1
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Kang Z, Luo Y, Xiao E, Li Q, Wang L. CD151 and prostate cancer progression: A review of current literature. Asia Pac J Clin Oncol 2022. [DOI: 10.1111/ajco.13890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 12/05/2022]
Affiliation(s)
- Zhen Kang
- Department of RadiologyTongji HospitalTongji Medical CollegeHuazhong University of Science and Technology WuhanChina
| | - Yanping Luo
- Department of Immunology School of Basic Medical Sciences Lanzhou University Lanzhou China
| | - Enhua Xiao
- Department of Radiology The Second Xiangya Hospital Central South University Changsha China
| | - Qiubai Li
- Department of Radiology University Hospitals Cleveland Medical Center Cleveland Ohio USA
| | - Liang Wang
- Department of RadiologyTongji HospitalTongji Medical CollegeHuazhong University of Science and Technology WuhanChina
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2
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Shao S, Piao L, Wang J, Guo L, Wang J, Wang L, Tong L, Yuan X, Han X, Fang S, Zhu J, Wang Y. Tspan9 Induces EMT and Promotes Osteosarcoma Metastasis via Activating FAK-Ras-ERK1/2 Pathway. Front Oncol 2022; 12:774988. [PMID: 35280793 PMCID: PMC8906905 DOI: 10.3389/fonc.2022.774988] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/21/2022] [Indexed: 01/14/2023] Open
Abstract
Object At present, there are few effective treatment options available to patients suffering from osteosarcoma (OS). Clarifying the signaling pathways that govern OS oncogenesis may highlight novel approaches to treating this deadly form of cancer. Recent experimental evidence suggests that the transmembrane protein tetraspanin-9 (Tspan9) plays a role in tumor development. This study was thus formulated to assess the molecular role of Tspan9 as a regulator of OS cell metastasis. Methods Gene expression in OS cell lines was evaluated via qRT-PCR, while CCK-8, colony formation, Transwell, and wound healing assays were used to explore the in vitro proliferative, invasive, and migratory activities of OS cells. The relationship between Tspan9 and in vivo OS cell metastasis was assessed by injecting these cells into the tail vein of nude mice. Interactions between the Tspan9 and integrin β1 proteins were explored through mass spectrometric and co-immunoprecipitation, and Western blotting to assess the functional mechanisms whereby Tspan9 shapes OS pathogenesis. Results Both primary OS tumors and OS cell lines commonly exhibited Tspan9 upregulation, and the knockdown of this tetraspanin suppressed the migration, invasion, and epithelial-mesenchymal transition (EMT) activity in OS cells, whereas Tspan9 overexpression resulted in opposite phenotypes. Tumor lung metastasis were significantly impaired in mice implanted with HOS cells in which Tspan9 was downregulated as compared to mice implanted with control HOS cells. Tspan9 was also found to interact with β1 integrin and to contribute to OS metastasis via the amplification of integrin-mediated downstream FAK/Ras/ERK1/2 signaling pathway. Conclusion These data suggest that Tspan9 can serve as a promising therapeutic target in OS.
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Affiliation(s)
- Shijie Shao
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Lianhua Piao
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Jiangsong Wang
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Liwei Guo
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jiawen Wang
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Luhui Wang
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Lei Tong
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiaofeng Yuan
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xu Han
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Sheng Fang
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Junke Zhu
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yimin Wang
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, China
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3
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Erfani S, Hua H, Pan Y, Zhou BP, Yang XH. The Context-Dependent Impact of Integrin-Associated CD151 and Other Tetraspanins on Cancer Development and Progression: A Class of Versatile Mediators of Cellular Function and Signaling, Tumorigenesis and Metastasis. Cancers (Basel) 2021; 13:cancers13092005. [PMID: 33919420 PMCID: PMC8122392 DOI: 10.3390/cancers13092005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/18/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Tetraspanins are a family of molecules abundantly expressed on the surface of normal or tumor cells. They have been implicated in recruiting or sequestering key molecular regulators of malignancy of a variety of human cancers, including breast and lung cancers, glioblastoma and leukemia. Yet, how their actions take place remains mysterious due to a lack of traditional platform for molecular interactions. The current review digs into this mystery by examining findings from recent studies of multiple tetraspanins, particularly CD151. The molecular basis for differential impact of tetraspanins on tumor development, progression, and spreading to secondary sites is highlighted, and the complexity and plasticity of their control over tumor cell activities and interaction with their surroundings is discussed. Finally, an outlook is provided regarding tetraspanins as candidate biomarkers and targets for the diagnosis and treatment of human cancer. Abstract As a family of integral membrane proteins, tetraspanins have been functionally linked to a wide spectrum of human cancers, ranging from breast, colon, lung, ovarian, prostate, and skin carcinomas to glioblastoma. CD151 is one such prominent member of the tetraspanin family recently suggested to mediate tumor development, growth, and progression in oncogenic context- and cell lineage-dependent manners. In the current review, we summarize recent advances in mechanistic understanding of the function and signaling of integrin-associated CD151 and other tetraspanins in multiple cancer types. We also highlight emerging genetic and epigenetic evidence on the intrinsic links between tetraspanins, the epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs), and the Wnt/β-catenin pathway, as well as the dynamics of exosome and cellular metabolism. Finally, we discuss the implications of the highly plastic nature and epigenetic susceptibility of CD151 expression, function, and signaling for clinical diagnosis and therapeutic intervention for human cancer.
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Affiliation(s)
- Sonia Erfani
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA;
- Markey Cancer Center, University of Kentucky Medical Center, Lexington, KY 40536, USA
- Pharmacy Department, St. Elizabeth Healthcare, Edgewood, KY 41017, USA
| | - Hui Hua
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230001, China; (H.H.); (Y.P.)
- Provincial Hospital, Hefei, Anhui 230001, China
| | - Yueyin Pan
- The First Affiliated Hospital of University of Science and Technology of China, Hefei, Anhui 230001, China; (H.H.); (Y.P.)
- Provincial Hospital, Hefei, Anhui 230001, China
| | - Binhua P. Zhou
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, USA;
| | - Xiuwei H. Yang
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536, USA;
- Markey Cancer Center, University of Kentucky Medical Center, Lexington, KY 40536, USA
- Correspondence: ; Tel.: +1-859-323-1996
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4
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Yunusova NV, Zambalova EA, Patysheva MR, Kolegova ES, Afanas'ev SG, Cheremisina OV, Grigor'eva AE, Tamkovich SN, Kondakova IV. Exosomal Protease Cargo as Prognostic Biomarker in Colorectal Cancer. Asian Pac J Cancer Prev 2021; 22:861-869. [PMID: 33773551 PMCID: PMC8286660 DOI: 10.31557/apjcp.2021.22.3.861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Objective: The aim of the study was to develop a model for predicting cancer risk in colorectal polyps’ patients (CPPs), as well as to reveal additional prognosis factors for Stage III colorectal cancer based on differences in subpopulations of tetraspanins, tetraspanin-associated and tetraspanin-non-associated proteases in blood plasma exosomes of CPPs and colorectal cancer patients (CRCPs). Methods: The subpopulations of CD151- and Tspan8-positive exosomes, the subpopulations of metalloproteinase at the surface of СD9-positive exosomes and the level of 20S proteasomes in plasma exosomes in 15 CPPs (tubulovillous adenomas) and 60 CRCPs were evaluated using flow cytometry and Western blotting. Logistic regression analysis was performed to predict cancer risk of CPPs. Results: The levels of 20S proteasomes in exosomes, MMP9+, MMP9+/MMP2+/EMMPRIN+ in CD9-positive blood plasma exosomes are associated with the risk of malignant transformation of colorectal tubulovillous adenomas. In patients with Stage III CRC, the levels of 20S proteasomes (less than 2 units) and MMP9+ subpopulations (more than 61%) in plasma exosomes are unfavorable prognostic factors for overall survival. The levels of 20S proteasomes and ADAM10+/ADAM17- subpopulations in CD9-positive blood plasma exosomes are the most significant values for predicting relapse-free survival. Conclusion: Protease cargo in CD9-positive blood plasma exosomes is prognostic biomarker for colorectal polyps and colorectal cancer.
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Affiliation(s)
- Natalia V Yunusova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.,Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk, Russia
| | - Elena A Zambalova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Marina R Patysheva
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Elena S Kolegova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Sergey G Afanas'ev
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Olga V Cheremisina
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Alina E Grigor'eva
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana N Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Clinical Biochemistry, V. Zelman Institute for the Medicine, Novosibirsk, Russia
| | - Irina V Kondakova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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5
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Han R, Hensley PJ, Li J, Zhang Y, Stark TW, Heller A, Qian H, Shi J, Liu Z, Huang JA, Jin T, Wei X, Zhou BP, Wu Y, Kyprianou N, Chen J, Yang XH. Integrin-associated CD151 is a suppressor of prostate cancer progression. Am J Transl Res 2020; 12:1428-1442. [PMID: 32355552 PMCID: PMC7191174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Owing to the complexity of interacting molecular networks on the cell surface, integrin-associated tetraspanin CD151 remains controversial regarding its clinical importance and functional impact in prostate cancer. The current study evaluated dynamics and clinical importance of CD151 expression and its function in prostate cancer by IHC analysis of two independent patient cohorts (n=80, 181), bioinformatic interrogation of the TCGA database, and evaluation of gene knockdown effect at the cellular level. Our data showed that aside from high mRNA expression, CD151 was primarily localized to intercellular junctions at the plasma membrane in normal prostate glands or benign tissues, regardless of nature of antibodies used. By contrast, in primary tumors from patients with metastatic disease, CD151 was largely localized in the cytosol. Furthermore, the level of the cell-cell junction-linked CD151 was inversely associated with Gleason grade and tumor stage (P<0.001 for both). The portion of primary tumors expressing junctional CD151 was also three-fold less in the metastatic patient population than its counterpart (P<0.001). In line with these observations, CD151 and its associated α3β1 or α6β4 integrin inversely correlated with androgen receptor (AR) at the mRNA level (Spearman coefficient: -0.44, -0.48 and -0.42) in the TCGA cohort. Expression of these adhesion molecules also correlated with DNA methylation in their promoters (Spearman coefficient: -0.37, -0.71 and -0.82). Combined, these data suggest that CD151 and associated integrins are linked to tumor metastasis through AR and the epigenetic program. Meanwhile, CD151 knockdown in E-cadherin-positive tumor cells led to increased cell proliferation and induction of the epithelial-mesenchymal transition (EMT)-like phenotype. Given the strong RGD-binding integrin dependence of EMT-featured tumor cells, we examined focal adhesion kinase (FAK), their key signaling effector, in the above patient cohorts. In contrast to CD151, FAK exhibited positive correlation with tumor grade and stage as well as AR and p53 inactivation at either mRNA, protein or genomic level. Taken together, our results suggest that CD151 represses prostate cancer by antagonizing cell proliferation, EMT and the signaling of RGD-binding integrins. Since this anti-tumorigenic role is prone to the AR-mediated transcriptional and epigenetic regulation, CD151 and possibly α3β1 and α6β4 integrins are of potential biomarkers for metastatic prostate cancer.
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Affiliation(s)
- Rongbo Han
- Department of Oncology, Nanjing First HospitalNanjing, Jiangsu, P. R. China
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
| | - Patrick J Hensley
- Department of Urology, University of Kentucky College of MedicineLexington 40536, KY, USA
| | - Jieming Li
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
- Center of Drug Discovery, China Pharmaceutical UniversityNanjing, Jiangsu, P. R. China
| | - Yang Zhang
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
- Department of Respiratory Medicine, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, P. R. China
| | - Timothy W Stark
- Department of Urology, University of Kentucky College of MedicineLexington 40536, KY, USA
| | - Allie Heller
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
| | - Hai Qian
- Center of Drug Discovery, China Pharmaceutical UniversityNanjing, Jiangsu, P. R. China
| | - Junfeng Shi
- Department of Oncology, Nanjing First HospitalNanjing, Jiangsu, P. R. China
| | - Zeyi Liu
- Department of Respiratory Medicine, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, P. R. China
| | - Jian-An Huang
- Department of Respiratory Medicine, First Affiliated Hospital of Soochow UniversitySuzhou, Jiangsu, P. R. China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, Division of Life Sciences and Medicine, University of Science and Technology of ChinaHefei, Anhui, P.R. China
| | - Xiaowei Wei
- Department of Oncology, Nanjing First HospitalNanjing, Jiangsu, P. R. China
| | - Binhua P Zhou
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
| | - Yadi Wu
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
| | - Natasha Kyprianou
- Department of Urology, University of Kentucky College of MedicineLexington 40536, KY, USA
| | - Jinfei Chen
- Cancer Center, Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, and Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical UniversityNanjing, Jiangsu, P. R. China
| | - Xiuwei H Yang
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, and Markey Cancer Center, University of KentuckyLexington 40536, KY, USA
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6
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Hayward S, Gachehiladze M, Badr N, Andrijes R, Molostvov G, Paniushkina L, Sopikova B, Slobodová Z, Mgebrishvili G, Sharma N, Horimoto Y, Burg D, Robertson G, Hanby A, Hoar F, Rea D, Eckhardt BL, Ueno NT, Nazarenko I, Long HM, van Laere S, Shaaban AM, Berditchevski F. The CD151-midkine pathway regulates the immune microenvironment in inflammatory breast cancer. J Pathol 2020; 251:63-73. [PMID: 32129471 DOI: 10.1002/path.5415] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/27/2020] [Accepted: 02/25/2020] [Indexed: 12/19/2022]
Abstract
The immune microenvironment in inflammatory breast cancer (IBC) is poorly characterised, and molecular and cellular pathways that control accumulation of various immune cells in IBC tissues remain largely unknown. Here, we discovered a novel pathway linking the expression of the tetraspanin protein CD151 in tumour cells with increased accumulation of macrophages in cancerous tissues. It is notable that elevated expression of CD151 and a higher number of tumour-infiltrating macrophages correlated with better patient responses to chemotherapy. Accordingly, CD151-expressing IBC xenografts were characterised by the increased infiltration of macrophages. In vitro migration experiments demonstrated that CD151 stimulates the chemoattractive potential of IBC cells for monocytes via mechanisms involving midkine (a heparin-binding growth factor), integrin α6β1, and production of extracellular vesicles (EVs). Profiling of chemokines secreted by IBC cells demonstrated that CD151 increases production of midkine. Purified midkine specifically stimulated migration of monocytes, but not other immune cells. Further experiments demonstrated that the chemoattractive potential of IBC-derived EVs is blocked by anti-midkine antibodies. These results demonstrate for the first time that changes in the expression of a tetraspanin protein by tumour cells can affect the formation of the immune microenvironment by modulating recruitment of effector cells to cancerous tissues. Therefore, a CD151-midkine pathway can be considered as a novel target for controlled changes of the immune landscape in IBC. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Steven Hayward
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Mariam Gachehiladze
- Department of Clinical and Molecular Pathology, Palacký Univerzity, Olomouc, Czech Republic
| | - Nahla Badr
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK.,Department of Pathology, Menoufia University School of Medicine, Menoufia, Egypt
| | - Regina Andrijes
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Guerman Molostvov
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Liliia Paniushkina
- Faculty of Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Barbora Sopikova
- Department of Clinical and Molecular Pathology, Palacký Univerzity, Olomouc, Czech Republic
| | - Zuzana Slobodová
- Department of Clinical and Molecular Pathology, Palacký Univerzity, Olomouc, Czech Republic
| | - Giorgi Mgebrishvili
- Department of Clinical and Molecular Pathology, Palacký Univerzity, Olomouc, Czech Republic
| | - Nisha Sharma
- Breast Unit, St James Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Yoshiya Horimoto
- Department of Breast Surgical Oncology, Juntendo University School of Medicine, Tokyo, Japan
| | | | | | - Andrew Hanby
- University of Leeds, Leeds Institute of Cancer and Pathology (LICAP) Leeds, Leeds, UK
| | - Fiona Hoar
- Hospital, Sandwell and West Birmingham Hospitals, Department of General and Breast Surgery, Birmingham, UK
| | - Daniel Rea
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Bedrich L Eckhardt
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX, USA
| | - Irina Nazarenko
- Faculty of Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heather M Long
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Steven van Laere
- Translational Cancer Research Unit Center for Oncological Research, University Antwerp, Antwerp, Belgium
| | - Abeer M Shaaban
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, UK
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7
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Wong AH, Tran T. CD151 in Respiratory Diseases. Front Cell Dev Biol 2020; 8:64. [PMID: 32117989 PMCID: PMC7020194 DOI: 10.3389/fcell.2020.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
The tetraspanin, Cluster of Differentiation 151 (CD151), is ubiquitously expressed in adult tissue, especially in the lungs where it has been implicated in lung cancer, asthma, influenza, and idiopathic pulmonary fibrosis (IPF). CD151 interacts with laminin-binding integrins and growth factor receptors, and is reported in cancer-promoting processes such as tumor initiation, metastasis, and angiogenesis. In asthma, CD151 was shown to promote airways hyperresponsiveness through calcium signaling whereas in influenza, CD151 was shown to be a novel host factor for nuclear viral export signaling. Furthermore, CD151 was shown to be associated with increased disease severity and poorer survival outcome in asthma and lung cancer, respectively. In this review, we provide an update on the current understanding of CD151 with regards to its contribution to lung pathophysiology. We also summarize factors that have been shown to regulate CD151 expression and identify key areas that need to be taken into consideration for its utility as a screening or prognostic tool in disease management and/or as a therapeutic target for the treatment of lung diseases.
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Affiliation(s)
- Amanda H Wong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Thai Tran
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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8
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Li H, Li J, Han R, Deng X, Shi J, Huang H, Hamad N, McCaughley A, Liu J, Wang C, Chen K, Wei D, Qiang J, Thatcher S, Wu Y, Liu C, Thibault O, Wei X, Chen S, Qian H, Zhou BP, Xu P, Yang XH. Deletion of tetraspanin CD151 alters the Wnt oncogene-induced mammary tumorigenesis: A cell type-linked function and signaling. Neoplasia 2019; 21:1151-1163. [PMID: 31783316 PMCID: PMC6888732 DOI: 10.1016/j.neo.2019.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022] Open
Abstract
Tetraspanin CD151 is increasingly implicated as a multifaceted mediator of cancer development and progression. Here we investigated the role of CD151 in breast cancer in the context of the Wnt oncogenic activation. Our data showed that removal of one or both of CD151 alleles in the MMTV-Wnt1 model significantly decreased the tumor-free survival of mice from 34 weeks on average to 22 weeks and 18 weeks, respectively. This effect coincided with an accelerated tumor growth and an increased number of Ki-67+ proliferative cells. Mechanistically, the CD151-deficient tumors were largely ER+, and exhibited hyperactivation of the Wnt pathway as reflected by a marked upregulation in β-catenin and Cyclin D1, and their target genes. In addition, E-cadherin displayed a cytosolic distribution and transcription factor Snail was markedly upregulated. Collectively, this data implies that CD151 suppresses the Wnt1-driven tumorigenesis, at least in part, via counteracting the epithelial-mesenchymal transition (EMT)-like program in luminal epithelial cells. Meanwhile, the proportion of tumor cells expressing CK5 or p63, the biomarkers of myoepithelial/basal cells, markedly decreased in the absence of CD151. This change was accompanied by a decreased invasiveness of tumors and their incompetence to form a long-term cell culture. Consistent with this basal cell-linked role, the CD151 downregulation impairs mammosphere formation in MCF-10A cells and the defect was rescued by re-expression of intact CD151 ORF, but not its integrin binding-defective mutant. Overall, our study suggests that CD151 is a key player in the Wnt oncogene-driven tumorigenesis and impacts breast cancer malignancy in a cell type-dependent manner.
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Affiliation(s)
- Hongxia Li
- Freshwater Fisheries Research Center, Ministry of Agriculture, and Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu Province, PR China; Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Jieming Li
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY; Center of Drug Discovery, China Pharmaceutical University, Nanjing, Jiangsu Province, PR China
| | - Rongbo Han
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY; Department of Oncology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Xinyu Deng
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Junfong Shi
- Department of Oncology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Huanhuan Huang
- Department of Oncology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Nevean Hamad
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Abigail McCaughley
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Jinpeng Liu
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Chi Wang
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Kuey Chen
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Dongping Wei
- Department of Oncology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Jun Qiang
- Freshwater Fisheries Research Center, Ministry of Agriculture, and Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu Province, PR China
| | - Sean Thatcher
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Yadi Wu
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Chunming Liu
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Olivier Thibault
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Xiaowei Wei
- Department of Oncology, Nanjing Medical University, Nanjing, Jiangsu Province, PR China
| | - Song Chen
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huaian, Jiangsu Province, PR China.
| | - Hai Qian
- Center of Drug Discovery, China Pharmaceutical University, Nanjing, Jiangsu Province, PR China.
| | - Binhua P Zhou
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY.
| | - Pao Xu
- Freshwater Fisheries Research Center, Ministry of Agriculture, and Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu Province, PR China.
| | - Xiuwei H Yang
- Department of Pharmacology and Nutritional Sciences, Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY.
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9
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Ramovs V, Secades P, Song JY, Thijssen B, Kreft M, Sonnenberg A. Absence of integrin α3β1 promotes the progression of HER2-driven breast cancer in vivo. Breast Cancer Res 2019; 21:63. [PMID: 31101121 PMCID: PMC6525362 DOI: 10.1186/s13058-019-1146-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023] Open
Abstract
Background HER2-driven breast cancer is correlated with poor prognosis, especially during its later stages. Numerous studies have shown the importance of the integrin α3β1 during the initiation and progression of breast cancer; however, its role in this disease is complex and often opposite during different stages and in different types of tumors. In this study, we aim to elucidate the role of integrin α3β1 in a genetically engineered mouse model of HER2-driven mammary tumorigenesis. Methods To investigate the role of α3β1 in HER2-driven tumorigenesis in vivo, we generated a HER2-driven MMTV-cNeu mouse model of mammary tumorigenesis with targeted deletion of Itga3 (Itga3 KO mice). We have further used several established triple-negative and HER2-overexpressing human mammary carcinoma cell lines and generated ITGA3-knockout cells to investigate the role of α3β1 in vitro. Invasion of cells was assessed using Matrigel- and Matrigel/collagen I-coated Transwell assays under static or interstitial fluid flow conditions. The role of α3β1 in initial adhesion to laminin and collagen was assessed using adhesion assays and immunofluorescence. Results Tumor onset in mice was independent of the presence of α3β1. In contrast, the depletion of α3β1 reduced the survival of mice and increased tumor growth and vascularization. Furthermore, Itga3 KO mice were significantly more likely to develop lung metastases and had an increased metastatic burden compared to WT mice. In vitro, the deletion of ITGA3 caused a significant increase in the cellular invasion of HER2-overexpressing SKBR3, AU565, and BT474 cells, but not of triple-negative MDA-MB-231. This invasion suppressing function of α3β1 in HER2-driven cells depended on the composition of the extracellular matrix and the interstitial fluid flow. Conclusion Downregulation of α3β1 in a HER2-driven mouse model and in HER2-overexpressing human mammary carcinoma cells promotes progression and invasiveness of tumors. The invasion-suppressive role of α3β1 was not observed in triple-negative mammary carcinoma cells, illustrating the tumor type-specific and complex function of α3β1 in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13058-019-1146-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Veronika Ramovs
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pablo Secades
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Oncode Institute and Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maaike Kreft
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arnoud Sonnenberg
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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10
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Yunusova NV, Tugutova EA, Tamkovich SN, Kondakova IV. [The role of exosomal tetraspanins and proteases in tumor progression]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 64:123-133. [PMID: 29723143 DOI: 10.18097/pbmc20186402123] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Major (CD9, CD63, CD81) and others (CD82, CD151, Tspan8) tetraspanins are widely represented in exosomes, where they interact with various proteins and form functional tetraspanin complexes. Tetraspanin complexes include proteases. Tetraspanin-associated exosomal proteases (ADAM proteases, MMPs, EMMPRIN) play an important role in the processes of cell motility, migration, invasion and formation of metastases. Also, a significant contribution to tumor progression is made by proteases that are not associated with tetraspanins. They destabilize intercellular contacts, promote migration and invasion of tumor cells, participate in the regulation of the expression IGF-I, VEGF and transcription factors activation/deactivation. The role of other proteases of exosomes in the processes of tumor progression is being clarified.
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Affiliation(s)
- N V Yunusova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia; Siberian State Medical University, Tomsk, Russia
| | - E A Tugutova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - S N Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia; Novosibirsk State Medical University, Novosibirsk, Russia
| | - I V Kondakova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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11
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Mieszkowska M, Piasecka D, Potemski P, Debska-Szmich S, Rychlowski M, Kordek R, Sadej R, Romanska HM. Tetraspanin CD151 impairs heterodimerization of ErbB2/ErbB3 in breast cancer cells. Transl Res 2019; 207:44-55. [PMID: 30639369 DOI: 10.1016/j.trsl.2018.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 01/07/2023]
Abstract
CD151/Tspan24 (SFS-1, PETA3) is one of the best characterized members of the tetraspanin family, whose involvement in breast cancer (BCa) progression was demonstrated both in vitro and in vivo. We have recently reported that in ErbB2-overexpressing BCa cells grown in 3D laminin-rich extracellular matrix, CD151 regulated basal phosphorylation and homodimerization of ErbB2 and sensitized the cells to Herceptin (trastuzumab). Following from these data, we have here analyzed an involvement of CD151 in regulation of ErbB2/ErbB3 heterodimerization and its impact on cell response to Herceptin. CD151 was found to: (1) impair ErbB2/ErbB3 heterodimerization, (2) inhibit heregulin-dependent cell growth in 3D and signaling, and (3) counteract the protective effect of heregulin on Herceptin-mediated growth inhibition. Analysis of tissue samples demonstrated for the first time clinical significance of CD151 in patients with ErbB2-overexpressing BCa undergone trastuzumab-based therapy. Consistent with in vitro results, CD151 impact on disease outcome was ErbB3-dependent. In patients with ErbB3-negative tumors, CD151 significantly improved both overall survival (OS) (hazard ratio [HR] = 0.19, P = 0.034) and progression-free survival (PFS) (HR = 0.36, P = 0.043), while in ErbB3-positive cases it had no significant effect on patient survival (OS: HR = 3.33, P = 0.283; PFS: HR = 2.40, P = 0.208). These results support previous findings and show that CD151 acts as an important component of ErbB2 signaling axis in BCa cells, affecting their sensitivity to ErbB2-targeting therapy.
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Affiliation(s)
- Magdalena Mieszkowska
- Department of Molecular Enzymology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Piotr Potemski
- Department of Chemotherapy, Medical University of Lodz and Copernicus Memorial Hospital in Lodz, Lodz, Poland
| | - Sylwia Debska-Szmich
- Department of Chemotherapy, Medical University of Lodz and Copernicus Memorial Hospital in Lodz, Lodz, Poland
| | - Michal Rychlowski
- Department of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Radzislaw Kordek
- Department of Pathology, Medical University of Lodz, Lodz, Poland
| | - Rafal Sadej
- Department of Molecular Enzymology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Hanna M Romanska
- Department of Pathology, Medical University of Lodz, Lodz, Poland.
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12
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Expression of tetraspanins NET-6 and CD151 in breast cancer as a potential tumor biomarker. Clin Exp Med 2019; 19:377-384. [PMID: 31004251 DOI: 10.1007/s10238-019-00554-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/12/2019] [Indexed: 02/07/2023]
Abstract
Tetraspanins have been implicated in multiple biological functions including protein networking and cell signaling. NET-6 (TSPAN 13) has been demonstrated to be a tumor suppressor gene in breast cancer, while CD151 is more likely to act as an oncogene. However, the biological function of both proteins is still inconclusive. Immunohistochemistry was used to analyze the expression of NET-6 and CD151 proteins in breast tumors and benign epithelial cells. The cellular expression of both markers was correlated with HER2, ER, and PR status as well as tumor grade, Ki-67 scores, invasion, and metastasis. Expression of NET-6 and CD151 was variable both in tumors and in benign epithelial cells. Expression of NET-6 and CD151 was stronger in tumors than in benign epithelial cells. The expression of NET-6 was also stronger in HER2-negative, low-grade, lymphovascular invasion-negative, and non-metastatic breast tumors. There was no correlation between NET-6 expression and ER, or PR, or triple-negative status. There was no correlation between CD151 expression and HER2, ER, PR, or triple-negative status, tumor grade, or Ki-67 scores, invasion, and metastasis. The expression of tetraspanins NET-6 and CD151 may indicate an alteration of their biological function during neoplastic transformation. NET-6 expression in tumors might be a potential marker indicating the outcome of breast cancer.
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13
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Abstract
A large variety of molecular pathways in melanoma progression suggests that no individual molecular alteration is crucial in itself. Our aim was to define the molecular alterations underlying metastasis formation. Gene expression profiling was performed using microarray and qRT-PCR to define alterations between matched primary and metastatic melanoma cell lines. These data were integrated with publicly available unmatched tissue data. The invasiveness of cell lines was determined by Matrigel invasion assays and invasive clones from primary melanoma-derived cell lines were also selected. Two metastatic cell line models were created: the regional lymph node WM983A-WM983A-WM983B and the distant lung WM793B-WM793B-1205Lu metastatic models. The majority of metastasis genes were downregulated and enriched in adhesion and ITGA6-B4 pathways. Upregulation of immune pathways was characteristic of distant metastases, whereas increased Rap1 signaling was specific for regional (sub)cutaneous metastases. qRT-PCR analysis of selected integrins (A2, A3, A4, A9, B5, B8, A6, B1, and B3) highlighted the possible importance of ITGA3/4 and B8 in the metastatic process, distinguishing regional and distant metastases. We identified functionally relevant gene clusters that influenced metastasis formation. Our data provide further evidence that integrin expression patterns may be important in distant metastasis formation.
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14
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Zeng P, Wang YH, Si M, Gu JH, Li P, Lu PH, Chen MB. Tetraspanin CD151 as an emerging potential poor prognostic factor across solid tumors: a systematic review and meta-analysis. Oncotarget 2018; 8:5592-5602. [PMID: 27888619 PMCID: PMC5354932 DOI: 10.18632/oncotarget.13532] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/02/2016] [Indexed: 02/01/2023] Open
Abstract
Tetraspanin CD151, also known as PETA-3 or SFA-1, has been reported to predict prognosis in various solid tumors. Yet, the results of these studies remained inconclusive. Here, we performed this meta-analysis of relevant studies published on the topic to quantitatively evaluate the clinicopathological significance of CD151 in solid tumors. The relevant articles were identified via searching the PubMed, Web of Science and Embase database. The pooled hazard ratios (HRs) and corresponding 95% confidence intervals (CI) of overall survival (OS) and disease-free survival (DFS) were calculated to evaluate the prognostic value of CD151 expression in patients with solid tumors. A total of 19 studies involving 4, 270 participants were included in the study, we drew the conclusion that CD151 overexpression was associated with statistically significant poor OS (pooled HR = 1.498, 95% CI = 1.346-1.667, P<0.001) and poor DFS (pooled HR = 1.488, 95% CI = 1.314-1.685, P<0.001). Furthermore, the subgroup analysis revealed that the associations between CD151 overexpression and the outcome endpoints (OS or TTP) were significant within the Asian region and European, as well in patients with breast cancer or gastric cancer. Taken together, the incorporative HR showed CD151 overexpression was associated with poor survival in human solid tumors. CD151 could be a valuable prognosis biomarker or a potential therapeutic target of solid tumors.
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Affiliation(s)
- Ping Zeng
- Department of Radiotherapy and Oncology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan 215300, Jiangsu Province, China
| | - Yin-Hua Wang
- Department of Radiotherapy and Oncology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan 215300, Jiangsu Province, China.,Department of Oncology, Changshu Second People's Hospital Affiliated to Yangzhou University, Changshu 215500, Jiangsu Province, China
| | - Meng Si
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China
| | - Jin-Hua Gu
- Department of Radiotherapy and Oncology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan 215300, Jiangsu Province, China
| | - Ping Li
- Department of Radiotherapy and Oncology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan 215300, Jiangsu Province, China
| | - Pei-Hua Lu
- Department of Medical Oncology, Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu Province, China
| | - Min-Bin Chen
- Department of Radiotherapy and Oncology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan 215300, Jiangsu Province, China
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15
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The opposing roles of laminin-binding integrins in cancer. Matrix Biol 2017; 57-58:213-243. [DOI: 10.1016/j.matbio.2016.08.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/02/2016] [Accepted: 08/17/2016] [Indexed: 02/06/2023]
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16
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Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics 2016; 17:263. [PMID: 27029813 PMCID: PMC4815211 DOI: 10.1186/s12864-016-2542-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation. RESULTS The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS). CONCLUSION The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.
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Affiliation(s)
- Matt R Paul
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd, Philadelphia, PA, USA.
| | - Nicholas P Levitt
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - David E Moore
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - Patricia M Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Robert C Wilson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Chadrick E Denlinger
- Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Surgery, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Dennis K Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
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