cons of the available methodologies and the potential response data in genomics, microRNA, epigenetics and proteomics with a focus on upper gastrointestinal cancers are considered herein to allow for an understanding of where these technologies stand with respect to cancer diagnosis, prognosis and treatment.
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Affiliation(s)
- Björn L D M Brücher
- Theodor-Billroth-Academy®, Munich, Germany. .,Theodor-Billroth-Academy®, Sacramento, CA, USA. .,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany. .,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA, USA. .,Bon Secours Cancer Institute, Richmond, VA, USA. .,Department of Surgery, Carl-Thiem-Klinikum, Cottbus, Germany.
| | - Yan Li
- Proteogenomics Research Institute for Systems Medicine, San Diego, CA, USA
| | - Philipp Schnabel
- Institute of Pathology, University of Homburg Saar, Homburg, Germany
| | - Martin Daumer
- Theodor-Billroth-Academy®, Munich, Germany.,Theodor-Billroth-Academy®, Sacramento, CA, USA.,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany.,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA, USA.,Sylvia Lawry Center for MS Research, Munich, Germany
| | | | - Rainer Kube
- Department of Surgery, Carl-Thiem-Klinikum, Cottbus, Germany
| | | | - Scott Steele
- Case Western Reserve University, Cleveland, OH, USA.,Department of Surgery, Madigan Army Medical Center, Tacoma, WA, USA
| | | | - Ijaz S Jamall
- Theodor-Billroth-Academy®, Munich, Germany.,Theodor-Billroth-Academy®, Sacramento, CA, USA.,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany.,INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA, USA.,Risk-Based Decisions, Inc., Sacramento, CA, USA
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Malik UU, Zarina S, Pennington SR. Oral squamous cell carcinoma: Key clinical questions, biomarker discovery, and the role of proteomics. Arch Oral Biol 2016; 63:53-65. [DOI: 10.1016/j.archoralbio.2015.11.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 09/08/2015] [Accepted: 11/20/2015] [Indexed: 12/19/2022]
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Lohmer LL, Clay MR, Naegeli KM, Chi Q, Ziel JW, Hagedorn EJ, Park JE, Jayadev R, Sherwood DR. A Sensitized Screen for Genes Promoting Invadopodia Function In Vivo: CDC-42 and Rab GDI-1 Direct Distinct Aspects of Invadopodia Formation. PLoS Genet 2016; 12:e1005786. [PMID: 26765257 PMCID: PMC4713207 DOI: 10.1371/journal.pgen.1005786] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/12/2015] [Indexed: 12/12/2022] Open
Abstract
Invadopodia are specialized membrane protrusions composed of F-actin, actin regulators, signaling proteins, and a dynamically trafficked invadopodial membrane that drive cell invasion through basement membrane (BM) barriers in development and cancer. Due to the challenges of studying invasion in vivo, mechanisms controlling invadopodia formation in their native environments remain poorly understood. We performed a sensitized genome-wide RNAi screen and identified 13 potential regulators of invadopodia during anchor cell (AC) invasion into the vulval epithelium in C. elegans. Confirming the specificity of this screen, we identified the Rho GTPase cdc-42, which mediates invadopodia formation in many cancer cell lines. Using live-cell imaging, we show that CDC-42 localizes to the AC-BM interface and is activated by an unidentified vulval signal(s) that induces invasion. CDC-42 is required for the invasive membrane localization of WSP-1 (N-WASP), a CDC-42 effector that promotes polymerization of F-actin. Loss of CDC-42 or WSP-1 resulted in fewer invadopodia and delayed BM breaching. We also characterized a novel invadopodia regulator, gdi-1 (Rab GDP dissociation inhibitor), which mediates membrane trafficking. We show that GDI-1 functions in the AC to promote invadopodia formation. In the absence of GDI-1, the specialized invadopodial membrane was no longer trafficked normally to the invasive membrane, and instead was distributed to plasma membrane throughout the cell. Surprisingly, the pro-invasive signal(s) from the vulval cells also controls GDI-1 activity and invadopodial membrane trafficking. These studies represent the first in vivo screen for genes regulating invadopodia and demonstrate that invadopodia formation requires the integration of distinct cellular processes that are coordinated by an extracellular cue. During animal development specialized cells acquire the ability move and invade into other tissues to form complex organs and structures. Understanding this cellular behavior is important medically, as cancer cells can hijack the developmental program of invasion to metastasize throughout the body. One of the most formidable barriers invasive cells face is basement membrane–-a thin, dense, sheet-like assembly of proteins and carbohydrates that surrounds most tissues. Cells deploy small, protrusive, membrane associated structures called invadopodia (invasive feet) to breach basement membranes. How invadopodia are formed and controlled during invasion has been challenging to understand, as it is difficult to examine these dynamic structures in live animals. Using the nematode worm Caenorhabditis elegans, we have conducted the first large-scale screen to isolate genes that control invadopodia in live animals. Our screen isolated 13 genes and we confirmed two are key invadopodia regulators: the Rho GTPase CDC-42 that promotes F-actin polymerization at invadopodia to generate the force to breach basement membranes, and the Rab GDI-1 that promotes membrane addition at invadopodia that may allow invadopodia to extend through basement membranes. This work provides new insights into invadopodia construction and identifies potential novel targets for anti-metastasis therapies.
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Affiliation(s)
- Lauren L. Lohmer
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Matthew R. Clay
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Kaleb M. Naegeli
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Qiuyi Chi
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Joshua W. Ziel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Elliott J. Hagedorn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jieun E. Park
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Ranjay Jayadev
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - David R. Sherwood
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Kashyap MK. Role of insulin-like growth factor-binding proteins in the pathophysiology and tumorigenesis of gastroesophageal cancers. Tumour Biol 2015; 36:8247-57. [PMID: 26369544 DOI: 10.1007/s13277-015-3972-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/21/2015] [Indexed: 02/07/2023] Open
Abstract
The insulin family of proteins include insulin-like growth factor binding proteins (IGFBPs) that are classified into two groups based on their differential affinities to IGFs: IGF high-affinity binding proteins (IGFBP1-6) and IGF low-affinity IGFBP-related proteins (IGFBP-rP1-10). IGFBPs interact with many proteins, including their canonical ligands insulin-like growth factor 1 (IGF-I) and IGF-II. Together with insulin-like growth factor 1 (IGF1) receptor (IGF1R), IGF2R, and ligands (IGF1 and IGF2), IGFBPs participate in a complex signaling axis called IGF-IGFR-IGFBP. Numerous studies have demonstrated that the IGF-IGFR-IGFBP axis is relevant in gastrointestinal (GI) and other cancers. The presence of different IGFBPs have been reported in gastrointestinal cancers, including esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAD or EAC), and gastric adenocarcinoma (GAD or GAC). A literature-based survey clearly indicates that an urgent need exists for a focused review of the role of IGFBPs in gastrointestinal cancers. The aim of this review is to present the biochemical and molecular characteristics of IGFBPs with an emphasis specifically on the role of these proteins in the pathophysiology and tumorigenesis of gastroesophageal cancers.
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Affiliation(s)
- Manoj K Kashyap
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, La Jolla, CA, 92093-0820, USA.
- Department of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.
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Syed N, Barbhuiya MA, Pinto SM, Nirujogi RS, Renuse S, Datta KK, Khan AA, Srikumar K, Prasad TSK, Kumar MV, Kumar RV, Chatterjee A, Pandey A, Gowda H. Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma. Proteomics 2015; 15:374-82. [PMID: 25366905 PMCID: PMC4309511 DOI: 10.1002/pmic.201400379] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/01/2014] [Accepted: 10/28/2014] [Indexed: 01/17/2023]
Abstract
Esophageal squamous‐cell carcinoma (ESCC) is one of the most common malignancies in Asia. Currently, surgical resection of early‐stage tumor is the best available treatment. However, most patients present late when surgery is not an option. Data suggest that chemotherapy regimens are inadequate for clinical management of advanced cancer. Targeted therapy has emerged as one of the most promising approaches to treat several malignancies. A prerequisite for developing targeted therapy is prior knowledge of proteins and pathways that drive proliferation in malignancies. We carried out phosphotyrosine profiling across four different ESCC cell lines and compared it to non‐neoplastic Het‐1A cell line to identify activated tyrosine kinase signaling pathways in ESCC. A total of 278 unique phosphopeptides were identified across these cell lines. This included several tyrosine kinases and their substrates that were hyperphosphorylated in ESCC. Ephrin receptor A2 (EPHA2), a receptor tyrosine kinase, was hyperphosphorylated in all the ESCC cell lines used in the study. EPHA2 is reported to be oncogenic in several cancers and is also known to promote metastasis. Immunohistochemistry‐based studies have revealed EPHA2 is overexpressed in nearly 50% of ESCC. We demonstrated EPHA2 as a potential therapeutic target in ESCC by carrying out siRNA‐based knockdown studies. Knockdown of EPHA2 in ESCC cell line TE8 resulted in significant decrease in cell proliferation and invasion, suggesting it is a promising therapeutic target in ESCC that warrants further evaluation.
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Affiliation(s)
- Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, India; Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
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Belousov PV, Bogolyubova AV, Kim YS, Abrosimov AY, Kopylov AT, Tvardovskiy AA, Lanshchakov KV, Sazykin AY, Dvinskikh NY, Bobrovskaya YI, Selivanova LS, Shilov ES, Schwartz AM, Shebzukhov YV, Severskaia NV, Vanushko VE, Moshkovskii SA, Nedospasov SA, Kuprash DV. Serum Immunoproteomics Combined With Pathological Reassessment of Surgical Specimens Identifies TCP-1ζ Autoantibody as a Potential Biomarker in Thyroid Neoplasia. J Clin Endocrinol Metab 2015. [PMID: 26196948 DOI: 10.1210/jc.2014-4260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Current methods of preoperative diagnostics frequently fail to discriminate between benign and malignant thyroid neoplasms. In encapsulated follicular-patterned tumors (EnFPT), this discrimination is challenging even using histopathological analysis. Autoantibody response against tumor-associated antigens is a well-documented phenomenon with prominent diagnostic potential; however, autoantigenicity of thyroid tumors remains poorly explored. OBJECTIVES Objectives were exploration of tumor-associated antigen repertoire of thyroid tumors and identification of candidate autoantibody biomarkers capable of discrimination between benign and malignant thyroid neoplasms. DESIGN, SETTING, AND PATIENTS Proteins isolated from FTC-133 cells were subjected to two-dimensional Western blotting using pooled serum samples of patients originally diagnosed with either papillary thyroid carcinoma (PTC) or EnFPT represented by apparently benign follicular thyroid adenomas, as well as healthy individuals. Immunoreactive proteins were identified using liquid chromatography-tandem mass-spectrometry. Pathological reassessment of EnFPT was performed applying nonconservative criteria for capsular invasion and significance of focal PTC nuclear changes (PTC-NCs). Recombinant T-complex protein 1 subunitζ (TCP-1ζ) was used to examine an expanded serum sample set of patients with various thyroid neoplasms (n = 89) for TCP-1ζ autoantibodies. All patients were included in tertiary referral centers. RESULTS A protein demonstrating a distinct pattern of EnFPT-specific seroreactivity was identified as TCP-1ζ protein. A subsequent search for clinicopathological correlates of TCP-1ζ seroreactivity revealed nonclassical capsular invasion or focal PTC-NC in all TCP-1ζ antibody-positive cases. Further studies in an expanded sample set confirmed the specificity of TCP-1ζ autoantibodies to malignant EnFPT. CONCLUSIONS We identified TCP-1ζ autoantibodies as a potential biomarker for presurgical discrimination between benign and malignant encapsulated follicular-patterned thyroid tumors. Our results suggest the use of nonconservative morphological criteria for diagnosis of malignant EnFPT in biomarker identification studies and provide a peculiar example of uncovering the diagnostic potential of a candidate biomarker using incorporation of pathological reassessment in the pipeline of immunoproteomic research.
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Affiliation(s)
- Pavel V Belousov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Apollinariya V Bogolyubova
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Yan S Kim
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Alexander Y Abrosimov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Arthur T Kopylov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrey A Tvardovskiy
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Kirill V Lanshchakov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Alexei Y Sazykin
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Nina Y Dvinskikh
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Yana I Bobrovskaya
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Lilia S Selivanova
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Evgeniy S Shilov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Anton M Schwartz
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Yuriy V Shebzukhov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Natalya V Severskaia
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Vladimir E Vanushko
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Sergei A Moshkovskii
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Sergei A Nedospasov
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Dmitry V Kuprash
- Department of Immunology (P.V.B., A.V.B., Y.S.K., A.Y.S., Y.I.B., E.S.S., S.A.N., D.V.K.) Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; Laboratory of Molecular Mechanisms of Immunity (A.V.B., S.A.N.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Department of Pathomorphology (A.Y.A., L.S.S.), Endocrinology Research Center, 117036 Moscow, Russia; Acousto-Optical Research Center (A.Y.A.), National University of Science & Technology "MISIS," 119049 Moscow, Russia; Laboratory of Systems Biology (A.T.K.), Institute of Biomedical Chemistry, 119121 Moscow, Russia; Department of Molecular Immunology (A.A.T., S.A.N.), A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; Department of Surgery (K.V.L., V.E.V.), Endocrinology Research Center, 117036 Moscow, Russia; Medical Radiology Research Center (N.Y.D., N.V.S.), 249036 Obninsk, Russia; Laboratory of Intracellular Signaling in Health and Disease (A.M.S., D.V.K.), Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; German Rheumatism Research Center (Y.V.S., S.A.N.), a Leibniz Institute, 10117 Berlin, Germany; and Laboratory of Personalized Medicine (S.A.M.), Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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Chen J, Kwong DL, Cao T, Hu Q, Zhang L, Ming X, Chen J, Fu L, Guan X. Esophageal squamous cell carcinoma (ESCC): advance in genomics and molecular genetics. Dis Esophagus 2015; 28:84-9. [PMID: 23796192 DOI: 10.1111/dote.12088] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal cancer is aggressive and has poor prognosis. Esophageal squamous cell carcinoma (ESCC) is histologically the most prevalent type of esophageal cancer and ranked as the sixth leading cause of cancer death worldwide. In recent years, cancer has been widely regarded as genetic disease, as well as epigenetic abnormalities including DNA methylation, histone deacetylation, chromatin remodeling, gene imprinting and noncoding RNA regulation. In this review, we will provide a general overview of genes, proteins and microRNAs that are involved in the development of ESCC, which aims to enhance our understanding of molecular mechanisms implicated in ESCC development and progression.
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Affiliation(s)
- J Chen
- Departments of Clinical Oncology, The University of Hong Kong, Hong Kong; Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Abstract
Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer.
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Affiliation(s)
- Hua Zhang
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN, UK
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Ren RJ, Dammer EB, Wang G, Seyfried NT, Levey AI. Proteomics of protein post-translational modifications implicated in neurodegeneration. Transl Neurodegener 2014; 3:23. [PMID: 25671099 PMCID: PMC4323146 DOI: 10.1186/2047-9158-3-23] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics has developed into a battery of approaches that is exceedingly adept at identifying with high mass accuracy and precision any of the following: oxidative damage to proteins (redox proteomics), phosphorylation (phosphoproteomics), ubiquitination (diglycine remnant proteomics), protein fragmentation (degradomics), and other posttranslational modifications (PTMs). Many studies have linked these PTMs to pathogenic mechanisms of neurodegeneration. To date, identifying PTMs on specific pathology-associated proteins has proven to be a valuable step in the evaluation of functional alteration of proteins and also elucidates biochemical and structural explanations for possible pathophysiological mechanisms of neurodegenerative diseases. This review provides an overview of methods applicable to the identification and quantification of PTMs on proteins and enumerates historic, recent, and potential future research endeavours in the field of proteomics furthering the understanding of PTM roles in the pathogenesis of neurodegeneration.
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Affiliation(s)
- Ru-Jing Ren
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Eric B Dammer
- />Department of Biochemistry, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Gang Wang
- />Department of Pharmacology, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T Seyfried
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
- />Department of Biochemistry, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
- />Emory Proteomics Service Center, Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Allan I Levey
- />Department of Neurology,Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA
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Läubli H, Alisson-Silva F, Stanczak MA, Siddiqui SS, Deng L, Verhagen A, Varki N, Varki A. Lectin galactoside-binding soluble 3 binding protein (LGALS3BP) is a tumor-associated immunomodulatory ligand for CD33-related Siglecs. J Biol Chem 2014; 289:33481-91. [PMID: 25320078 DOI: 10.1074/jbc.m114.593129] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Lectin galactoside-binding soluble 3 binding protein (LGALS3BP, also called Mac-2 binding protein) is a heavily glycosylated secreted molecule that has been shown previously to be up-regulated in many cancers and has been implicated in tumor metastatic processes, as well as in other cell adhesion and immune functions. The CD33-related subset of sialic acid-binding immunoglobulin-like lectins (Siglecs) consists of immunomodulatory molecules that have recently been associated with the modulation of immune responses to cancer. Because up-regulation of Siglec ligands in cancer tissue has been observed, the characterization of these cancer-associated ligands that bind to inhibitory CD33-related Siglecs could provide novel targets for cancer immunomodulatory therapy. Here we used affinity chromatography of tumor cell extracts to identify LGALS3BP as a novel sialic acid-dependent ligand for human Siglec-9 and for other immunomodulatory Siglecs, such as Siglec-5 and Siglec-10. In contrast, the mouse homolog Siglec-E binds to murine LGALS3BP with lower affinity. LGALS3BP has been observed to be up-regulated in human colorectal and prostate cancer specimens, particularly in the extracellular matrix. Finally, LGALS3BP was able to inhibit neutrophil activation in a sialic acid- and Siglec-dependent manner. These findings suggest a novel immunoinhibitory function for LGALS3BP that might be important for immune evasion of tumor cells during cancer progression.
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Affiliation(s)
- Heinz Läubli
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Frederico Alisson-Silva
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Michal A Stanczak
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Shoib S Siddiqui
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Liwen Deng
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Andrea Verhagen
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Nissi Varki
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
| | - Ajit Varki
- From the Departments of Medicine and Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093
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Sahasrabuddhe NA, Huang TC, Ahmad S, Kim MS, Yang Y, Ghosh B, Leach SD, Gowda H, Somani BL, Chaerkady R, Pandey A. Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis. J Proteomics 2014; 108:306-15. [DOI: 10.1016/j.jprot.2014.04.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/31/2014] [Accepted: 04/13/2014] [Indexed: 12/22/2022]
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Henningsen J, Blagoev B, Kratchmarova I. Analysis of secreted proteins using SILAC. Methods Mol Biol 2014; 1188:313-26. [PMID: 25059621 DOI: 10.1007/978-1-4939-1142-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Secreted proteins serve a crucial role in the communication between cells, tissues, and organs. Proteins released to the extracellular environment exert their function either locally or at distant points of the organism. Proteins are secreted in a highly dynamic fashion by cells and tissues in the body responding to the stimuli and requirements presented by the extracellular milieu. Characterization of secretomes derived from various cell types has been performed using different quantitative mass spectrometry-based proteomics strategies, several of them taking advantage of labeling with stable isotopes. Here, we describe the use of Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for the quantitative analysis of the skeletal muscle secretome during myogenesis.
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Affiliation(s)
- Jeanette Henningsen
- Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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Abstract
AbstractLung cancer is one of the most common cancers in terms of both incidence and mortality.The major reasons for the increasing number of deaths from lung cancer are late detection and lack of effective therapies. To improve our understanding of lung cancer biology, there is urgent need for blood-based, non-invasive molecular tests to assist in its detection in a cost-effective manner at an early stage when curative interventions are still possible. Recent advances in proteomic technology have provided extensive, high throughput analytical tools for identification, characterization and functional studies of proteomes. Changes in protein expression patterns in response to stimuli can serve as indicators or biomarkers of biological and pathological processes as well as physiological and pharmacological responses to drug treatment, thus aiding in early diagnosis and prognosis of disease. However, only a few biomarkers have been approved by the FDA to date for screening and diagnostic purposes. This review provides a brief overview of currently available proteomic techniques, their applications and limitations and the current state of knowledge about important serum biomarkers in lung cancer and their potential value as prognostic and diagnostic tools.
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Cheng JCH, Graber MS, Hsu FM, Tsai CL, Castaneda L, Lee JM, Chang DT, Koong AC. High Serum Levels of Vascular Endothelial Growth Factor-A and Transforming Growth Factor-β1 Before Neoadjuvant Chemoradiotherapy Predict Poor Outcomes in Patients with Esophageal Squamous Cell Carcinoma Receiving Combined Modality Therapy. Ann Surg Oncol 2014; 21:2361-8. [DOI: 10.1245/s10434-014-3611-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 12/28/2022]
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Patel S, Ngounou Wetie AG, Darie CC, Clarkson BD. Cancer secretomes and their place in supplementing other hallmarks of cancer. Adv Exp Med Biol 2014; 806:409-42. [PMID: 24952195 DOI: 10.1007/978-3-319-06068-2_20] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The secretome includes all macromolecules secreted by cells, in particular conditions at defined times, allowing cell-cell communication. Cancer cell secretomes that are altered compared to normal cells have shown significant potential for elucidating cancer biology. Proteins of secretomes are secreted by various secretory pathways and can be studied using different methods. Cancer secretomes seem to play an important role in known hallmarks of cancers such as excessive proliferation, reduced apoptosis, immune invasion, angioneogenesis, alteration in energy metabolism, and development of resistance against anti-cancer therapy [1, 2]. If a significant role of an altered secretome can be identified in cancer cells, using advanced mass spectrometry-based techniques, this may allow researchers to screen and characterize the secretome proteins involved in cancer progression and open up new opportunities to develop new therapies. We aim to elaborate upon recent advances in cancer cell secretome analysis using different proteomics techniques. In this review, we highlight the role of the altered secretome in contributing to already recognized and emerging hallmarks of cancer and we discuss new challenges in the field of secretome analysis.
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Affiliation(s)
- Sapan Patel
- Memorial Sloan Kettering Cancer Center, Molecular Pharmacology and Chemistry Program, 415 East 68th Street, New York, NY, 10065, USA
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Stampolidis P, Ullrich A, Iacobelli S. LGALS3BP, lectin galactoside-binding soluble 3 binding protein, promotes oncogenic cellular events impeded by antibody intervention. Oncogene 2013; 34:39-52. [DOI: 10.1038/onc.2013.548] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 10/21/2013] [Accepted: 11/15/2013] [Indexed: 02/08/2023]
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