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Li Q, Zhu Z, Zhang H, Wu X, Yang H, Li X, Li W, Zhao Y, Du F, Chen Y, Shen J, Xiao Z, Chen M, Wang F, Gu L, Sun Y, Lu L, Jia Y, Li M. LncRNA RP11-93B14.5 promotes gastric cancer cell growth through PI3K/AKT signaling pathway. Mol Biotechnol 2024; 66:2332-2340. [PMID: 37682457 DOI: 10.1007/s12033-023-00844-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/29/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVE Emerging evidence indicates that long non-coding RNA (lncRNA) RP11-93B14.5 facilitates tumor progression in variety of malignancies. The present study proposed to study the functional effect of lncRNA RP11-93B14.5 in gastric cancer (GC) as well as the underlying mechanism. METHODS Bioinformatics analysis was utilized to analyze lncRNA expression in GC tissues. siRNA was used for knockdown of RP11-93B14.5 in GC cells MKN45 and KATO III. The stable knockdown cell lines were constructed by CRISPR-Cas9. Cell counting kit-8 (CCK-8) assay and soft agar colony formation assay were used to analyze GC cell viability. Flow cytometry analysis was performed to analyze the cell cycle distribution of MKN45 and KATO III. RNA sequencing (RNA-seq) was employed to detect differential genes after transfection with siRP11-93B14.5. Quantitative PCR (Q-PCR) was used to examine gene expression in GC cell lines. Western-blot assay was used to measure protein levels. RNA fluorescent in situ hybridization (FISH) was conducted for lncRNA cellular location and expression. RESULTS Based on the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, RP11-93B14.5 was upregulated in GC tissue, which was also verified in GC cell lines in comparison to the normal gastric epithelial HFE145 cells. Knockdown of RP11-93B14.5 decreased cell viability and the colony number of MKN45 and KATO III cells, and altered cell cycle distribution in vitro. RNA-seq analysis revealed RP11-93B14.5 may modulate genes expression of S100A2 and TIMP2 in MKN45 and KATO III cells. Mechanistically, RP11-93B14.5 may drive the progression of GC via S100A2 related-PI3K/AKT signaling pathway. CONCLUSIONS LncRNA RP11-93B14.5 knockdown alleviated the malignant phenotypes of GC cells through regulating PI3K/AKT. Our results provide evidence for the role of lncRNAs in regulating tumor progression.
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Affiliation(s)
- Qianxiu Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Zhongxiu Zhu
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, 250000, Shandong, China
| | - Hanyu Zhang
- Nanchong Key Laboratory of Individualized Drug Therapy, Department of Pharmacy, The Second Clinical Medical College, Nanchong Central Hospital, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Huan Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Fang Wang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China
| | - Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Yuliang Jia
- Department of Gastroenterology, The first affiliated hospital of Wannan Medical College, Wuhu, 241000, Anhui, China.
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, Sichuan, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, Sichuan, China.
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Peeney D, Kumar S, Singh TP, Liu Y, Jensen SM, Chowdhury A, Coates-Park S, Rich J, Gurung S, Fan Y, Meerzaman D, Stetler-Stevenson WG. Timp2 loss-of-function mutation and TIMP2 treatment in murine model of NSCLC: modulation of immunosuppression and oncogenic signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.29.573636. [PMID: 38234759 PMCID: PMC10793420 DOI: 10.1101/2023.12.29.573636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Mounting evidence suggests that the tissue inhibitor of metalloproteinases-2 (TIMP2) can reduce tumor burden and metastasis. However, the demonstration of such anti-tumor activity and associated mechanisms using in vivo tumor models is lacking. The effects of a Timp2 functional mutation and administration of recombinant TIMP2 were examined in both orthotopic and heterotopic murine models of lung cancer using C57Bl/6 syngeneic Lewis Lung 2-luciferase 2 cells (LL2-luc2) cells. Mice harboring a functional mutation of TIMP2 (mT2) display markedly increased primary lung tumor growth, increased mortality, enriched vasculature, and enhanced infiltration of pro-tumorigenic, immunosuppressive myeloid cells. Treatment with recombinant TIMP2 reduced primary tumor growth in both mutant and wild-type (wt) mice. Comparison of transcriptional profiles of lung tissues from tumor-free, wt versus mT2 mice reveals only minor changes. However, lung tumor-bearing mice of both genotypes demonstrate significant genotype-dependent changes in gene expression following treatment with TIMP. In tumor-bearing wt mice, TIMP2 treatment reduced the expression of upstream oncogenic mediators, whereas treatment of mT2 mice resulted in an immunomodulatory phenotype. A heterotopic subcutaneous model generating metastatic pulmonary tumors demonstrated that daily administration of recombinant TIMP2 significantly downregulates the expression of heat shock proteins, suggesting a reduction of cell-stress responses. In summary, we describe how TIMP2 exerts novel, anti-tumor effects in a murine model of lung cancer and that rTIMP2 treatment supports a normalizing effect on the tumor microenvironment. Our findings show that TIMP2 treatment demonstrates significant potential as an adjuvant in the treatment of NSCLC.
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Affiliation(s)
- David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Sarvesh Kumar
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Tej Pratap Singh
- Laboratory of Molecular Immunology, National Institute for Allergy, and Infectious Disease (NIAID); Bethesda, MD 20892
| | - Yueqin Liu
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Sandra M. Jensen
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Ananda Chowdhury
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Sasha Coates-Park
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Joshua Rich
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Sadeechya Gurung
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
| | - Yu Fan
- Computational Genomics and Bioinformatics Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute; Rockville, MD 20850
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute; Rockville, MD 20850
| | - William G. Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI); Bethesda, MD, 20892
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Xu W, Chen S, Jiang Q, He J, Zhang F, Wang Z, Ruan C, Shi B. LUM as a novel prognostic marker and its correlation with immune infiltration in gastric cancer: a study based on immunohistochemical analysis and bioinformatics. BMC Gastroenterol 2023; 23:455. [PMID: 38129820 PMCID: PMC10740220 DOI: 10.1186/s12876-023-03075-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is considered the sixth highly prevailing malignant neoplasm and is ranked third in terms of cancer mortality rates. To enable an early and efficient diagnosis of GC, it is important to detect the fundamental processes involved in the oncogenesis and progression of gastric malignancy. The understanding of molecular signaling pathways can facilitate the development of more effective therapeutic strategies for GC patients. METHODS The screening of genes that exhibited differential expression in early and advanced GC was performed utilizing the Gene Expression Omnibus databases (GSE3438). Based on this, the protein and protein interaction network was constructed to screen for hub genes. The resulting list of hub genes was evaluated with bioinformatic analysis and selected genes were validated the protein expression by immunohistochemistry (IHC). Finally, a competing endogenous RNA network of GC was constructed. RESULTS The three genes (ITGB1, LUM, and COL5A2) overexpressed in both early and advanced GC were identified for the first time. Their upregulation has been linked with worse overall survival (OS) time in patients with GC. Only LUM was identified as an independent risk factor for OS among GC patients by means of additional analysis. IHC results demonstrated that the expression of LUM protein was increased in GC tissue, and was positively associated with the pathological T stage. LUM expression can effectively differentiate tumorous tissue from normal tissue (area under the curve = 0.743). The area under 1-, 3-, and 5-year survival relative operating characteristics were greater than 0.6. Biological function enrichment analyses suggested that the genes related to LUM expression were involved in extracellular matrix development-related pathways and enriched in several cancer-related pathways. LUM affects the infiltration degree of cells linked to the immune system in the tumor microenvironment. In GC progression, the AC117386.2/hsa-miR-378c/LUM regulatory axis was also identified. CONCLUSION Collectively, a thorough bioinformatics analysis was carried out and an AC117386.2/hsa-miR-378c/LUM regulatory axis in the stomach adenocarcinoma dataset was detected. These findings should serve as a guide for future experimental investigations and warrant confirmation from larger studies.
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Affiliation(s)
- Wu Xu
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Shasha Chen
- Department of Pathology, Longyan Second Hospital, No.8 Shuangyang West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Qiuju Jiang
- Department of Pathology, Longyan Second Hospital, No.8 Shuangyang West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Jinlan He
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Feifei Zhang
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Zhuying Wang
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Caishun Ruan
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China
| | - Bin Shi
- Department of Medical Oncology, Longyan People's Hospital, No.31 Denggao West Road, Longyan, Fujian, 364000, People's Republic of China.
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Escalona RM, Chu S, Kadife E, Kelly JK, Kannourakis G, Findlay JK, Ahmed N. Knock down of TIMP-2 by siRNA and CRISPR/Cas9 mediates diverse cellular reprogramming of metastasis and chemosensitivity in ovarian cancer. Cancer Cell Int 2022; 22:422. [PMID: 36585738 PMCID: PMC9805260 DOI: 10.1186/s12935-022-02838-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The endogenous tissue inhibitor of metalloproteinase-2 (TIMP-2), through its homeostatic action on certain metalloproteinases, plays a vital role in remodelling extracellular matrix (ECM) to facilitate cancer progression. This study investigated the role of TIMP-2 in an ovarian cancer cell line in which the expression of TIMP-2 was reduced by either siRNA or CRISPR/Cas9. METHODS OVCAR5 cells were transiently and stably transfected with either single or pooled TIMP-2 siRNAs (T2-KD cells) or by CRISPR/Cas9 under the influence of two distinct guide RNAs (gRNA1 and gRNA2 cell lines). The expression of different genes was analysed at the mRNA level by quantitative real time PCR (qRT-PCR) and at the protein level by immunofluorescence (IF) and western blot. Proliferation of cells was investigated by 5-Ethynyl-2'-deoxyuridine (EdU) assay or staining with Ki67. Cell migration/invasion was determined by xCELLigence. Cell growth in vitro was determined by 3D spheroid cultures and in vivo by a mouse xenograft model. RESULTS Approximately 70-90% knock down of TIMP-2 expression were confirmed in T2-KD, gRNA1 and gRNA2 OVCAR5 ovarian cancer cells at the protein level. T2-KD, gRNA1 and gRNA2 cells exhibited a significant downregulation of MMP-2 expression, but concurrently a significant upregulation in the expression of membrane bound MMP-14 compared to control and parental cells. Enhanced proliferation and invasion were exhibited in all TIMP-2 knocked down cells but differences in sensitivity to paclitaxel (PTX) treatment were observed, with T2-KD cells and gRNA2 cell line being sensitive, while the gRNA1 cell line was resistant to PTX treatment. In addition, significant differences in the growth of gRNA1 and gRNA2 cell lines were observed in in vitro 3D cultures as well as in an in vivo mouse xenograft model. CONCLUSIONS Our results suggest that the inhibition of TIMP-2 by siRNA and CRISPR/Cas-9 modulate the expression of MMP-2 and MMP-14 and reprogram ovarian cancer cells to facilitate proliferation and invasion. Distinct disparities in in vitro chemosensitivity and growth in 3D culture, and differences in tumour burden and invasion to proximal organs in a mouse model imply that selective suppression of TIMP-2 expression by siRNA or CRISPR/Cas-9 alters important aspects of metastasis and chemosensitivity in ovarian cancer.
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Affiliation(s)
- Ruth M. Escalona
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia ,Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - Simon Chu
- grid.1002.30000 0004 1936 7857Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia
| | - Elif Kadife
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - Jason K. Kelly
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia ,grid.1040.50000 0001 1091 4859School of Science, Psychology and Sport, Federation University, Mt Helen, VIC 3350 Australia
| | - Jock K. Findlay
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia
| | - Nuzhat Ahmed
- grid.1008.90000 0001 2179 088XDepartment of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC 3052 Australia ,grid.1002.30000 0004 1936 7857Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Clayton, VIC 3168 Australia ,Fiona Elsey Cancer Research Institute, Suites 23, 106-110 Lydiard Street South, Ballarat Technology Park Central, Ballarat, VIC 3350 Australia ,grid.1040.50000 0001 1091 4859School of Science, Psychology and Sport, Federation University, Mt Helen, VIC 3350 Australia
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EBV persistence in gastric cancer cases conventionally classified as EBER-ISH negative. Infect Agent Cancer 2022; 17:57. [DOI: 10.1186/s13027-022-00469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
The Epstein-Barr virus (EBV) causes various B-cell lymphomas and epithelial malignancies, including gastric cancer (GC) at frequencies ranging from 5 to 10% in adenocarcinomas (ADK) to 80% in GC with lymphoid stroma (GCLS). Using high-sensitivity methods, we recently detected EBV traces in a large cohort of EBV-negative B-cell lymphomas, suggesting a hit-and-run mechanism.
Methods
Here, we used routine and higher-sensitivity methods [droplet digital PCR (ddPCR) for EBV segments on microdissected tumour cells and RNAscope for EBNA1 mRNA] to assess EBV infection in a cohort of 40 GCs (28 ADK and 12 GCLS).
Results
ddPCR documented the presence of EBV nucleic acids in rare tumour cells of several cases conventionally classified as EBV-negative (ADK, 8/26; GCLS, 6/7). Similarly, RNAscope confirmed EBNA1 expression in rare tumour cells (ADK, 4/26; GCLS, 3/7). Finally, since EBV induces epigenetic changes that are heritable and retained after complete loss of the virus from the host cell, we studied the methylation pattern of EBV-specifically methylated genes (Timp2, Eya1) as a mark of previous EBV infection. Cases with EBV traces showed a considerable level of methylation in Timp2 and Eya1 genes that was similar to that observed in EBER-ISH positive cases and greater than cases not featuring any EBV traces.
Conclusions
These findings suggest that: (a) EBV may contribute to gastric pathogenesis more widely than currently acknowledged and (b) indicate the methylation changes as a mechanistic framework for how EBV can act in a hit-and-run manner. Finally, we found that the viral state was of prognostic significance in univariate and multivariate analyses.
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Identification of TIMP2 as a Prognostic Biomarker and Its Correlation with Tumor Immune Microenvironment: A Comprehensive Pan-Cancer Analysis. JOURNAL OF ONCOLOGY 2022; 2022:9133636. [DOI: 10.1155/2022/9133636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/29/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022]
Abstract
Background. Tissue inhibitor of metalloproteinase-2 (TIMP2), an endogenous inhibitor of matrix metalloproteinases, has been disclosed to participate in the development and carcinogenesis of multiple malignancies. However, the prognosis of TIMP2 in different cancers and its correlation with tumor microenvironment and immunity have not been clarified. Methods. In this study, we conducted a comprehensive bioinformatics analysis to evaluate the prognostic and therapeutic value of TIMP2 in cancer patients by utilizing a series of databases, including Oncomine, GEPIA, cBioPortal, GeneMANIA, Metascape, and Sangerbox online tool. The expression of TIMP2 in different cancers was analyzed by Oncomine, TCGA, and GTEx databases, and mutation status of TIMP2 in cancers was then verified using the cBioPortal database. The protein-protein interaction (PPI) network of the TIMP family was exhibited by GeneMANIA. The prognosis of TIMP2 in cancers was performed though the GEPIA database and Cox regression. Additionally, the correlations between TIMP2 expression and immunity (immune cells, gene markers of immune cells, TMB, MSI, and neoantigen) were explored using Sangerbox online tool. Results. The transcriptional level of TIMP2 in most cancerous tissues was significantly elevated. Survival analysis revealed that an elevated expression of TIMP2 is associated with unfavorable survival outcome in multiple cancers. Enrichment analysis demonstrated the possible mechanisms of TIMPs and their associated genes mainly involved in pathways including extracellular matrix (ECM) regulators, degradation of ECM and ECM disassembly, and several other signaling pathways. Conclusions. Our findings systematically dissected that TIMP2 is a potential prognostic maker in various cancers and use the inhibitor of TIMP2, which may be an effective strategy for cancer therapy to improve the poor cancer survival and prognostic accuracy, but concrete mechanisms need to be validated by subsequent experiments.
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TIMP2 is associated with prognosis and immune infiltrates of gastric and colon cancer. Int Immunopharmacol 2022; 110:109008. [DOI: 10.1016/j.intimp.2022.109008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/07/2023]
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Escalona RM, Kannourakis G, Findlay JK, Ahmed N. Expression of TIMPs and MMPs in Ovarian Tumors, Ascites, Ascites-Derived Cells, and Cancer Cell Lines: Characteristic Modulatory Response Before and After Chemotherapy Treatment. Front Oncol 2022; 11:796588. [PMID: 35047406 PMCID: PMC8762252 DOI: 10.3389/fonc.2021.796588] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Background The tissue inhibitors of metalloproteinase (TIMPs) and their associated metalloproteinase (MMPs) are essential regulators of tissue homeostasis and are essential for cancer progression. This study analyzed the expression of TIMP-1,-2,-3 and the associated MMPs (MMP-2,-9,-11,-14) in different Stages, Grades and World Health Organization (WHO) classifications of serous ovarian tumors, ascites, ascites-derived cells from chemo-naïve (CN) and relapsed (CR) patients, and in ovarian cancer cell lines. The status of TIMPs and associated MMPs in response to chemotherapy treatment was assessed in cancer cell lines; TCGA data was interrogated to gauge TIMPs and associated MMPs as prognostic and platinum-response indicators. Methods The levels of TIMP-1, -2 and -3 were assessed by immunohistochemistry. The mRNA expression of TIMPs and MMPs was quantified by real time PCR (qRT-PCR). The chemosensitivity (IC50 values) to Cisplatin or Paclitaxel in cell lines was evaluated by MTT assay. The levels of TIMPs in ascites and cell lysates were analyzed by an ELISA assay. Results The expression of TIMP-2 was significantly upregulated in Type 2 compared to Type 1 tumors and normal/benign ovarian tissues. TIMP-3 expression was significantly enhanced in Stage III, Grade 3 and Type 2 tumors compared to normal/benign ovarian tissues. The mRNA expression of MMP-9,-11 and -14 was significantly upregulated in Stage IV compared to normal/benign ovarian tissues. The expression of TIMP-1 was highest, followed by TIMP-2 and then TIMP-3 in CN ascites. At the cellular level, TIMP-2 mRNA expression was significantly higher in CN compared to CR epithelial cells in patients. The expression of TIMP-1 and -2, MMPs and cancer stem cells (CSCs) were upregulated in response to chemotherapy treatments in cancer cell lines. Interrogation of the TCGA dataset suggests shifts in platinum responses in patients consistent with genetic alterations in TIMP-2, -3 and MMP-2, -11 genes in tumors; and decreased overall survival (OS) and progression-free survival (PFS) in patients with altered MMP-14 genes. Conclusions TIMPs and related MMPs are differentially expressed in serous ovarian tumors, ascites, ascites-derived cells and ovarian cancer cell lines. Chemotherapy treatment modulates expression of TIMPs and MMPs in association with increased expression of genes related to cancer stem cells.
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Affiliation(s)
- Ruth M Escalona
- Fiona Elsey Cancer Research Institute, Ballarat, VIC, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Melbourne, VIC, Australia.,Department of Translational Medicine, Monash University, Melbourne, VIC, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat, VIC, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, Australia
| | - Jock K Findlay
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Melbourne, VIC, Australia.,Department of Translational Medicine, Monash University, Melbourne, VIC, Australia
| | - Nuzhat Ahmed
- Fiona Elsey Cancer Research Institute, Ballarat, VIC, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Melbourne, VIC, Australia.,Department of Translational Medicine, Monash University, Melbourne, VIC, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, Australia
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Role of Calcium Signaling Pathway-Related Gene Regulatory Networks in Ischemic Stroke Based on Multiple WGCNA and Single-Cell Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2021:8060477. [PMID: 34987704 PMCID: PMC8720592 DOI: 10.1155/2021/8060477] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/20/2021] [Accepted: 11/27/2021] [Indexed: 01/28/2023]
Abstract
Background This study is aimed at investigating the changes in relevant pathways and the differential expression of related gene expression after ischemic stroke (IS) at the single-cell level using multiple weighted gene coexpression network analysis (WGCNA) and single-cell analysis. Methods The transcriptome expression datasets of IS samples and single-cell RNA sequencing (scRNA-seq) profiles of cerebrovascular tissues were obtained by searching the Gene Expression Omnibus (GEO) database. First, gene pathway scoring was calculated via gene set variation analysis (GSVA) and was imported into multiple WGCNA to acquire key pathways and pathway-related hub genes. Furthermore, SCENIC was used to identify transcription factors (TFs) regulating these core genes using scRNA-seq data. Finally, the pseudotemporal trajectory analysis was used to analyse the role of these TFs on various cell types under hypoxic and normoxic conditions. Results The scores of 186 KEGG pathways were obtained via GSVA using microarray expression profiles of 40 specimens. WGCNA of the KEGG pathways revealed the two following pathways: calcium signaling pathway and neuroactive ligand-receptor interaction pathways. Subsequently, WGCNA of the gene expression matrix of the samples revealed the calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) that were identified as core genes via correlation analysis. Furthermore, SCENIC and pseudotemporal analysis revealed JUN, IRF9, ETV5, and PPARA score gene-related TFs. Jun was found to be associated with hypoxia in endothelial cells, whereas Irf9 and Etv5 were identified as astrocyte-specific TFs associated with oxygen concentration in the mouse cerebral cortex. Conclusions Calcium signaling pathway-related genes (AC079305.10, BCL10, BCL2A1, BRE-AS1, DYNLL2, EREG, and PTGS2) and TFs (JUN, IRF9, ETV5, and PPARA) were identified to play a key role in IS. This study provides a new perspective and basis for investigating the pathogenesis of IS and developing new therapeutic approaches.
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10
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Peeney D, Liu Y, Lazaroff C, Gurung S, Stetler-Stevenson WG. OUP accepted manuscript. Carcinogenesis 2022; 43:405-418. [PMID: 35436325 PMCID: PMC9167030 DOI: 10.1093/carcin/bgac037] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022] Open
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a conserved family of proteins that were originally identified as endogenous inhibitors of matrixin and adamalysin endopeptidase activity. The matrixins and adamalysins are the major mediators of extracellular matrix (ECM) turnover, thus making TIMPs important regulators of ECM structure and composition. Despite their high sequence identity and relative redundancy in inhibitory profiles, each TIMP possesses unique biological characteristics that are independent of their regulation of metalloproteinase activity. As our understanding of TIMP biology has evolved, distinct roles have been assigned to individual TIMPs in cancer progression. In this respect, data regarding TIMP2's role in cancer have borne conflicting reports of both tumor suppressor and, to a lesser extent, tumor promoter functions. TIMP2 is the most abundant TIMP family member, prevalent in normal and diseased mammalian tissues as a constitutively expressed protein. Despite its apparent stable expression, recent work highlights how TIMP2 is a cell stress-induced gene product and that its biological activity can be dictated by extracellular posttranslational modifications. Hence an understanding of TIMP2 molecular targets, and how its biological functions evolve in the progressing tumor microenvironment may reveal new therapeutic opportunities. In this review, we discuss the continually evolving functions of TIMP proteins, future perspectives in TIMP research, and the therapeutic utility of this family, with a particular focus on TIMP2.
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Affiliation(s)
- David Peeney
- To whom correspondence should be addressed. Tel: 240-858-3233;
| | - Yueqin Liu
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Carolyn Lazaroff
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sadeechya Gurung
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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Han J, Jing Y, Han F, Sun P. Comprehensive analysis of expression, prognosis and immune infiltration for TIMPs in glioblastoma. BMC Neurol 2021; 21:447. [PMID: 34781885 PMCID: PMC8591954 DOI: 10.1186/s12883-021-02477-1] [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: 05/31/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Tissue inhibitors of metalloproteinase (TIMP) family proteins are peptidases involved in extracellular matrix (ECM) degradation. Various diseases are related to TIMPs, and the primary reason is that TIMPs can indirectly regulate remodelling of the ECM and cell signalling by regulating matrix metalloproteinase (MMP) activity. However, the link between TIMPs and glioblastoma (GBM) is unclear. Objective This study aimed to explore the role of TIMP expression and immune infiltration in GBM. Methods Oncomine, GEPIA, OSgbm, LinkedOmics, STRING, GeneMANIA, Enrichr, and TIMER were used to conduct differential expression, prognosis, and immune infiltration analyses of TIMPs in GBM. Results All members of the TIMP family had significantly higher expression levels in GBM. High TIMP3 expression correlated with better overall survival (OS) and disease-specific survival (DSS) in GBM patients. TIMP4 was associated with a long OS in GBM patients. We found a positive relationship between TIMP3 and TIMP4, identifying gene sets with similar or opposite expression directions to those in GBM patients. TIMPs and associated genes are mainly associated with extracellular matrix organization and involve proteoglycan pathways in cancer. The expression levels of TIMPs in GBM correlate with the infiltration of various immune cells, including CD4+ T cells, macrophages, neutrophils, B cells, CD8+ T cells, and dendritic cells. Conclusions Our study inspires new ideas for the role of TIMPs in GBM and provides new directions for multiple treatment modalities, including immunotherapy, in GBM. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02477-1.
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Affiliation(s)
- Jinkun Han
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yajun Jing
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fubing Han
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Peng Sun
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, China.
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Zheng H, Liu H, Li H, Dou W, Wang X. Weighted Gene Co-expression Network Analysis Identifies a Cancer-Associated Fibroblast Signature for Predicting Prognosis and Therapeutic Responses in Gastric Cancer. Front Mol Biosci 2021; 8:744677. [PMID: 34692770 PMCID: PMC8531434 DOI: 10.3389/fmolb.2021.744677] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Cancer-associated fibroblasts (CAFs) are the most prominent cellular components in gastric cancer (GC) stroma that contribute to GC progression, treatment resistance, and immunosuppression. This study aimed at exploring stromal CAF-related factors and developing a CAF-related classifier for predicting prognosis and therapeutic effects in GC. Methods: We downloaded mRNA expression and clinical information of 431 GC samples from Gene Expression Omnibus (GEO) and 330 GC samples from The Cancer Genome Atlas (TCGA) databases. CAF infiltrations were quantified by the estimate the proportion of immune and cancer cells (EPIC) method, and stromal scores were calculated via the Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE) algorithm. Stromal CAF-related genes were identified by weighted gene co-expression network analysis (WGCNA). A CAF risk signature was then developed using the univariate and least absolute shrinkage and selection operator method (LASSO) Cox regression model. We applied the Spearman test to determine the correlation among CAF risk score, CAF markers, and CAF infiltrations (estimated via EPIC, xCell, microenvironment cell populations-counter (MCP-counter), and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms). The TIDE algorithm was further used to assess immunotherapy response. Gene set enrichment analysis (GSEA) was applied to clarify the molecular mechanisms. Results: The 4-gene (COL8A1, SPOCK1, AEBP1, and TIMP2) prognostic CAF model was constructed. GC patients were classified into high– and low–CAF-risk groups in accordance with their median CAF risk score, and patients in the high–CAF-risk group had significant worse prognosis. Spearman correlation analyses revealed the CAF risk score was strongly and positively correlated with stromal and CAF infiltrations, and the four model genes also exhibited positive correlations with CAF markers. Furthermore, TIDE analysis revealed high–CAF-risk patients were less likely to respond to immunotherapy. GSEA revealed that epithelial–mesenchymal transition (EMT), TGF-β signaling, hypoxia, and angiogenesis gene sets were significantly enriched in high–CAF-risk group patients. Conclusion: The present four-gene prognostic CAF signature was not only reliable for predicting prognosis but also competent to estimate clinical immunotherapy response for GC patients, which might provide significant clinical implications for guiding tailored anti-CAF therapy in combination with immunotherapy for GC patients.
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Affiliation(s)
- Hang Zheng
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Heshu Liu
- Department of Oncology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Huayu Li
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Weidong Dou
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, China
| | - Xin Wang
- Department of General Surgery, Peking University First Hospital, Peking University, Beijing, China
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Zeng W, Wu L, Sun Y, Wang Y, Wang J, Ye D. Ratiometric Imaging of MMP-2 Activity Facilitates Tumor Detection Using Activatable Near-Infrared Fluorescent Semiconducting Polymer Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101924. [PMID: 34309199 DOI: 10.1002/smll.202101924] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-activatable ratiometric near-infrared (NIR) fluorescent probes enabling noninvasive imaging of enzyme activity in vivo are promising for biomedical research; however, such probes with ratiometric fluorescence emissions both in NIR window under a single NIR light excitation are largely unexplored. Here, a quenched NIR fluorophore of Cy5.5 is integrated with NIR fluorescent poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b']dithiophene)-alt-4,7(2,1,3-benzothiadiazole)] (PCPDTBT)-based semiconducting polymer nanoparticles (SPNs), and an αv β3 integrin-targeting and matrix metalloproteinase-2 (MMP-2)-activatable ratiometric fluorescent probe (SPN-MMP-RGD) is developed. Under excitation at 660 nm, SPN-MMP-RGD shows "always-on" fluorescence of PCPDTBT (830 nm) and activatable fluorescence of Cy5.5 (690 nm) toward MMP-2, affording a remarkable ≈176-fold enhancement in fluorescence intensity ratio between 690 and 830 nm (I690 /I830 ) for sensitive detection of MMP-2 activity in vitro and in tumor cells. By virtue of ratiometric fluorescence imaging independently of probe's concentration, SPN-MMP-RGD can not only accurately report on MMP-2 levels regarding different tumor sizes, but also noninvasively delineate MMP-2-positive tiny gastric tumors metastasis in vivo. The authors' study reveals the potential of SPN-MMP-RGD for ratiometric fluorescence imaging of MMP-2 activity via combining two independent NIR fluorophores, which can be amenable for the design of other enzyme-activatable ratiometric NIR fluorescent probes for reliable in vivo imaging.
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Affiliation(s)
- Wenhui Zeng
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Luyan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yidan Sun
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jinfang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Research Center of Resources and Environment, School of Chemical Engineering and Materials, Changzhou Institute of Technology, Changzhou, 213022, China
| | - Deju Ye
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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Tan R, Zhang G, Liu R, Hou J, Dong Z, Deng C, Wan S, Lai X, Cui H. Identification of Early Diagnostic and Prognostic Biomarkers via WGCNA in Stomach Adenocarcinoma. Front Oncol 2021; 11:636461. [PMID: 34221961 PMCID: PMC8249817 DOI: 10.3389/fonc.2021.636461] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/27/2021] [Indexed: 01/11/2023] Open
Abstract
Stomach adenocarcinoma (STAD) is a leading cause of cancer deaths, and the outcome of the patients remains dismal for the lack of effective biomarkers of early detection. Recent studies have elucidated the landscape of genomic alterations of gastric cancer and reveal some biomarkers of advanced-stage gastric cancer, however, information about early-stage biomarkers is limited. Here, we adopt Weighted Gene Co-expression Network Analysis (WGCNA) to screen potential biomarkers for early-stage STAD using RNA-Seq and clinical data from TCGA database. We find six gene clusters (or modules) are significantly correlated with the stage-I STADs. Among these, five hub genes, i.e., MS4A1, THBS2, VCAN, PDGFRB, and KCNA3 are identified and significantly de-regulated in the stage-I STADs compared with the normal stomach gland tissues, which suggests they can serve as potential early diagnostic biomarkers. Moreover, we show that high expression of VCAN and PDGFRB is associated with poor prognosis of STAD. VCAN encodes a large chondroitin sulfate proteoglycan that is the main component of the extracellular matrix, and PDGFRB encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor (PDGF) family. Consistently, Gene Ontology (GO) analysis of differentially expressed genes in the STADs indicates terms associated with extracellular matrix and receptor ligand activity are significantly enriched. Protein-protein network interaction analysis (PPI) and Gene Set Enrichment Analysis (GSEA) further support the core role of VCAN and PDGFRB in the tumorigenesis. Collectively, our study identifies the potential biomarkers for early detection and prognosis of STAD.
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Affiliation(s)
- Ruoyue Tan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Guanghui Zhang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Jianbing Hou
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaowei Deng
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Sicheng Wan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Xiaodong Lai
- Department of Critical Care Medicine, The Thirteenth People’s Hospital of Chongqing, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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Meng Z, Wang M, Zhao Z, Zhou Y, Wu Y, Guo S, Li M, Zhou Y, Yang S, Li W, Ying B. Development and Validation of a Predictive Model for Severe COVID-19: A Case-Control Study in China. Front Med (Lausanne) 2021; 8:663145. [PMID: 34113636 PMCID: PMC8185163 DOI: 10.3389/fmed.2021.663145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Predicting the risk of progression to severe coronavirus disease 2019 (COVID-19) could facilitate personalized diagnosis and treatment options, thus optimizing the use of medical resources. Methods: In this prospective study, 206 patients with COVID-19 were enrolled from regional medical institutions between December 20, 2019, and April 10, 2020. We collated a range of data to derive and validate a predictive model for COVID-19 progression, including demographics, clinical characteristics, laboratory findings, and cytokine levels. Variation analysis, along with the least absolute shrinkage and selection operator (LASSO) and Boruta algorithms, was used for modeling. The performance of the derived models was evaluated by specificity, sensitivity, area under the receiver operating characteristic (ROC) curve (AUC), Akaike information criterion (AIC), calibration plots, decision curve analysis (DCA), and Hosmer–Lemeshow test. Results: We used the LASSO algorithm and logistic regression to develop a model that can accurately predict the risk of progression to severe COVID-19. The model incorporated alanine aminotransferase (ALT), interleukin (IL)-6, expectoration, fatigue, lymphocyte ratio (LYMR), aspartate transaminase (AST), and creatinine (CREA). The model yielded a satisfactory predictive performance with an AUC of 0.9104 and 0.8792 in the derivation and validation cohorts, respectively. The final model was then used to create a nomogram that was packaged into an open-source and predictive calculator for clinical use. The model is freely available online at https://severeconid-19predction.shinyapps.io/SHINY/. Conclusion: In this study, we developed an open-source and free predictive calculator for COVID-19 progression based on ALT, IL-6, expectoration, fatigue, LYMR, AST, and CREA. The validated model can effectively predict progression to severe COVID-19, thus providing an efficient option for early and personalized management and the allocation of appropriate medical resources.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shuyu Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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Li Z, Jing Q, Wu L, Chen J, Huang M, Qin Y, Wang T. The prognostic and diagnostic value of tissue inhibitor of metalloproteinases gene family and potential function in gastric cancer. J Cancer 2021; 12:4086-4098. [PMID: 34093812 PMCID: PMC8176236 DOI: 10.7150/jca.57808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/23/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Tissue inhibitor of metalloproteinases (TIMP) gene family, including TIMP1, TIMP2, TIMP3 and TIMP4, was found to be correlated with serval cancers. Still the diagnostic and prognostic study of it in gastric cancer (GC) have few reports. Methods and materials: In this study, the gene expression and clinical data were acquired from the Cancer Gene Atlas (TCGA), function enrichment was used by several databases for verifying known function. Operating characteristic (ROC) curves with area under the curve (AUC) used to assess diagnostic value. Survival analysis and joint-effects survival analysis was performed by the Kaplan-Meier curve. The results were adjusted by cox-regression model. Nomogram is used to directly predict the survival rate for individual GC patient. The potential mechanism for diagnostic and prognostic value was assessed by gene set enrichment analysis (GSEA). Further functions of gene were verified by cell proliferation, migration and invasion assays in human gastric cancer cell line. Results:TIMP1 was expressed in GC tissue was higher than normal gastric tissue. TIMP3 and TIMP4 have expressed in normal gastric tissue were higher than GC tissue. TIMP1, TIMP3 and TIMP4 have potential diagnostic value (AUC=0.842, 0.729, 0.786 respectively; all P<0.01). Low expression of TIMP2 and TIMP3 associated with favorable overall survival (all P<0.05). TIMP2 and TIMP3, which had significantly affection of prognosis were found having some function such as tRNA processing, cell cycle pathway ncRNA processing. The silencing of TIMP3 could inhibit the migration and invasion of gastric cancer cell. Conclusion: We analyzed the TIMP gene family in GC, and the prognostic and diagnostic value. TIMP1 and TIMP2 could be used as diagnostic biomarkers in GC. TIMP2 and TIMP3 could be used as potential biomarkers for GC's prognosis.
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Affiliation(s)
- Zhao Li
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Qinwen Jing
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Liucheng Wu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Jiansi Chen
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Mingwei Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yuzhou Qin
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Tingan Wang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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Pan T, He Y, Chen H, Pei J, Li Y, Zeng R, Xia J, Zuo Y, Qin L, Chen S, Xiao L, Zhou H. Identification and Validation of a Prognostic Gene Signature for Diffuse Large B-Cell Lymphoma Based on Tumor Microenvironment-Related Genes. Front Oncol 2021; 11:614211. [PMID: 33692952 PMCID: PMC7938316 DOI: 10.3389/fonc.2021.614211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an extremely heterogeneous tumor entity, which makes prognostic prediction challenging. The tumor microenvironment (TME) has a crucial role in fostering and restraining tumor development. Consequently, we performed a systematic investigation of the TME and genetic factors associated with DLBCL to identify prognostic biomarkers for DLBCL. Data for a total of 1,084 DLBCL patients from the Gene Expression Omnibus database were included in this study, and patients were divided into a training group, an internal validation group, and two external validation groups. We calculated the abundance of immune–stromal components of DLBCL and found that they were related to tumor prognosis and progression. Then, differentially expressed genes were obtained based on immune and stromal scores, and prognostic TME‐related genes were further identified using a protein–protein interaction network and univariate Cox regression analysis. These genes were analyzed by the least absolute shrinkage and selection operator Cox regression model to establish a seven-gene signature, comprising TIMP2, QKI, LCP2, LAMP2, ITGAM, CSF3R, and AAK1. The signature was shown to have critical prognostic value in the training and validation sets and was also confirmed to be an independent prognostic factor. Subgroup analysis also indicated the robust prognostic ability of the signature. A nomogram integrating the seven-gene signature and components of the International Prognostic Index was shown to have value for prognostic prediction. Gene set enrichment analysis between risk groups demonstrated that immune-related pathways were enriched in the low-risk group. In conclusion, a novel and reliable TME relevant gene signature was proposed and shown to be capable of predicting the survival of DLBCL patients at high risk of poor survival.
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Affiliation(s)
- Tao Pan
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yizi He
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Huan Chen
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Junfei Pei
- Department of Gastrointestinal Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yajun Li
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruolan Zeng
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiliang Xia
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang School of Medicine, University of South China, Hengyang, China
| | - Yilang Zuo
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Liping Qin
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Siwei Chen
- Department of Histology and Embryology of School of Basic Medical Science, Central South University, Changsha, China
| | - Ling Xiao
- Department of Histology and Embryology of School of Basic Medical Science, Central South University, Changsha, China
| | - Hui Zhou
- Department of Lymphoma & Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
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18
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Zhang J, Gu J, Guo S, Huang W, Zheng Y, Wang X, Zhang T, Zhao W, Ni B, Fan Y, Wang H. Establishing and validating a pathway prognostic signature in pancreatic cancer based on miRNA and mRNA sets using GSVA. Aging (Albany NY) 2020; 12:22840-22858. [PMID: 33197892 PMCID: PMC7746356 DOI: 10.18632/aging.103965] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
Abstract
Pancreatic cancer (PC) is a severe disease with the highest mortality rate among various cancers. It is urgent to find an effective and accurate way to predict the survival of PC patients. Gene set variation analysis (GSVA) was used to establish and validate a miRNA set-based pathway prognostic signature for PC (miPPSPC) and a mRNA set-based pathway prognostic signature for PC (mPPSPC) in independent datasets. An optimized miPPSPC was constructed by combining clinical parameters. The miPPSPC, optimized miPPSPC and mPPSPC were established and validated to predict the survival of PC patients and showed excellent predictive ability. Four metabolic pathways and one oxidative stress pathway were identified in the miPPSPC, whereas linoleic acid metabolism and the pentose phosphate pathway were identified in the mPPSPC. Key factors of the pentose phosphate pathway and linoleic acid metabolism, G6PD and CYP2C8/9/18/19, respectively, are related to the survival of PC patients according to our tissue microarray. Thus, the miPPSPC, optimized miPPSPC and mPPSPC can predict the survival of PC patients efficiently and precisely. The metabolic and oxidative stress pathways may participate in PC progression.
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Affiliation(s)
- Junfeng Zhang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
| | - Jianyou Gu
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, P R China
| | - Shixiang Guo
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
| | - Wenjie Huang
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, P R China
| | - Yao Zheng
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
| | - Xianxing Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
| | - Tao Zhang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
| | - Weibo Zhao
- PLA Strategic Support Force Characteristic Medical Center (The 306th Hospital of PLA), Beijing 100101, P R China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing 400038, P R China.,Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing 400038, P R China.,Key Laboratory of High Altitude Medicine, PLA, Chongqing 400038, P R China
| | - Yingfang Fan
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, Guangdong Province, P R China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 401120, P R China
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Kipkeeva F, Muzaffarova T, Korotaeva A, Nikulin M, Grishina K, Mansorunov D, Apanovich P, Karpukhin A. MicroRNA in Gastric Cancer Development: Mechanisms and Biomarkers. Diagnostics (Basel) 2020; 10:E891. [PMID: 33142817 PMCID: PMC7692123 DOI: 10.3390/diagnostics10110891] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/20/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer (GC) is one of the most common and difficult diseases to treat. The study of signaling pathway regulation by microRNA provides information on the mechanisms of GC development and is the basis for biomarker creation. In this study, a circuit of microRNA interactions with signaling pathways was constructed. The microRNAs, associated with metastasis and chemoresistance, are described. In most cases, microRNAs in GC regulate the Wnt/β-catenin, PI3K/AKT/mTOR, RAS/RAF/ERK/MAPK, NF-kB, TGF-β, and JAK/STAT pathways. Part of the microRNA acts on several target genes that function in different pathways. This often leads to an intensification of the induced processes. MicroRNAs have also been described that have the opposite effect on different pathways, causing different functional consequences. By acting on several target genes, or genes associated with several pathways, microRNAs can function in a signaling network. MicroRNAs associated with metastasis most often interact with the Wnt/β-catenin pathway. MicroRNAs affecting chemoresistance, in most cases, affect the regulators of apoptosis and are associated with the PI3K/AKT/mTOR pathway. The characteristics of microRNAs proposed as candidates for GC biomarkers were analyzed. The currently developed diagnostic and prognostic panels of microRNAs are also considered.
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Affiliation(s)
- Fatimat Kipkeeva
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Tatyana Muzaffarova
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Alexandra Korotaeva
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Maxim Nikulin
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia;
| | - Kristina Grishina
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Danzan Mansorunov
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Pavel Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
| | - Alexander Karpukhin
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (F.K.); (T.M.); (A.K.); (K.G.); (D.M.); (P.A.)
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20
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Zhou J, Song Y, Gan W, Liu L, Chen G, Chen Z, Luo G, Zhang L, Zhang G, Wang P, Cao Y. Upregulation of COL8A1 indicates poor prognosis across human cancer types and promotes the proliferation of gastric cancer cells. Oncol Lett 2020; 20:34. [PMID: 32774507 PMCID: PMC7405348 DOI: 10.3892/ol.2020.11895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/13/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) was one of the most common types of the digestive system. COL8A1 was reported to be associated with cancer progression. The present study showed COL8A1 was overexpressed and correlated to shorter overall survival (OS) time across human cancer types. Specially, our results showed COL8A1 was up-regulated in advanced stage GC compared to low stage GC samples. Higher expression of COL8A1 was significantly correlated to shorter OS time in patients with GC. Bioinformatics analysis revealed COL8A1 was involved in regulating cell proliferation and metastasis. Experimental validations of COL8A1 showed that silencing of COL8A1 could significantly suppressed cell proliferation, migration and invasion in GC. These results provided a potential target for the clinical prognosis and treatment of gastric cancer.
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Affiliation(s)
- Jun Zhou
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Yaning Song
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Wei Gan
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Liye Liu
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Guibing Chen
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Zhenyu Chen
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Guode Luo
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Lin Zhang
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Guohu Zhang
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Peihong Wang
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Yongkuan Cao
- Department of Gastrointestinal Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
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21
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Azevedo Martins JM, Rabelo-Santos SH, do Amaral Westin MC, Zeferino LC. Tumoral and stromal expression of MMP-2, MMP-9, MMP-14, TIMP-1, TIMP-2, and VEGF-A in cervical cancer patient survival: a competing risk analysis. BMC Cancer 2020; 20:660. [PMID: 32669083 PMCID: PMC7364527 DOI: 10.1186/s12885-020-07150-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/07/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Expression of matrix metalloproteases 2, 9 and 14 (MMP-2, MMP-9, MMP-14), tissue inhibitors of metalloprotease 1 and 2 (TIMP-1, TIMP-2) and vascular endothelial growth factor A (VEGF-A) is involved in tumor invasion and metastasis via extracellular matrix degradation and angiogenesis. This study aimed to assess whether the expression of MMP-2, MMP-9, MMP-14, TIMP-1, and TIMP-2 in tumors and in the adjacent stroma is associated with cervical cancer prognosis. METHODS This study analyzed a retrospective cohort of 64 patients. Protein expression was previously obtained by immunohistochemistry from biopsies containing both tumor and stroma. The expression and percentage of stained cells were categorized as high or low according to the cutoff points by using ROC curves. The follow-up data was collected from diagnosis to the last clinical visit. Clinical status categorized as alive without disease, alive with disease, death due to other causes, and death from the disease. The relative risk of death from the disease was evaluated according to the proteins expression using a cause-specific Cox regression model with a 95% confidence interval (95%CI). For the significant associations (p < 0.05), survival curves of patients with low and high expression were plotted for the competing risk survival curve analyses. RESULTS High expression levels of stromal MMP-2 (RR; 95%CI: 3.91; 1.17-13.02) and stromal TIMP-2 (RR, 95%CI: 8.67; 1.15-65.27) were associated with a greater relative risk of death from the disease and with lower survival (p = 0.03; p = 0.04) than lower expression levels. Low expression levels of stromal MMP-9 (RR, 95%CI: 0.19; 0.05-0.65) and tumoral MMP-9 (HR, 95%CI: 0.19; 0.04-0.90) were protective factors against death from the disease and were associated with poorer survival. CONCLUSIONS High expression levels of MMP-2 and TIMP-2 in the stroma were significantly associated with poor survival in cervical cancer patients. High expression of MMP-9 was associated with a favorable cervical cancer prognosis.
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Affiliation(s)
- Jordana Maria Azevedo Martins
- Department of Gynecology and Obstetrics, School of Medical Sciences, State University of Campinas, UNICAMP, Tessalia Vieira de Camargo Street, 126, Campinas, Sao Paulo 13083-887 Brazil
| | - Silvia Helena Rabelo-Santos
- School of Pharmacy, Federal University of Goias, 240 Street, Leste Universitario, Goiania, Goias 74605-170 Brazil
| | - Maria Cristina do Amaral Westin
- Laboratory of Cytopathology, Women’s Health Hospital Professor Jose Aristodemo Pinotti – (CAISM), University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-881 Brazil
| | - Luiz Carlos Zeferino
- Department of Gynecology and Obstetrics, School of Medical Sciences, State University of Campinas, UNICAMP, Tessalia Vieira de Camargo Street, 126, Campinas, Sao Paulo 13083-887 Brazil
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22
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Plasma Extracellular Vesicle-Derived TIMP-1 mRNA as a Prognostic Biomarker in Clear Cell Renal Cell Carcinoma: A Pilot Study. Int J Mol Sci 2020; 21:ijms21134624. [PMID: 32610589 PMCID: PMC7370073 DOI: 10.3390/ijms21134624] [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] [Received: 05/22/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
The tumor microenvironment has gained a lot of attention from the scientific community since it has a proven impact in the development of tumor progression and metastasis. Extracellular vesicles (EVs) are now considered one of the key players of tumor microenvironment modulation. Clear cell renal cell carcinoma (ccRCC) is the most lethal urological neoplasia and presents a high metastatic potential, which reinforces the need for the development of more effective predictive biomarkers. Our goal was to evaluate the applicability of EV-derived matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) as prognostic biomarkers for ccRCC. To do so, we studied the plasma EV content of 32 patients with localized ccRCC and 29 patients with metastatic ccRCC. We observed that patients with localized disease and tumors larger than 7 cm presented higher levels of plasma EV-derived TIMP-1 mRNA when compared with patients presenting smaller tumors (p = 0.020). Moreover, patients with metastatic disease presented higher levels of EV-derived TIMP-1 mRNA when compared with patients with localized disease (p = 0.002) and when we stratified those patients in high and low levels of TIMP-1 EV-derived mRNA, the ones presenting higher levels had a lower overall survival (p = 0.030). EV-derived TIMP-1 mRNA may be a good prognostic biomarker candidate for ccRCC.
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23
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Wang W, Li D, Xiang L, Lv M, Tao L, Ni T, Deng J, Gu X, Masatara S, Liu Y, Zhou Y. TIMP-2 inhibits metastasis and predicts prognosis of colorectal cancer via regulating MMP-9. Cell Adh Migr 2020; 13:273-284. [PMID: 31293204 PMCID: PMC6629184 DOI: 10.1080/19336918.2019.1639303] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer has a common cause of morbidity and mortality. Therefore, it is urgent to detect reliable biomarkers to predict prognosis in CRC. Here, we determined the expression of TIMP-2 and MMP-9 in a CRC tissue microarray by immunohistochemistry. We found that lower TIMP-2 or/and higher MMP-9 expression in cancer tissues was correlated with poorer overall survival (OS). TIMP-2 or MMP-9 expression was independent prognostic factors for CRC. Furthermore, TIMP-2 and MMP-9 expression had a synergistic role as efficient prognostic indicators for CRC patients. In vitro and in vivo, TIMP-2 could inhibit HCT 116 cells invasion and migration by regulating MMP-9. In sum, a combined expression of TIMP-2 and MMP-9 as efficient prognostic indicators was found for the first time.
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Affiliation(s)
- Weimin Wang
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China.,c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
| | - Dan Li
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China.,c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
| | - Liangliang Xiang
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China
| | - Mengying Lv
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China
| | - Li Tao
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China
| | - Tengyang Ni
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China
| | - Jianliang Deng
- c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
| | - Xiancheng Gu
- c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
| | - Sunagawa Masatara
- d Department of Physiology , School of Medicine, Showa University , Tokyo , Japan
| | - Yanqing Liu
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China.,c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
| | - Yan Zhou
- a Institute of Traslational Medicine , Medical College, Yangzhou University , Yangzhou , PR China.,b The Key Laboratory of Syndrome Differentiation and Treatment of Gastric Cancer of the State Administration of Traditional Chinese Medicine , Yangzhou , PR China.,c Department of Oncology , Yixing Hospital Affiliated to Medical College of Yangzhou University , Yixing , Jiangsu , PR China
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24
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Su X, Zhang J, Yang W, Liu Y, Liu Y, Shan Z, Wang W. Identification of the Prognosis-Related lncRNAs and Genes in Gastric Cancer. Front Genet 2020; 11:27. [PMID: 32117443 PMCID: PMC7027194 DOI: 10.3389/fgene.2020.00027] [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] [Received: 11/07/2019] [Accepted: 01/08/2020] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer is a common malignant tumor with high occurrence and recurrence and is the leading cause of death worldwide. However, the prognostic value of protein-coding and non-coding RNAs in stage III gastric cancer has not been systematically analyzed. In this study, using TCGA data, we identified 585 long noncoding RNAs (lncRNAs) and 927 protein-coding genes (PCGs) correlated with the overall survival rate of gastric cancer. Functional enrichment analysis revealed that the prognostic genes positively correlated with death rates were enriched in pathways, including gap junction, focal adhesion, cell adhesion molecules (CAMs), and neuroactive ligand-receptor interaction, that are involved in the tumor microenvironment and cell-cell communications, suggesting that their dysregulation may promote the tumor progression. To evaluate the performance of the prognostic genes in risk prediction, we built three multivariable Cox models based on prognostic genes selected from the prognostic PCGs and lncRNAs. The performance of the three models based on features from only PCGs or lncRNAs or from all prognostic genes were systematically compared, which revealed that the features selected from all the prognostic genes showed higher performance than the features selected only from lncRNAs or PCGs. Furthermore, the multivariable Cox regression analysis revealed that the stratification with the highest performance was an independent prognostic factor in stage III gastric cancer. In addition, we explored the underlying mechanism of the prognostic lncRNAs in the Cox model by predicting the lncRNA and protein interaction. Specifically, CTD-2218G20.2 was predicted to interact with PSG4, PSG5, and PSG7, which could also interact with cancer-related proteins, including KISS1, TIMP2, MMP11, IGFBP1, EGFR, and CDKN1C, suggesting that CTD-2218G20.2 might participate in the cancer progression via these cancer-related proteins. In summary, the systematic analysis of the prognostic lncRNAs and PCGs was of great importance to the understanding of the progression of stage III gastric cancer.
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Affiliation(s)
- Xiaohui Su
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Jianjun Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Wei Yang
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Yanqing Liu
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Yang Liu
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Zexing Shan
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
| | - Wentao Wang
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning, China
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25
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Peeney D, Fan Y, Nguyen T, Meerzaman D, Stetler-Stevenson WG. Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer. Sci Rep 2019; 9:20142. [PMID: 31882975 PMCID: PMC6934702 DOI: 10.1038/s41598-019-56632-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
Remodeling of the extracellular matrix (ECM) to facilitate invasion and metastasis is a universal hallmark of cancer progression. However, a definitive therapeutic target remains to be identified in this tissue compartment. As major modulators of ECM structure and function, matrix metalloproteinases (MMPs) are highly expressed in cancer and have been shown to support tumor progression. MMP enzymatic activity is inhibited by the tissue inhibitor of metalloproteinase (TIMP1-4) family of proteins, suggesting that TIMPs may possess anti-tumor activity. TIMP2 is a promiscuous MMP inhibitor that is ubiquitously expressed in normal tissues. In this study, we address inconsistencies in the literature regarding the role of TIMP2 in tumor progression by analyzing co-expressed genes in tumor vs. normal tissue. Utilizing data from The Cancer Genome Atlas and Genotype-Tissue expression studies, focusing on breast and lung carcinomas, we analyzed the correlation between TIMP2 expression and the transcriptome to identify a list of genes whose expression is highly correlated with TIMP2 in tumor tissues. Bioinformatic analysis of the identified gene list highlights a core of matrix and matrix-associated genes that are of interest as potential modulators of TIMP2 function, thus ECM structure, identifying potential tumor microenvironment biomarkers and/or therapeutic targets for further study.
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Affiliation(s)
- David Peeney
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA.
| | - Yu Fan
- Computational Genomics and Bioinformatics Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland, USA
| | - Trinh Nguyen
- Computational Genomics and Bioinformatics Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Group, Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institute of Health, Rockville, Maryland, USA
| | - William G Stetler-Stevenson
- Extracellular Matrix Pathology Section, Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
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Function of p21 (Cip1/Waf1/ CDKN1A) in Migration and Invasion of Cancer and Trophoblastic Cells. Cancers (Basel) 2019; 11:cancers11070989. [PMID: 31311187 PMCID: PMC6678555 DOI: 10.3390/cancers11070989] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 11/18/2022] Open
Abstract
Tumor progression and pregnancy have several features in common. Tumor cells and placental trophoblasts share many signaling pathways involved in migration and invasion. Preeclampsia, associated with impaired differentiation and migration of trophoblastic cells, is an unpredictable and unpreventable disease leading to maternal and perinatal mortality and morbidity. Like in tumor cells, most pathways, in which p21 is involved, are deregulated in trophoblasts of preeclamptic placentas. The aim of the present study was to enlighten p21’s role in tumorigenic choriocarcinoma and trophoblastic cell lines. We show that knockdown of p21 induces defects in chromosome movement during mitosis, though hardly affecting proliferation and cell cycle distribution. Moreover, suppression of p21 compromises the migration and invasion capability of various trophoblastic and cancer cell lines mediated by, at least partially, a reduction of the extracellular signal-regulated kinase 3, identified using transcriptome-wide profiling, real-time PCR, and Western blot. Further analyses show that downregulation of p21 is associated with reduced matrix metalloproteinase 2 and tissue inhibitor of metalloproteinases 2. This work evinces that p21 is involved in chromosome movement during mitosis as well as in the motility and invasion capacity of trophoblastic and cancer cell lines.
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27
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Chao Y, Hu K, Wang X, Wang L. MicroRNA-552 promotes migration and invasion of osteosarcoma through targeting TIMP2. Biochem Biophys Res Commun 2019; 511:63-68. [PMID: 30765222 DOI: 10.1016/j.bbrc.2019.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 02/01/2019] [Indexed: 12/16/2022]
Abstract
Aberrant miRNAs play important roles in tumor development and progression. Previous studies reported that miR-552 was dysregulated expressed in multiple cancers. However, its biological effects and underlying mechanism in osteosarcoma remains largely unknown. In present research, we demonstrated that miR-552 was significantly up-regulated in both osteosarcoma cell lines and tissues for the first time. Its high-expression was significantly associated with poor prognostic features and overall survival of osteosarcoma patients. Gain- and loss-of-function experiment confirmed that miR-552 promoted cell migration, invasion and MMPs expression. Moreover, TIMP2 was a direct downstream target of miR-552. miR-552 inversely correlated with TIMP2 in osteosarcoma tissues. TIMP2 restoration at least partially abolished the migration, invasion and MMPs expression of miR-552 on osteosarcoma cells. Above all, our data suggest that miR-552 promoted migration, invasion and MMPs expression of osteosarcoma by targeting TIMP2, and represent a novel potential therapeutic target for osteosarcoma.
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Affiliation(s)
- Yu Chao
- Department of Orthopaedics, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710077, China
| | - Kejun Hu
- Department of Orthopaedics, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710077, China
| | - Xueli Wang
- Department of Radiology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710077, China
| | - Lei Wang
- Department of Orthopaedics, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi, 710077, China.
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