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Samiminemati A, Aprile D, Siniscalco D, Di Bernardo G. Methods to Investigate the Secretome of Senescent Cells. Methods Protoc 2024; 7:52. [PMID: 39051266 PMCID: PMC11270363 DOI: 10.3390/mps7040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/27/2024] Open
Abstract
The word "secretome" was first used to describe the proteins that cells secrete under different circumstances; however, recent studies have proven the existence of other molecules such as RNA and chemical compounds in the secretome. The study of secretome has significance for the diagnosis and treatment of disease as it provides insight into cellular functions, including immune responses, development, and homeostasis. By halting cell division, cellular senescence plays a role in both cancer defense and aging by secreting substances known as senescence-associated secretory phenotypes (SASP). A variety of techniques could be used to analyze the secretome: protein-based approaches like mass spectrometry and protein microarrays, nucleic acid-based methods like RNA sequencing, microarrays, and in silico prediction. Each method offers unique advantages and limitations in characterizing secreted molecules. Top-down and bottom-up strategies for thorough secretome analysis are became possible by mass spectrometry. Understanding cellular function, disease causes, and proper treatment targets is aided by these methodologies. Their approaches, benefits, and drawbacks will all be discussed in this review.
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Affiliation(s)
- Afshin Samiminemati
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Domenico Aprile
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Dario Siniscalco
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Giovanni Di Bernardo
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
- Sbarro Health Research Organization, Temple University, Philadelphia, PA 19122, USA
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2
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Luu JK, Johnson FD, Jajarmi J, Sihota T, Shi R, Lu D, Farnsworth D, Spencer SE, Negri GL, Morin GB, Lockwood WW. Characterizing the secretome of EGFR mutant lung adenocarcinoma. Front Oncol 2024; 13:1286821. [PMID: 38260835 PMCID: PMC10801028 DOI: 10.3389/fonc.2023.1286821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background Lung cancer is the leading cause of cancer related death worldwide, mainly due to the late stage of disease at the time of diagnosis. Non-invasive biomarkers are needed to supplement existing screening methods to enable earlier detection and increased patient survival. This is critical to EGFR-driven lung adenocarcinoma as it commonly occurs in individuals who have never smoked and do not qualify for current screening protocols. Methods In this study, we performed mass spectrometry analysis of the secretome of cultured lung cells representing different stages of mutant EGFR driven transformation, from normal to fully malignant. Identified secreted proteins specific to the malignant state were validated using orthogonal methods and their clinical activity assessed in lung adenocarcinoma patient cohorts. Results We quantified 1020 secreted proteins, which were compared for differential expression between stages of transformation. We validated differentially expressed proteins at the transcriptional level in clinical tumor specimens, association with patient survival, and absolute concentration to yield three biomarker candidates: MDK, GDF15, and SPINT2. These candidates were validated using ELISA and increased levels were associated with poor patient survival specifically in EGFR mutant lung adenocarcinoma patients. Conclusions Our study provides insight into changes in secreted proteins during EGFR driven lung adenocarcinoma transformation that may play a role in the processes that promote tumor progression. The specific candidates identified can harnessed for biomarker use to identify high risk individuals for early detection screening programs and disease management for this molecular subgroup of lung adenocarcinoma patients.
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Affiliation(s)
- Jennifer K. Luu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fraser D. Johnson
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jana Jajarmi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Tianna Sihota
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Daniel Lu
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dylan Farnsworth
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sandra E. Spencer
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gian Luca Negri
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Gregg B. Morin
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia (BC), Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia (UBC), Vancouver, BC, Canada
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3
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Zhu Y, Pu Z, Wang G, Li Y, Wang Y, Li N, Peng F. FAM3C: an emerging biomarker and potential therapeutic target for cancer. Biomark Med 2021; 15:373-384. [PMID: 33666514 DOI: 10.2217/bmm-2020-0179] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
FAM3C is a member of the FAM3 family. Recently, overexpression of FAM3C has been reported in numerous types of cancer, including breast and colon cancer. Increasing evidence suggests that elevated FAM3C and its altered subcellular localization are closely associated with tumor formation, invasion, metastasis and poor survival. Moreover, FAM3C has been found to be the regulator of various proteins that associate with cancer, including Ras, STAT3, TGF-β and LIFR. This review summarizes the current knowledge regarding FAM3C, including its structure, expression patterns, regulation, physiological roles and regulatory functions in various malignancies. These findings highlight the importance of FAM3C in cancer development and provide evidence that FAM3C is a novel biomarker and potential therapeutic target for various cancers.
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Affiliation(s)
- Yuanyuan Zhu
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Zhangya Pu
- Department of Infectious Diseases & Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Guoqiang Wang
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Yubin Li
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Yinmiao Wang
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
| | - Fang Peng
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, China
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4
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Shnaider PV, Ivanova OM, Malyants IK, Anufrieva KS, Semenov IA, Pavlyukov MS, Lagarkova MA, Govorun VM, Shender VO. New Insights into Therapy-Induced Progression of Cancer. Int J Mol Sci 2020; 21:E7872. [PMID: 33114182 PMCID: PMC7660620 DOI: 10.3390/ijms21217872] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
The malignant tumor is a complex heterogeneous set of cells functioning in a no less heterogeneous microenvironment. Like any dynamic system, cancerous tumors evolve and undergo changes in response to external influences, including therapy. Initially, most tumors are susceptible to treatment. However, remaining cancer cells may rapidly reestablish the tumor after a temporary remission. These new populations of malignant cells usually have increased resistance not only to the first-line agent, but also to the second- and third-line drugs, leading to a significant decrease in patient survival. Multiple studies describe the mechanism of acquired therapy resistance. In past decades, it became clear that, in addition to the simple selection of pre-existing resistant clones, therapy induces a highly complicated and tightly regulated molecular response that allows tumors to adapt to current and even subsequent therapeutic interventions. This review summarizes mechanisms of acquired resistance, such as secondary genetic alterations, impaired function of drug transporters, and autophagy. Moreover, we describe less obvious molecular aspects of therapy resistance in cancers, including epithelial-to-mesenchymal transition, cell cycle alterations, and the role of intercellular communication. Understanding these molecular mechanisms will be beneficial in finding novel therapeutic approaches for cancer therapy.
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Affiliation(s)
- Polina V. Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (P.V.S.); (O.M.I.); (K.S.A.); (M.A.L.)
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Olga M. Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (P.V.S.); (O.M.I.); (K.S.A.); (M.A.L.)
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
| | - Irina K. Malyants
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow 125047, Russia
| | - Ksenia S. Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (P.V.S.); (O.M.I.); (K.S.A.); (M.A.L.)
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
- Moscow Institute of Physics and Technology (State University), Dolgoprudny 141701, Russia
| | - Ilya A. Semenov
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
| | - Marat S. Pavlyukov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia;
| | - Maria A. Lagarkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (P.V.S.); (O.M.I.); (K.S.A.); (M.A.L.)
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
| | - Vadim M. Govorun
- Laboratory of Simple Systems, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia;
| | - Victoria O. Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (P.V.S.); (O.M.I.); (K.S.A.); (M.A.L.)
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia; (I.K.M.); (I.A.S.)
- Laboratory of Molecular Oncology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
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Heffner K, Hizal DB, Majewska NI, Kumar S, Dhara VG, Zhu J, Bowen M, Hatton D, Yerganian G, Yerganian A, O'Meally R, Cole R, Betenbaugh M. Expanded Chinese hamster organ and cell line proteomics profiling reveals tissue-specific functionalities. Sci Rep 2020; 10:15841. [PMID: 32985598 PMCID: PMC7522264 DOI: 10.1038/s41598-020-72959-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are the predominant production vehicle for biotherapeutics. Quantitative proteomics data were obtained from two CHO cell lines (CHO-S and CHO DG44) and compared with seven Chinese hamster (Cricetulus griseus) tissues (brain, heart, kidney, liver, lung, ovary and spleen) by tandem mass tag (TMT) labeling followed by mass spectrometry, providing a comprehensive hamster tissue and cell line proteomics atlas. Of the 8470 unique proteins identified, high similarity was observed between CHO-S and CHO DG44 and included increases in proteins involved in DNA replication, cell cycle, RNA processing, and chromosome processing. Alternatively, gene ontology and pathway analysis in tissues indicated increased protein intensities related to important tissue functionalities. Proteins enriched in the brain included those involved in acidic amino acid metabolism, Golgi apparatus, and ion and phospholipid transport. The lung showed enrichment in proteins involved in BCAA catabolism, ROS metabolism, vesicle trafficking, and lipid synthesis while the ovary exhibited enrichments in extracellular matrix and adhesion proteins. The heart proteome included vasoconstriction, complement activation, and lipoprotein metabolism enrichments. These detailed comparisons of CHO cell lines and hamster tissues will enhance understanding of the relationship between proteins and tissue function and pinpoint potential pathways of biotechnological relevance for future cell engineering.
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Affiliation(s)
- Kelley Heffner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Natalia I Majewska
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Swetha Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jie Zhu
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | - Michael Bowen
- Allogene Therapeutics, Product and Process Development, South San Francisco, CA, USA
| | - Diane Hatton
- AstraZeneca, Cell Culture and Fermentation Sciences, Gaithersburg, MD, USA
| | | | | | - Robert O'Meally
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert Cole
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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6
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Yan M, Wang W, Zhou J, Chang M, Peng W, Zhang G, Li J, Li H, Bai C. Knockdown of PLAT enhances the anticancer effect of gefitinib in non-small cell lung cancer. J Thorac Dis 2020; 12:712-723. [PMID: 32274137 PMCID: PMC7139041 DOI: 10.21037/jtd.2019.12.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Tyrosine kinase inhibitors (TKIs), such as gefitinib, are widely used as standard treatments for non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations. However, the subsequent inevitable drug resistance has become a major challenge in clinical treatment. The aim of this study was to investigate the role of tissue-type plasminogen activator (PLAT) in gefitinib resistance in NSCLC. Methods The function of PLAT was determined using gefitinib-resistant cells and a nude mouse model. The gene knockdown was achieved by Lentivirus based RNA silence technique. Expression of relevant genes and proteins, cell viability, proliferation, apoptosis, cell cycle, reactive oxygen species levels, mitochondrial membrane potential and differential gene expression was detected by RT-qPCR, western blot, cell counting kit-8 assay, EdU incorporation, flow cytometry, JC-1 dye assay and complementary DNA arrays. The effects of PLAT knockdown on tumorigenesis was analyzed in vivo. Results Gefitinib-resistant cells expressed higher levels of PLAT and that knockdown of PLAT in resistant cells restored gefitinib sensitivity. Tumor proliferation was limited in vivo following PLAT knockdown. Moreover, PLAT knockdown affected mitochondrial function, caused caspase activation and cell cycle arrest, and activated TNF-α signaling, leading to apoptosis of gefitinib-resistant PC9 cells. Conclusions Our results suggest that PLAT reduces apoptosis of NSCLC cells and knockdown of PLAT enhances anticancer effect of gefitinib by upregulating TNF-α signaling.
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Affiliation(s)
- Mengnan Yan
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Wang
- Department of Pathology, Affiliated Yantai Yuhuangding Hospital, Medical College of Qingdao University, Yantai 264000, China
| | - Jian Zhou
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Meijia Chang
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wenjun Peng
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ge Zhang
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jing Li
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Huayin Li
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunxue Bai
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Zubair H, Patel GK, Khan MA, Azim S, Zubair A, Singh S, Srivastava SK, Singh AP. Proteomic Analysis of MYB-Regulated Secretome Identifies Functional Pathways and Biomarkers: Potential Pathobiological and Clinical Implications. J Proteome Res 2020; 19:794-804. [PMID: 31928012 DOI: 10.1021/acs.jproteome.9b00641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Earlier we have shown important roles of MYB in pancreatic tumor pathobiology. To better understand the role of MYB in the tumor microenvironment and identify MYB-associated secreted biomarker proteins, we conducted mass spectrometry analysis of the secretome from MYB-modulated and control pancreatic cancer cell lines. We also performed in silico analyses to determine MYB-associated biofunctions, gene networks, and altered biological pathways. Our data demonstrated significant modulation (p < 0.05) of 337 secreted proteins in MYB-silenced MiaPaCa cells, whereas 282 proteins were differentially present in MYB-overexpressing BxPC3 cells, compared to their respective control cells. Alteration of several phenotypes such as cellular movement, cell death and survival, inflammatory response, protein synthesis, etc. was associated with MYB-induced differentially expressed proteins (DEPs) in secretomes. DEPs from MYB-silenced MiaPaCa PC cells were suggestive of the downregulation of genes primarily associated with glucose metabolism, PI3K/AKT signaling, and oxidative stress response, among others. DEPs from MYB-overexpressing BxPC3 cells suggested the enhanced release of proteins associated with glucose metabolism and cellular motility. We also observed that MYB positively regulated the expression of four proteins with potential biomarker properties, i.e., FLNB, ENO1, ITGB1, and INHBA. Mining of publicly available databases using Oncomine and UALCAN demonstrated that these genes are overexpressed in pancreatic tumors and associated with reduced patient survival. Altogether, these data provide novel avenues for future investigations on diverse biological functions of MYB, specifically in the tumor microenvironment, and could also be exploited for biomarker development.
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Affiliation(s)
- Haseeb Zubair
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Girijesh Kumar Patel
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Mohammad Aslam Khan
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Shafquat Azim
- Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Asif Zubair
- Molecular and Computational Biology, School of Biological Sciences, Dornsife College of Letters, Arts and Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Seema Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
| | - Sanjeev Kumar Srivastava
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States
| | - Ajay Pratap Singh
- Department of Pathology, College of Medicine , University of South Alabama , Mobile , Alabama 36617 , United States.,Mitchell Cancer Institute , University of South Alabama , 1660 Springhill Avenue , Mobile , Alabama 36604 , United States.,Department of Biochemistry and Molecular Biology, College of Medicine , University of South Alabama , Mobile , Alabama 36688 , United States
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8
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Wang Z, Liu G, Jiang J. Profiling of apoptosis- and autophagy-associated molecules in human lung cancer A549 cells in response to cisplatin treatment using stable isotope labeling with amino acids in cell culture. Int J Oncol 2019; 54:1071-1085. [PMID: 30664195 DOI: 10.3892/ijo.2019.4690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 10/01/2018] [Indexed: 11/06/2022] Open
Abstract
Cis‑diammine‑dichloro‑platinum II‑based adjuvant chemotherapy provides an alternative therapy to improve the survival of patients with lung tumors, especially those with non‑small cell lung cancer (NSCLC). However, drug resistance is a large clinical problem and its underlying mechanism remains unclear. In the present study, NSCLC A549 cells were treated with a low concentration of cisplatin in order to observe and determine the development of chemoresistance, via growth curves, colony forming assays and apoptosis assays. Then the induction of autophagy was examined in the cisplatin‑treated A549 cells with a fluorescence reporter. Profiled proteins in the cisplatin‑treated A549 cells were also assessed using the stable isotope labeling by amino acids in cell culture (SILAC) method, and then the differentially expressed molecules were verified. The results demonstrated that A549 cells became less sensitive to cisplatin [resistant A549 cells (A549R)] following 20 passages in the medium containing a low concentration of cisplatin, with less apoptotic cells post‑cisplatin treatment. A549R cells grew more efficiently in the cisplatin medium, with more colony formation and more cells migrating across the baseline. In addition, NSCLC results demonstrated that more autophagy‑related proteins (ATGs) were expressed in the A549R cells. Furthermore, the western blotting results confirmed this upregulation of ATGs in A549R cells. In addition, two repeated SILAC screening experiments recognized 15 proteins [glucose‑regulated protein, 78 kDa (GRP78), heat shock protein 71, pre‑mRNA processing factor 19, polypyrimidine tract binding protein 1, translationally controlled tumor protein, Cathepsin D, Cytochrome c, thioredoxin domain containing 5, MutS homolog (MSH) 6, Annexin A2 (ANXA2), BRCA2 and Cyclin dependent kinase inhibitor 1A interacting protein, MSH2, protein phosphatase 2A 55 kDa regulatory subunit Bα, Rho glyceraldehyde‑3‑phosphate‑dissociation inhibitor 1 and ANXA4] that were upregulated by >1.5‑fold in heavy (H)‑ and light (L)‑labeled A549R cells. In addition, 16 and 14 proteins were downregulated by >1.5‑fold in the H‑ and L‑labeled A549R cells, respectively. The majority of the downregulated proteins were associated with apoptosis. In conclusion, the present study isolated a cisplatin‑resistant human lung cancer A549 cell clone, with reduced apoptosis and high levels of autophagy, in response to cisplatin treatment. In cisplatin‑resistant A549R cells, SILAC proteomics recognized the high expression of GRP78 and other proteins that are associated with anti‑apoptosis and/or autophagy promotion.
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Affiliation(s)
- Zongqiang Wang
- Department of Medical Services, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Guifeng Liu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Jinlan Jiang
- Science Research Center, Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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9
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Piotrowski C, Sinz A. Structural Investigation of Proteins and Protein Complexes by Chemical Cross-Linking/Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:101-121. [PMID: 30617826 DOI: 10.1007/978-981-13-2200-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During the last two decades, cross-linking combined with mass spectrometry (MS) has evolved as a valuable tool to gain structural insights into proteins and protein assemblies. Structural information is obtained by introducing covalent connections between amino acids that are in spatial proximity in proteins and protein complexes. The distance constraints imposed by the cross-linking reagent provide information on the three-dimensional arrangement of the covalently connected amino acid residues and serve as basis for de-novo or homology modeling approaches. As cross-linking/MS allows investigating protein 3D-structures and protein-protein interactions not only in-vitro, but also in-vivo, it is especially appealing for studying protein systems in their native environment. In this chapter, we describe the principles of cross-linking/MS and illustrate its value for investigating protein 3D-structures and for unraveling protein interaction networks.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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10
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Zhu Y, Bradic J. Significance testing in non-sparse high-dimensional linear models. Electron J Stat 2018. [DOI: 10.1214/18-ejs1443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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