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Doghish AS, Radwan AF, Zaki MB, Elfar N, Moussa R, Walash Z, Alhamshry NAA, Mohammed OA, Abdel-Reheim MA, Elimam H. Decoding the role of long non-coding RNAs in gallbladder cancer pathogenesis: A review focus on signaling pathways interplay. Int J Biol Macromol 2024; 264:130426. [PMID: 38428766 DOI: 10.1016/j.ijbiomac.2024.130426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Gallbladder cancer (GBC) is one of the most aggressive types of biliary tree cancers and the commonest despite its rarity. It is infrequently diagnosed at an early stage, further contributing to its poor prognosis and low survival rate. The lethal nature of the disease has underlined a crucial need to discern the underlying mechanisms of GBC carcinogenesis which are still largely unknown. However, with the continual evolution in the research of cancer biology and molecular genetics, studies have found that non-coding RNAs (ncRNAs) play an active role in the molecular pathophysiology of GBC development. Dysregulated long non-coding RNAs (lncRNAs) and their interaction with intracellular signaling pathways contribute to malignancy and disease development. LncRNAs, a subclass of ncRNAs with over 200 nucleotides, regulate gene expression at transcriptional, translational, and post-translational levels and especially as epigenetic modulators. Thus, their expression abnormalities have been linked to malignancy and therapeutic resistance. lnsRNAs have also been found in GBC patients' serum and tumor tissue biopsies, highlighting their potential as novel biomarkers and for targeted therapy. This review will examine the growing involvement of lncRNAs in GBC pathophysiology, including related signaling pathways and their wider clinical use.
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Affiliation(s)
- Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
| | - Abdullah F Radwan
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Nourhan Elfar
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital 11578, Cairo, Egypt; Egyptian Drug Authority (EDA), Ministry of Health and Population, Cairo 11567, Egypt
| | - Rewan Moussa
- Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Zahraa Walash
- Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Nora A A Alhamshry
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt.
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Mahdi-Esferizi R, Shiasi Z, Heidari R, Najafi A, Mahmoudi I, Elahian F, Tahmasebian S. Single-cell transcriptional signature-based drug repurposing and in vitro evaluation in colorectal cancer. BMC Cancer 2024; 24:371. [PMID: 38528462 DOI: 10.1186/s12885-024-12142-8] [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: 11/12/2023] [Accepted: 03/18/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The need for intelligent and effective treatment of diseases and the increase in drug design costs have raised drug repurposing as one of the effective strategies in biomedicine. There are various computational methods for drug repurposing, one of which is using transcription signatures, especially single-cell RNA sequencing (scRNA-seq) data, which show us a clear and comprehensive view of the inside of the cell to compare the state of disease and health. METHODS In this study, we used 91,103 scRNA-seq samples from 29 patients with colorectal cancer (GSE144735 and GSE132465). First, differential gene expression (DGE) analysis was done using the ASAP website. Then we reached a list of drugs that can reverse the gene signature pattern from cancer to normal using the iLINCS website. Further, by searching various databases and articles, we found 12 drugs that have FDA approval, and so far, no one has reported them as a drug in the treatment of any cancer. Then, to evaluate the cytotoxicity and performance of these drugs, the MTT assay and real-time PCR were performed on two colorectal cancer cell lines (HT29 and HCT116). RESULTS According to our approach, 12 drugs were suggested for the treatment of colorectal cancer. Four drugs were selected for biological evaluation. The results of the cytotoxicity analysis of these drugs are as follows: tezacaftor (IC10 = 19 µM for HCT-116 and IC10 = 2 µM for HT-29), fenticonazole (IC10 = 17 µM for HCT-116 and IC10 = 7 µM for HT-29), bempedoic acid (IC10 = 78 µM for HCT-116 and IC10 = 65 µM for HT-29), and famciclovir (IC10 = 422 µM for HCT-116 and IC10 = 959 µM for HT-29). CONCLUSIONS Cost, time, and effectiveness are the main challenges in finding new drugs for diseases. Computational approaches such as transcriptional signature-based drug repurposing methods open new horizons to solve these challenges. In this study, tezacaftor, fenticonazole, and bempedoic acid can be introduced as promising drug candidates for the treatment of colorectal cancer. These drugs were evaluated in silico and in vitro, but it is necessary to evaluate them in vivo.
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Affiliation(s)
- Roohallah Mahdi-Esferizi
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zahra Shiasi
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Razieh Heidari
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Issa Mahmoudi
- Information Technology Department, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fatemeh Elahian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Shahram Tahmasebian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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Tan S, Chen X, Liu W. Tumor-suppressive role of miR-139-5p in angiogenesis and tumorigenesis of ovarian cancer: Based on GEO microarray analysis and experimental validation. Cell Signal 2023; 109:110730. [PMID: 37244634 DOI: 10.1016/j.cellsig.2023.110730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/03/2023] [Accepted: 05/21/2023] [Indexed: 05/29/2023]
Abstract
This study clarified the possible molecular mechanisms by which the miR-139-5p/SOX4/TMEM2 axis affected angiogenesis and tumorigenesis of ovarian cancer (OC) based on GEO microarray datasets and experimental support. The expression of miR-139-5p and SOX4 was examined in clinical OC samples. Human umbilical vein endothelial cells (HUVECs) and human OC cell lines were included in vitro experiments. Tube formation assay was conducted in HUVECs. The expression of SOX4, SOX4, and VEGF in OC cells was identified using Western blot and immunohistochemistry. Luciferase assays were conducted to validate the targeting relationship between miR-139-5p and SOX4 and between SOX4 and TMEM2. A RIP assay assessed the binding of SOX4 and miR-139-5p. The impact of miR-139-5p and SOX4 on OC tumorigenesis in vivo was evaluated in nude mice. SOX4 was up-regulated, while miR-139-5p was down-regulated in OC tissues and cells. Ectopic miR-139-5p expression or SOX4 knockdown inhibited angiogenesis and tumorigenicity of OC. By targeting SOX4 in OC, miR-139-5p lowered VEGF expression, angiogenesis, and TMEM2 expression. The miR-139-5p/SOX4/TMEM2 axis also reduced VEGF expression and angiogenesis, which might curtail OC growth in vivo. Collectively, miR-139-5p represses VEGF expression and angiogenesis by targeting the transcription factor SOX4 and down-regulating TMEM2 expression, thereby impeding OC tumorigenesis.
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Affiliation(s)
- Shu Tan
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, PR China
| | - Xiuwei Chen
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, PR China
| | - Wei Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, PR China.
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Khan AS, Campbell KJ, Cameron ER, Blyth K. The RUNX/CBFβ Complex in Breast Cancer: A Conundrum of Context. Cells 2023; 12:641. [PMID: 36831308 PMCID: PMC9953914 DOI: 10.3390/cells12040641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Dissecting and identifying the major actors and pathways in the genesis, progression and aggressive advancement of breast cancer is challenging, in part because neoplasms arising in this tissue represent distinct diseases and in part because the tumors themselves evolve. This review attempts to illustrate the complexity of this mutational landscape as it pertains to the RUNX genes and their transcription co-factor CBFβ. Large-scale genomic studies that characterize genetic alterations across a disease subtype are a useful starting point and as such have identified recurring alterations in CBFB and in the RUNX genes (particularly RUNX1). Intriguingly, the functional output of these mutations is often context dependent with regards to the estrogen receptor (ER) status of the breast cancer. Therefore, such studies need to be integrated with an in-depth understanding of both the normal and corrupted function in mammary cells to begin to tease out how loss or gain of function can alter the cell phenotype and contribute to disease progression. We review how alterations to RUNX/CBFβ function contextually ascribe to breast cancer subtypes and discuss how the in vitro analyses and mouse model systems have contributed to our current understanding of these proteins in the pathogenesis of this complex set of diseases.
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Affiliation(s)
- Adiba S. Khan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Kirsteen J. Campbell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
| | - Ewan R. Cameron
- School of Biodiversity One Health & Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK;
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Rd, Glasgow G61 1BD, UK; (A.S.K.); (K.J.C.)
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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Prokineticins as a Prognostic Biomarker for Low-Grade Gliomas: A Study Based on The Cancer Genome Atlas Data. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2309339. [PMID: 35845958 PMCID: PMC9283042 DOI: 10.1155/2022/2309339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022]
Abstract
Lower-grade glioma (LGG) is a crucial pathological type of glioma. Prokineticins have not been reported in LGG. Prokineticins as a member of the multifunctional chemokine-like peptide family are divided into two ligands: PROK1 and PROK2. We evaluated the role of PROK1 and PROK2 in LGG using TCGA database. We downloaded the datasets of LGG from TCGA and evaluated the influence of prokineticins on LGG survival by survival module. Correlations between clinical information and prokineticins expression were analyzed using logistic regression. Univariable survival and multivariate Cox analysis was used to compare several clinical characteristics with survival. Correlation between prokineticins and cancer immune infiltrates was explored using CIBERSORT and correlation module of GEPIA. We analyzed genes of PROK1 and PROK2 affecting LGG, screened differentially expressed genes (DEGs), interacted protein-protein with DEGs through the STRING website, then imported the results into the Cytospace software, and calculated the hub genes. To analyze whether hub genes and prokineticins are related, the relationship between PROK1 and PROK2 and hub genes was assessed and shown by heat map. In addition, gene set enrichment analysis (GSEA) was performed using the TCGA dataset. The univariate analysis using logistic regression and PROK1 and PROK2 showed opposite expression differences between tumor and normal tissues (
). PRO1 and PROK2 expressions showed significant differences in tumor grade, age, Iiscitrate DeHydrogenase (IDH) status, histological type, and 1P/19q codeletion. Multivariate analysis revealed that the up-regulated PROK1 and PROK2 expression is an independent prognostic factor for bad prognosis. Specifically, prokineticin expression level has significant correlations with infiltrating levels of Th1 cells, NK CD 56bright cells, and Mast cells in LGG. We screened 21 DEGs and obtained 5 hub genes (HOXC10, HOXD13, SOX4, GATA4, HOXA9). GSEA-identified FCMR activation, creation of C4 and C2 activators, and CD22-mediated BCR regulation in gene ontology (GO) were differentially enriched in high PROK1 and PROK2 expression phenotype pathway, cytoplasmic ribosomal proteins, and ribosome and were differentially enriched in the low PROK1 and PROK2 expression phenotype pathway. Prokineticins are a prognostic biomarker and the correlation between hub genes and LGG requires further attention.
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Wei Z, Xu J, Li W, Ou L, Zhou Y, Wang Y, Shi B. SMARCC1 Enters the Nucleus via KPNA2 and Plays an Oncogenic Role in Bladder Cancer. Front Mol Biosci 2022; 9:902220. [PMID: 35669562 PMCID: PMC9163745 DOI: 10.3389/fmolb.2022.902220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background: SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily C member 1 (SMARCC1), a component of the SWI/SNF complex, is thought to be an oncogene in several kinds of cancer. Materials and methods: The potential interaction between SMARCC1 and KPNA2 was inquired by Spearman’s correlation analysis, immunofluorescence staining and co-immunoprecipitation (Co-IP) assays. The immunohistochemistry staining, RT-PCR and western blot assay were taken for determining the expression levels of SMARCC1. And CCK-8, transwell assay, cell apoptosis assay, cell cycle analysis and subcutaneous tumor model were conducted to explore the role of SMARCC1 in carcinogenesis of bladder cancer. Results: In our experiments, Spearman’s correlation analysis, immunofluorescence staining and co-immunoprecipitation (Co-IP) assays showed that SMARCC1 interacted with KPNA2, and after knockdown of KPNA2, Nup50 and Nup153, the nuclear content of SMARCC1 decreased while the amount of SMARCC1 protein remaining in the cytoplasm increased, indicating that SMARCC1 could be transported into the nucleus via KPNA2 and thus acted as an oncogene. We found that both the mRNA and protein expression levels of SMARCC1 were increased in bladder cancer, and increased SMARCC1 expression was significantly associated with a higher T stage and poorer prognosis in bladder cancer patients. Knockdown of SMARCC1 slowed the growth of the two tested cell lines and clearly arrested the cell cycle at the G0/G1 phase checkpoint. Moreover, the migratory ability was significantly decreased and the number of apoptotic cells was increased. Conclusion: On the whole, our results demonstrate KPNA2, Nup50 and Nup153 regulate the process of SMARCC1 nuclear translocation in BC. SMARCC1 may be a competent candidate as a diagnostic and therapeutic target for BC. Further studies are required to research the mechanism and assess the role of SMARCC1 in vivo.
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Affiliation(s)
- Zhengmao Wei
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jinming Xu
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiqing Li
- Karamay Central Hospital of Xinjiang, Karamay, China
| | - Longhua Ou
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yingchen Zhou
- Department of Surgery, Fuwai Hospital Chinese Academy of Medical Sciences Shenzhen, University of South China, Shenzhen, China
| | - Yan Wang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Yan Wang, ; Bentao Shi,
| | - Bentao Shi
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Yan Wang, ; Bentao Shi,
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Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML. Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme. Cancer Res 2021; 81:5401-5412. [PMID: 34493595 PMCID: PMC8563450 DOI: 10.1158/0008-5472.can-21-0730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 01/07/2023]
Abstract
Glioblastoma is an aggressive cancer of the brain and spine. While analysis of glioblastoma 'omics data has somewhat improved our understanding of the disease, it has not led to direct improvement in patient survival. Cancer survival is often characterized by differences in gene expression, but the mechanisms that drive these differences are generally unknown. We therefore set out to model the regulatory mechanisms associated with glioblastoma survival. We inferred individual patient gene regulatory networks using data from two different expression platforms from The Cancer Genome Atlas. We performed comparative network analysis between patients with long- and short-term survival. Seven pathways were identified as associated with survival, all of them involved in immune signaling; differential regulation of PD1 signaling was validated to correspond with outcome in an independent dataset from the German Glioma Network. In this pathway, transcriptional repression of genes for which treatment options are available was lost in short-term survivors; this was independent of mutational burden and only weakly associated with T-cell infiltration. Collectively, these results provide a new way to stratify patients with glioblastoma that uses network features as biomarkers to predict survival. They also identify new potential therapeutic interventions, underscoring the value of analyzing gene regulatory networks in individual patients with cancer. SIGNIFICANCE: Genome-wide network modeling of individual glioblastomas identifies dysregulation of PD1 signaling in patients with poor prognosis, indicating this approach can be used to understand how gene regulation influences cancer progression.
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Affiliation(s)
- Camila M. Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Tatiana Belova
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | | | - Marouen Ben Guebila
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Daniel Osorio
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.,Corresponding Author: Marieke L. Kuijjer, Centre for Molecular Medicine Norway, University of Oslo, Guastadalléen 21, Oslo 0318, Norway. Phone: 47-22840528; E-mail:
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Agapito G, Cannataro M. Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. BMC Bioinformatics 2021; 22:376. [PMID: 34592927 PMCID: PMC8482563 DOI: 10.1186/s12859-021-04297-z] [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: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous work in which we introduced a preliminary comparative analysis of pathway enrichment analysis tools. We extended the earlier work by providing more case studies, comparing BiP enrichment performance with other well-known PEA software tools. METHODS PEA uses pathway information to discover connections between a list of genes and proteins as well as biological mechanisms, helping researchers to overcome the problem of explaining biological entity lists of interest disconnected from the biological context. RESULTS We compared the results of BiP with some existing pathway enrichment analysis tools comprising Centrality-based Pathway Enrichment, pathDIP, and Signaling Pathway Impact Analysis, considering three cancer types (colorectal, endometrial, and thyroid), for a total of six datasets (that is, two datasets per cancer type) obtained from the The Cancer Genome Atlas and Gene Expression Omnibus databases. We measured the similarities between the overlap of the enrichment results obtained using each couple of cancer datasets related to the same cancer. CONCLUSION As a result, BiP identified some well-known pathways related to the investigated cancer type, validated by the available literature. We also used the Jaccard and meet-min indices to evaluate the stability and the similarity between the enrichment results obtained from each couple of cancer datasets. The obtained results show that BiP provides more stable enrichment results than other tools.
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Affiliation(s)
- Giuseppe Agapito
- Department of Legal, Economic and Social Sciences, University "Magna Graecia", Catanzaro, Italy. .,Data Analytics Research Center, University "Magna Graecia", Catanzaro, Italy.
| | - Mario Cannataro
- Department of Medical and Surgical Sciences, University "Magna Graecia", Catanzaro, Italy. .,Data Analytics Research Center, University "Magna Graecia", Catanzaro, Italy.
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Rezayi Soufiani A, Dolatkhah R, Raeisi M, Chavoshi H, Mohammadi P, Mehdinavaz Aghdam A. Hypermethylation of MIR129-2 Regulates SOX4 Transcription and Associates with Metastasis in Patients with Colorectal Cancer. J Gastrointest Cancer 2021; 53:718-724. [PMID: 34499308 DOI: 10.1007/s12029-021-00708-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND MicroRNA-129-2 (miR-129-2), targeting SOX4, has been shown to be involved in the pathogenesis of different cancers. Here in this study, we examined the methylation levels of the promoter region of MIR19-2 gene as well as transcription of miR-129-2 and mRNA expression of SOX4 in the tumoral tissues from colorectal cancer (CRC) patients and compared those in the normal marginal tissues. METHODS Fifty CRC patients with Iranian Azari ethnicity were recruited. Genomic DNAs were extracted from the tumoral and normal tissues and the methylation level of the promoter regions of the MIR129-2 gene was determined using methylation-specific PCR (MSP) by evaluating 100 CG sites. The RNA content of the samples was isolated and the transcript levels of miR-129-2 and SOX4 were measured using quantitative real-time PCR. RESULTS Methylation level of the MIR192-2 promoter was significantly higher in the tumoral tissues compared to that in the normal marginal tissues (84% vs. 28%; P = 0.0041). The expression level of miR-192-2 was significantly downregulated (fold change = 0.34, P = 0.028) but SOX4 mRNA expression was upregulated (fold change = 2.7, P = 0.019) in the tumoral tissues compared to that in the normal marginal tissues. There was a significant correlation between the methylation level of the MIR192-2 promoter and the expression levels of miR-192-2 and SOX4 in the tumoral tissues. Associations were observed between the methylation of the MIR192-2 promoter and lymph node and liver metastasis. CONCLUSIONS It seems that MIR192-2 promoter hypermethylation might regulate the expression of SOX4 and therefore modulate metastasis in CRC.
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Affiliation(s)
- Alireza Rezayi Soufiani
- Tuberculosis and Lung Disease Research Center, Daneshgah St, Tabriz University of Medical Science, Tabriz, Iran
| | - Roya Dolatkhah
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Chavoshi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Payam Mohammadi
- Tuberculosis and Lung Disease Research Center, Daneshgah St, Tabriz University of Medical Science, Tabriz, Iran
| | - Abdolreza Mehdinavaz Aghdam
- Tuberculosis and Lung Disease Research Center, Daneshgah St, Tabriz University of Medical Science, Tabriz, Iran.
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10
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Xiao ZM, Lv DJ, Yu YZ, Wang C, Xie T, Wang T, Song XL, Zhao SC. SMARCC1 Suppresses Tumor Progression by Inhibiting the PI3K/AKT Signaling Pathway in Prostate Cancer. Front Cell Dev Biol 2021; 9:678967. [PMID: 34249931 PMCID: PMC8267926 DOI: 10.3389/fcell.2021.678967] [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: 03/10/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
Background SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily C member 1 (SMARCC1) protein is a potential tumor suppressor in various cancers. However, its role in prostate cancer (PCa) remains controversial. The aim of this study was to determine the biological function of SMARCC1 in PCa and explore the underlying regulatory mechanisms. Methods The expression of SMARCC1 was validated in PCa tissues by immunohistochemistry. Meanwhile, function experiments were used to evaluate the regulatory role on cell proliferation and metastasis in PCa cells with SMARCC1 depletion both in vitro and in vivo. The expression levels of relevant proteins were detected by Western blotting. Results Our finding showed that SMARCC1 was significantly downregulated in prostate adenocarcinoma, with a higher Gleason score (GS) than that in low GS. The decreased expression of SMARCC1 was significantly correlated with a higher GS and poor prognosis. Additionally, we found that silencing of SMARCC1 dramatically accelerated cell proliferation by promoting cell cycle progression and enhancing cell migration by inducing epithelial mesenchymal transition (EMT). Furthermore, depletion of SMARCC1 facilitated PCa xenograft growth and lung metastasis in murine models. Mechanistically, the loss of SMARCC1 activated the PI3K/AKT pathway in PCa cells. Conclusion SMARCC1 suppresses PCa cell proliferation and metastasis via the PI3K/AKT signaling pathway and is a novel therapeutic target.
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Affiliation(s)
- Zhao-Ming Xiao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dao-Jun Lv
- Guangdong Key Laboratory of Urology, Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu-Zhong Yu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Xie
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xian-Lu Song
- Department of Radiotherapy, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Urology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
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11
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Rossouw SC, Bendou H, Blignaut RJ, Bell L, Rigby J, Christoffels A. Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues. Pathol Oncol Res 2021; 27:622855. [PMID: 34257588 PMCID: PMC8262168 DOI: 10.3389/pore.2021.622855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/17/2022]
Abstract
To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterization of large individual patient tissue cohorts are required. Since most pathology institutes routinely preserve biopsy tissues by standardized methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient metadata, such as medical history and treatments. FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. In addition, the optimal sample preparation techniques required for accurate and reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. This study investigated protein extraction efficiency of 1, 5, and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free protein purification methods for label-free LC-MS/MS analysis. A sample size of n = 17 patients per experimental group (with experiment power = 0.7 and α = 0.05, resulting in 70% confidence level) was selected. Data were evaluated in terms of protein concentration extracted, peptide/protein identifications, method reproducibility and efficiency, sample proteome integrity (due to storage time), as well as protein/peptide distribution according to biological processes, cellular components, and physicochemical properties. Data are available via ProteomeXchange with identifier PXD017198. The results indicate that the amount of protein extracted is significantly dependent on block age (p < 0.0001), with older blocks yielding less protein than newer blocks. Detergent removal plates were the most efficient and overall reproducible protein purification method with regard to number of peptide and protein identifications, followed by the MagReSyn® SP3/HILIC method (with on-bead enzymatic digestion), and lastly the acetone precipitation and formic acid resolubilization method. Overall, the results indicate that long-term storage of FFPE tissues (as measured by methionine oxidation) does not considerably interfere with retrospective proteomic analysis (p > 0.1). Block age mainly affects initial protein extraction yields and does not extensively impact on subsequent label-free LC-MS/MS analysis results.
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Affiliation(s)
- Sophia C. Rossouw
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Hocine Bendou
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Renette J. Blignaut
- Department of Statistics and Population Studies, University of the Western Cape, Bellville, South Africa
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Observatory, Cape Town, South Africa
| | - Jonathan Rigby
- Division of Anatomical Pathology, Department of Pathology, Faculty of Health Sciences, University of Stellenbosch, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
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12
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Nuclear Expression Loss of SSBP2 Is Associated with Poor Prognostic Factors in Colorectal Adenocarcinoma. Diagnostics (Basel) 2020; 10:diagnostics10121097. [PMID: 33339271 PMCID: PMC7766200 DOI: 10.3390/diagnostics10121097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022] Open
Abstract
Single-stranded DNA binding protein 2 (SSBP2) is involved in DNA damage response and may induce growth arrest in cancer cells, having a potent tumor suppressor role. SSBP2 is ubiquitously expressed and the loss of its expression has been reported in various tumor types. However, the correlation between SSBP2 expression and colorectal cancer (CRC) prognosis remains unclear. SSBP2 nuclear expression was evaluated immunohistochemically in 48 normal colonic mucosae, 47 adenomas, 391 primary adenocarcinomas, and 131 metastatic carcinoma tissue samples. The clinicopathological factors, overall survival (OS), and recurrence-free survival were evaluated, and associations with the clinicopathological parameters were analyzed in 391 colorectal adenocarcinoma patients. A diffuse nuclear SSBP2 expression was detected in all normal colonic mucosa and adenoma samples. SSBP2 expression loss was observed in 131 (34.3%) primary adenocarcinoma and 100 (76.3%) metastatic carcinoma samples. SSBP2 expression was significantly associated with poor prognostic factors, such as vascular invasion (p = 0.005), high pT category (p = 0.045), and shorter OS (p = 0.038), using univariate survival analysis. Nuclear SSBP2 expression loss was significantly observed in colorectal carcinoma and metastatic carcinoma tissues, being associated with poor prognostic factors. SSBP2 acts as a tumor suppressor and may be used as a CRC prognostic biomarker.
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13
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Comprehensive genomic profile of Chinese lung cancer patients and mutation characteristics of individuals resistant to icotinib/gefitinib. Sci Rep 2020; 10:20243. [PMID: 33219256 PMCID: PMC7679461 DOI: 10.1038/s41598-020-76791-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the leading causes of cancer-related death worldwide. Precise treatment based on next-generation sequencing technology has shown advantages in the diagnosis and treatment of lung cancer. This cohort study included 371 lung cancer patients. The lung cancer subtype was related to the smoking status and sex of the patients. The most common mutated genes were TP53 (62%), EGFR (55%), and KRAS (11%). The mutation frequencies of EGFR, TP53, PIK3CA, NFE2L2, KMT2D, FGFR1, CCND1, and CDKN2A were significantly different between lung adenocarcinoma and lung squamous cell carcinoma. We identified the age-associated mutations in ALK, ERBB2, KMT2D, RBM10, NRAS, NF1, PIK3CA, MET, PBRM1, LRP2, and CDKN2B; smoking-associated mutations in CDKN2A, FAT1, FGFR1, NFE2L2, CCNE1, CCND1, SMARCA4, KEAP1, KMT2C, and STK11; tumor stage-associated mutations in ARFRP1, AURKA, and CBFB; and sex-associated mutations in EGFR. Tumor mutational burden (TMB) is associated with tumor subtype, age, sex, and smoking status. TMB-associated mutations included CDKN2A, LRP1B, LRP2, TP53, and EGFR. EGFR amplification was commonly detected in patients with acquired lcotinib/gefitinib resistance. DNMT3A and NOTCH4 mutations may be associated with the benefit of icotinib/gefitinib treatment.
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14
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [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: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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15
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Chromatin remodelling factor BAF155 protects hepatitis B virus X protein (HBx) from ubiquitin-independent proteasomal degradation. Emerg Microbes Infect 2020; 8:1393-1405. [PMID: 31533543 PMCID: PMC6758689 DOI: 10.1080/22221751.2019.1666661] [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] [Indexed: 02/08/2023]
Abstract
HBx is a short-lived protein whose rapid turnover is mainly regulated by ubiquitin-dependent proteasomal degradation pathways. Our prior work identified BAF155 to be one of the HBx binding partners. Since BAF155 has been shown to stabilize other members of the SWI/SNF chromatin remodelling complex by attenuating their proteasomal degradation, we proposed that BAF155 might also contribute to stabilizing HBx protein in a proteasome-dependent manner. Here we report that BAF155 protected hepatitis B virus X protein (HBx) from ubiquitin-independent proteasomal degradation by competing with the 20S proteasome subunit PSMA7 to bind to HBx. BAF155 was found to directly interact with HBx via binding of its SANT domain to the HBx region between amino acid residues 81 and 120. Expression of either full-length BAF155 or SANT domain increased HBx protein levels whereas siRNA-mediated knockdown of endogenous BAF155 reduced HBx protein levels. Increased HBx stability and steady-state level by BAF155 were attributable to inhibition of ubiquitin-independent and PSMA7-mediated protein degradation. Consequently, overexpression of BAF155 enhanced the transcriptional transactivation function of HBx, activated protooncogene expression and inhibited hepatoma cell clonogenicity. These results suggest that BAF155 plays important roles in ubiquitin-independent degradation of HBx, which may be related to the pathogenesis and carcinogenesis of HBV-associated HCC.
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16
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Alam MM, Chakma K, Mahmud S, Hossain MN, Ahsan T. A systemic analysis reveals TRIM24-SMARCC1 dependent poor prognosis of hepatocellular carcinoma. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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Shannon NB, Tan JWS, Tan HL, Wang W, Chen Y, Lim HJ, Tan QX, Hendrikson J, Ng WH, Loo LY, Skanthakumar T, Wasudevan SD, Kon OL, Lim TKH, Tan GHC, Chia CS, Soo KC, Ong CAJ, Teo MCC. A set of molecular markers predicts chemosensitivity to Mitomycin-C following cytoreductive surgery and hyperthermic intraperitoneal chemotherapy for colorectal peritoneal metastasis. Sci Rep 2019; 9:10572. [PMID: 31332257 PMCID: PMC6646658 DOI: 10.1038/s41598-019-46819-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) is associated with significant perioperative morbidity and mortality. We aim to generate and validate a biomarker set predicting sensitivity to Mitomycin-C to refine selection of patients with colorectal peritoneal metastasis (CPM) for this treatment. A signature predicting Mitomycin-C sensitivity was generated using data from Genomics of Drug Sensitivity in Cancer and The Cancer Genome Atlas. Validation was performed on CPM patients who underwent CRS-HIPEC (n = 62) using immunohistochemistry (IHC). We determined predictive significance of our set using overall survival as a surrogate endpoint via a logistic regression model. Three potential biomarkers were identified and optimized for IHC. Patients exhibiting lower expression of PAXIP1 and SSBP2 had poorer survival than those with higher expression (p = 0.045 and 0.140, respectively). No difference was observed in patients with differing DTYMK expression (p = 0.715). Combining PAXIP1 and SSBP2 in a set, patients with two dysregulated protein markers had significantly poorer survival than one or no dysregulated marker (p = 0.016). This set independently predicted survival in a Cox regression model (HR 5.097; 95% CI 1.731–15.007; p = 0.003). We generated and validated an IHC prognostic set which could potentially identify patients who are likely to benefit from HIPEC using Mitomycin-C.
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Affiliation(s)
| | - Joey Wee-Shan Tan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Hwee Leong Tan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weining Wang
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Yudong Chen
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Hui Jun Lim
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Qiu Xuan Tan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Josephine Hendrikson
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wai Har Ng
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Li Yang Loo
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Seettha D Wasudevan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Grace Hwei Ching Tan
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Claramae Shulyn Chia
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Khee Chee Soo
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chin-Ann Johnny Ong
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore.
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18
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SOX4: Epigenetic regulation and role in tumorigenesis. Semin Cancer Biol 2019; 67:91-104. [PMID: 31271889 DOI: 10.1016/j.semcancer.2019.06.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
Sex-determining region Y-related (SRY) high-mobility group box 4 (SOX4) is a member of the group C subfamily of SOX transcription factors and promotes tumorigenesis by endowing cancer cells with survival, migratory, and invasive capacities. Emerging evidence has highlighted an unequivocal role for this transcription factor in mediating various signaling pathways involved in tumorigenesis, epithelial-to-mesenchymal transition (EMT), and tumor progression. During the last decade, numerous studies have highlighted the epigenetic interplay between SOX4-targeting microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and SOX4 and the subsequent modulation of tumorigenesis, invasion and metastasis. In this review, we summarize the current state of knowledge about the role of SOX4 in cancer development and progression, the epigenetic regulation of SOX4, and the potential utilization of SOX4 as a diagnostic and prognostic biomarker and its depletion as a therapeutic target.
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19
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Ai K, Jia Y, Li J, Wang C, Wang Y. Systematic analysis of multigene predictors in gastric cancer exploiting gene expression signature. J Cell Biochem 2019; 120:8069-8077. [PMID: 30426570 DOI: 10.1002/jcb.28085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 10/29/2018] [Indexed: 01/24/2023]
Abstract
Gastric cancer (GC) is the second most common cause of cancer death worldwide but could be more curable if diagnosed at an earlier stage. At present, the capability to predict the efficaciousness of molecular diagnosis for GC for each patient remains elusive. The purpose of this study was to identify tumor biomarkers through systems analysis of multigene predictors exploiting the available data resource. In this study, we investigated the top 10% overexpressed genes in GC from five data sets of the Oncomine platform, with 265 GC samples versus 174 normal gastric mucosa samples. Sixteen candidate genes were identified as predictors of GC, of which 14 genes were verified through the comparison of expression levels in specimens from normal (chronic gastritis, 21 samples) and GC groups (38 samples). In addition, unique molecular portraits of diffuse adenocarcinoma (DA), intestinal adenocarcinoma (IA), and mixed adenocarcinoma (MA) were studied through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, where DA showed higher extracellular matrix alteration while IA and MA showed higher cell-cycle alteration than other types. We also found that the elevated expressions of genes during GC progression were independent of gene mutations, and high core-binding factor subunit β expression is correlated with a high overall survival rate in GC patients. Our research may provide an efficient clinical diagnosis of GC at an early stage with high accuracy and thus help improve the overall survival rate through early therapeutic interventions.
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Affiliation(s)
- Kuankuan Ai
- Department of Gastroenterology, Affiliated Hospital of Jining Medical College, Jining, China
| | - Yanli Jia
- Department of Gastroenterology, Yanzhou Hospital of Affiliated Hospital of Jining Medical College, Yanzhou, China
| | - Jin Li
- Department of Gastroenterology, Heze Municipal Hospital, Heze, China
| | - Chong Wang
- Department of Endocrinology, Heze Municipal Hospital, Heze, China
| | - Yan Wang
- Department of Gastroenterology, Affiliated Hospital of Jining Medical College, Jining, China
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20
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Wei D, Wang W, Shen B, Zhou Y, Yang X, Lu G, Yang J, Shao Y. MicroRNA‑199a‑5p suppresses migration and invasion in oral squamous cell carcinoma through inhibiting the EMT‑related transcription factor SOX4. Int J Mol Med 2019; 44:185-195. [PMID: 31059001 PMCID: PMC6559314 DOI: 10.3892/ijmm.2019.4174] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 04/19/2019] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRs) are small, non-coding RNAs that can act as oncogenes or tumor suppressor genes in human cancer. Recent studies have revealed that miR-199a-5p is abnormally expressed in various types of human cancer; however, the potential role of miR-199a-5p in oral squamous cell carcinoma (OSCC) remains elusive. The present study investigated the role of miR-199a-5p in OSCC cells and explored the potential molecular mechanism. Reverse transcription-quantitative polymerase chain reaction was used to measure miR-199a-5p expression in OSCC tissues and adjacent normal oral epithelial tissues. Cell invasion and migration were evaluated using Transwell invasion and wound-healing assays in OSCC cells post-transfection with miR-199a-5p mimics or negative control mimics. In addition, a luciferase reporter assay was conducted to identify the target gene of miR-199a-5p in OSCC cells. The results demonstrated that miR-199a-5p expression was significantly downregulated in OSCC tissues and cell lines, and was associated with tumor progression in OSCC. Furthermore, overexpression of miR-199a-5p inhibited cell invasion and migration, and blocked the epithelial-mesenchymal transition (EMT) cascade. Notably, the results revealed that the EMT-related transcription factor SRY-box 4 (SOX4) was a direct target gene of miR-199a-5p, as determined by the direct binding of miR-199a-5p with the 3′-untranslated region of SOX4. In addition, knockdown of SOX4 by small interfering RNA-SOX4 suppressed proliferation, migration and invasion of OSCC cells. Conversely, overexpression of SOX4 rescued the suppressive effects of miR-199a-5p on cell migration and invasion. Collectively, these data indicated that miR-199a-5p may inhibit the migration and invasion of OSCC cells via targeting the EMT-related transcription factor SOX4, thus suggesting that miR-199a-5p may serve as a prognostic biomarker and therapeutic target in the treatment of OSCC.
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Affiliation(s)
- Dongyi Wei
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Weixin Wang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Baohong Shen
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Yanjun Zhou
- Clinical Laboratory, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Xiaodong Yang
- Clinical Laboratory, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Guangjian Lu
- Clinical Laboratory, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Jianbin Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Yuebao Shao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
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21
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Zhao Z, Liu W, Li J. miR-140-5p inhibits cell proliferation and invasion in colorectal carcinoma by targeting SOX4. Oncol Lett 2018; 17:2215-2220. [PMID: 30675286 PMCID: PMC6341654 DOI: 10.3892/ol.2018.9834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) have been reported to influence the occurrence and development of colorectal carcinoma (CRC). In the current research, we explored miR-140-5p function in CRC. In addition, the molecular mechanisms of miR-140-5p/SOX4 axis for CRC were investigated. The miR-140-5p and SOX4 expression levels were evaluated via RT-qPCR or western blot analysis. The MTT and Transwell assay assessed cell proliferation and invasion. Luciferase assay confirmed that miR-140-5p directly targeted SOX4. Moreover, the results showed that miR-140-5p expression was obviously declined in CRC. The low expression of miR-140-5p was related to tumor stage or metastasis. The miR-140-5p overexpression suppressed cell proliferation and invasion in CRC. Moreover, miR-140-5p was identified to directly target SOX4 and the SOX4 expression was increased in CRC. In addition, the high expression of SOX4 promoted cell proliferation and invasion in CRC. The inhibiting effect of miR-140-5p on SOX4 was identified for CRC, and it inhibited the proliferation and invasion. The novel miR-140-5p/SOX4 axis may provide a new therapy for CRC.
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Affiliation(s)
- Zhongsong Zhao
- Digestive System Department, Shandong Provincial Third Hospital, Jinan, Shandong 250000, P.R. China
| | - Weiwei Liu
- Digestive System Department, Shandong Provincial Third Hospital, Jinan, Shandong 250000, P.R. China
| | - Jianhua Li
- Digestive System Department, Shandong Provincial Third Hospital, Jinan, Shandong 250000, P.R. China
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22
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Ke SB, Qiu H, Chen JM, Shi W, Chen YS. MicroRNA-202-5p functions as a tumor suppressor in colorectal carcinoma by directly targeting SMARCC1. Gene 2018; 676:329-335. [PMID: 30144500 DOI: 10.1016/j.gene.2018.08.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023]
Abstract
Recently, microRNAs (miRNAs) have been emerged as critical regulators for human diseases and as prognostic markers in several tumors, including colorectal carcinoma (CRC). Herein, we identified a tumor-suppressive miRNA, miR-202-5p, which may suppress CRC tumorigenesis. SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 (SMARCC1) is a susceptibility gene in CRC. However, the role of SMARCC1 in CRC tumorigenesis has not been elucidated. In our present study, we demonstrated that miR-202-5p was a tumor-suppressive miRNA in CRC progression. We found that expression of miR-202-5p was obviously decreased in CRC tissues. Down-regulation of miR-202-5p was associated with postoperative survival. Overexpression of miR-202-5p inhibited the growth and metastasis of CRC cells. The SMARCC1 was a direct target of miR-202-5p and promoted the growth and metastasis of CRC cells. Further study showed that SMARCC1 could reverse the inhibitory effect of miR-202-5p on growth and metastasis of CRC cells. In conclusion, our data highlight the key role of miR-202-5p in the progression of CRC. Thus, miR-202-5p may be a potential prognostic marker and of treatment relevance for CRC progression intervention.
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Affiliation(s)
- Shao-Bo Ke
- Renmin Hospital of Wuhan University, Cancer Center, Wuhan 430071, PR China
| | - Hu Qiu
- Renmin Hospital of Wuhan University, Cancer Center, Wuhan 430071, PR China
| | - Jia-Mei Chen
- Renmin Hospital of Wuhan University, Cancer Center, Wuhan 430071, PR China
| | - Wei Shi
- Renmin Hospital of Wuhan University, Cancer Center, Wuhan 430071, PR China
| | - Yong-Shun Chen
- Renmin Hospital of Wuhan University, Cancer Center, Wuhan 430071, PR China.
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23
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Zhao J, Xu J, Zhang R. MicroRNA-539 inhibits colorectal cancer progression by directly targeting SOX4. Oncol Lett 2018; 16:2693-2700. [PMID: 30013665 DOI: 10.3892/ol.2018.8892] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer and the fourth most common cause of cancer-associated mortality in males and females globally. Aberrant expression of microRNA-539 (miR-539) has been reported in multiple types of cancer. However, miR-539 expression, function and underlying mechanisms have not been clearly elucidated in CRC. In the present study, miR-539 expression was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in CRC tissues and cell lines. The effects of miR-539 on CRC cells were further examined in in vitro studies. In addition, the direct targets of miR-539 in CRC were investigated using bioinformatics, luciferase reporter assays, RT-qPCR and western blotting. miR-539 was revealed to be significantly downregulated in CRC cell lines and tissues. Decreased miR-539 expression was associated with lymph node metastasis and tumor-node-metastasis stage in patients with CRC. Functional assays revealed that the rescue of miR-539 expression attenuated CRC cell proliferation and invasion in vitro. Additionally, SRY-box 4 (SOX4) was validated as a direct target gene of miR-539 in CRC. Furthermore, SOX4 was revealed to be upregulated in CRC tissues at the mRNA and protein level. A significant negative correlation between miR-539 and SOX4 mRNA expression levels was observed in CRC tissues. Furthermore, upregulation of SOX4 partially restored the tumor suppressive effects of miR-539 on CRC cell proliferation and invasion. Taken together, this suggests that miR-539 may serve tumor-suppressive functions in CRC during the process of malignant transformation, by directly targeting SOX4. miR-539/SOX4-based targeted therapy may represent a potential novel treatment for patients with CRC.
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Affiliation(s)
- Jian Zhao
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Jian Xu
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Rui Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
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Soliman B, Salem A, Ghazy M, Abu-Shahba N, El Hefnawi M. Bioinformatics functional analysis of let-7a, miR-34a, and miR-199a/b reveals novel insights into immune system pathways and cancer hallmarks for hepatocellular carcinoma. Tumour Biol 2018; 40:1010428318773675. [PMID: 29775159 DOI: 10.1177/1010428318773675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression. There were 87 common target messenger RNAs (p ≤ 0.05) that were predicted to be regulated by the three micro-RNAs using miRror 2.0 target prediction tool. In addition, the functional enrichment analysis of these targets that was performed by DAVID functional annotation and REACTOME tools revealed two major immune-related pathways, eight hepatocellular carcinoma hallmarks-linked pathways, and two pathways that mediate interconnected processes between immune system and hepatocellular carcinoma hallmarks. Moreover, protein-protein interaction network for the predicted common targets was obtained by using STRING database. The individual analysis of target genes and pathways for the three micro-RNAs of interest using miRGator V3.0 and GeneTrail servers revealed some novel predicted target oncogenes such as SOX4, which we validated experimentally, in addition to some regulated pathways of immune system and hepatocarcinogenesis such as insulin signaling pathway and adipocytokine signaling pathway. In general, our results demonstrate that let-7a, miR-34a, and miR-199 a/b have novel interactions in different immune system pathways and major hepatocellular carcinoma hallmarks. Thus, our findings shed more light on the roles of these miRNAs as cancer silencers.
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Affiliation(s)
- Bangly Soliman
- 1 Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt.,2 Informatics and Systems Department, Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), Division of Engineering Research, National Research Centre, Cairo, Egypt
| | - Ahmed Salem
- 1 Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed Ghazy
- 1 Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nourhan Abu-Shahba
- 3 Stem Cells Research Group, Medical Centre of Excellence, Medical Molecular Genetics Department, National Research Centre, Cairo, Egypt
| | - Mahmoud El Hefnawi
- 2 Informatics and Systems Department, Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), Division of Engineering Research, National Research Centre, Cairo, Egypt.,4 Centre for Informatics, Nile University, Sheikh Zayed City, Egypt
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Chen X, Chen Z, Yu S, Nie F, Yan S, Ma P, Chen Q, Wei C, Fu H, Xu T, Ren S, Sun M, Wang Z. Long Noncoding RNA LINC01234 Functions as a Competing Endogenous RNA to Regulate CBFB Expression by Sponging miR-204-5p in Gastric Cancer. Clin Cancer Res 2018; 24:2002-2014. [PMID: 29386218 DOI: 10.1158/1078-0432.ccr-17-2376] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/04/2017] [Accepted: 01/24/2018] [Indexed: 12/13/2022]
Abstract
Purpose: Long noncoding RNAs (lncRNAs) have emerged as important regulators in a variety of human diseases, including cancers. However, the overall biological roles and clinical significance of most lncRNAs in gastric carcinogenesis are not fully understood. We investigated the clinical significance, biological function, and mechanism of LINC01234 in gastric cancer.Experimental Design: First, we analyzed LINC01234 alterations in gastric cancerous and noncancerous tissues through an analysis of sequencing data obtained from The Cancer Genome Atlas. Next, we evaluated the effect of LINC01234 on the gastric cancer cell proliferation and apoptosis, and its regulation of miR-204-5p by acting as a competing endogenous RNA (ceRNA). The animal model was used to support the in vitro experimental findings.Results: We found that LINC01234 expression was significantly upregulated in gastric cancer tissues and was associated with larger tumor size, advanced TNM stage, lymph node metastasis, and shorter survival time. Furthermore, knockdown of LINC01234-induced apoptosis and growth arrest in vitro and inhibited tumorigenesis in mouse xenografts. Mechanistic investigations indicated that LINC01234 functioned as a ceRNA for miR-204-5p, thereby leading to the derepression of its endogenous target core-binding factor β (CBFB).Conclusions: LINC01234 is significantly overexpressed in gastric cancer, and LINC01234-miR-204-5p-CBFB axis plays a critical role in gastric cancer tumorigenesis. Our findings may provide a potential new target for gastric cancer diagnosis and therapy. Clin Cancer Res; 24(8); 2002-14. ©2018 AACR.
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Affiliation(s)
- Xin Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenyao Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shanxun Yu
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fengqi Nie
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuai Yan
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qinnan Chen
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenchen Wei
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hangjiang Fu
- Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Tianwei Xu
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shengnan Ren
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, Texas.
| | - Zhaoxia Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China. .,Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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26
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He P, Jin X. SOX10 induces epithelial-mesenchymal transition and contributes to nasopharyngeal carcinoma progression. Biochem Cell Biol 2017; 96:326-331. [PMID: 29035684 DOI: 10.1139/bcb-2017-0160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the role of SOX10 in nasopharyngeal carcinoma (NPC) and the underlying molecular mechanisms. METHODS The expression of SOX10 was initially assessed in human NPC tissues and a series of NPC cell lines through quantitative real-time PCR (qRT-PCR) and Western blot. Then, cell proliferation, cycle, migration, and the invasiveness of NPC cells with knockdown of SOX10 were examined by MTT, flow cytometry, and Transwell migration and invasion assays, respectively. Finally, nude mice tumorigenicity experiments were performed to evaluate the effects of SOX10 on NPC growth and metastasis in vivo. RESULTS SOX10 was significantly increased in NPC tissues and cell lines. In-vitro experiments revealed that loss of SOX10 obviously inhibited cell proliferation, migration, and invasiveness, as well as the epithelial-mesenchymal transition (EMT) process in NPC cells. In-vivo experiments further demonstrated that disrupted SOX10 expression restrained NPC growth and metastasis, especially in lung and liver. CONCLUSION Taken together, our data confirmed the role of SOX10 as an oncogene in NPC progression, and revealed that SOX10 may serve as a novel biomarker for diagnosis of NPC, as well as a potential therapeutic target against this disease.
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Affiliation(s)
- Ping He
- Department of Otolaryngology, South Campus RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Otolaryngology, South Campus RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Jin
- Department of Otolaryngology, South Campus RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Otolaryngology, South Campus RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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27
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Mullany LE, Herrick JS, Wolff RK, Stevens JR, Samowitz W, Slattery ML. Transcription factor-microRNA associations and their impact on colorectal cancer survival. Mol Carcinog 2017; 56:2512-2526. [PMID: 28667784 PMCID: PMC5633497 DOI: 10.1002/mc.22698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/06/2017] [Accepted: 06/29/2017] [Indexed: 01/16/2023]
Abstract
MicroRNAs (miRNAs) and Transcription Factors (TFs) both influence messenger RNA (mRNA) expression, disrupting biological pathways involved in carcinogenesis and prognosis. As many miRNAs target multiple mRNAs, thus influencing a multitude of biological pathways, deciphering which miRNAs are important for cancer development and survival is difficult. In this study, we (i) determine associations between TF and survival (N = 168 colon cancer cases); (ii) identify miRNAs associated with TFs related to survival; and (iii) determine if factors derived from TF-specific miRNA principal component analysis (PCA) influence survival. Cox Proportional hazard models were run for each PCA factor to determine Hazard Ratios (HR) and 95% Confidence Intervals (CI) adjusting for age, center, and AJCC stage. Thirty TFs improved survival when differential expression increased; 27 of these were associated significantly with normal colonic mucosa expression of 65 unique miRNAs when an FDR q-value of <0.05 was applied. Five factors, comprising 21 miRNAs, altered survival in rectal cancer subjects; four of these five factors improved survival and one factor reduced survival. One factor comprising four miRNAs reduced survival in colon cancer subjects. In summary, our data suggest that expression of TFs and their related miRNAs influence survival after diagnosis with colorectal cancer.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah
| | - Wade Samowitz
- Department of Pathology, University of Utah School, Salt Lake City, Utah
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
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28
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Liu Y, Zeng S, Jiang X, Lai D, Su Z. SOX4 induces tumor invasion by targeting EMT-related pathway in prostate cancer. Tumour Biol 2017; 39:1010428317694539. [PMID: 28466783 DOI: 10.1177/1010428317694539] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
SOX4 (sex-determining region Y-related high-mobility group box 4) is associated with tumor progression and poor clinical outcome in several cancers. This study aims to evaluate whether SOX4 affects the biological behaviors of prostate cancer and further elucidate whether this effect works through the epithelial-mesenchymal transition pathway. We investigated the expression of SOX4 in a series of prostate cancer tissues and adjacent noncancerous tissues, as well as in a panel of prostate cancer cell lines. Cell proliferation, migration, and invasion were evaluated in SOX4 knockdown prostate cancer cell lines by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and Transwell assay. Our results showed that the expression of SOX4 was remarkably upregulated both in prostate cancer tissues and in cell lines. Knockdown of SOX4 repressed the ability of cell proliferation and migration of DU145 cells. Moreover, inhibition of SOX4 could reverse the epithelial-mesenchymal transition processes through upregulation of E-cadherin and downregulation of vimentin. This study provided evidence that SOX4 could serve as a potential therapeutic target in prostate cancer.
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Affiliation(s)
- Yifan Liu
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Zeng
- 2 Department of Pharmacy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xianhan Jiang
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dehui Lai
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhengming Su
- 1 Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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29
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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30
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Yan M, Song M, Bai R, Cheng S, Yan W. Identification of potential therapeutic targets for colorectal cancer by bioinformatics analysis. Oncol Lett 2016; 12:5092-5098. [PMID: 28105216 PMCID: PMC5228398 DOI: 10.3892/ol.2016.5328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/04/2016] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to identify potential therapeutic targets for colorectal cancer (CRC). The gene expression profile GSE32323, containing 34 samples, including 17 specimens of CRC tissues and 17 of paired normal tissues from CRC patients, was downloaded from the Gene Expression Omnibus database. Following data preprocessing using the Affy and preprocessCore packages, the differentially-expressed genes (DEGs) between the two types of samples were identified with the Linear Models for Microarray Analysis package. Next, functional and pathway enrichment analysis of the DEGs was performed using the Database for Annotation Visualization and Integrated Discovery. The protein-protein interaction (PPI) network was established using the Search Tool for the Retrieval of Interacting Genes database. Utilizing WebGestalt, the potential microRNAs (miRNAs/miRs) of the DEGs were screened and the integrated miRNA-target network was built. A cohort of 1,347 DEGs was identified, the majority of which were mainly enriched in cell cycle-related biological processes and pathways. Cyclin-dependent kinase 1 (CDK1), cyclin B1 (CCNB1), MAD2 mitotic arrest deficient-like 1 (MAD2L1) and BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B) were prominent in the PPI network, while the over-represented genes in the integrated miRNA-target network were SRY (sex determining region Y)-box 4 (SOX4; targeted by hsa-mir-129), v-myc avian myelocytomatosis viral oncogene homolog (MYC; targeted by hsa-let-7c and hsa-mir-145) and cyclin D1 (CCND1; targeted by hsa-let-7b). CDK1, CCNB1 and CCND1 were also associated with the p53 signaling pathway. Overall, several genes associated with the cell cycle and p53 pathway were identified as biomarkers for CRC. CDK1, CCNB1, MAD2L1, BUB1B, SOX4, collagen type I α2 chain and MYC may play significant roles in CRC progression by affecting the cell cycle-related pathways, while CDK1, CCNB1 and CCND1 may serve as crucial regulators in the p53 signaling pathway. Furthermore, SOX4, MYC and CCND1 may be targets of miR-129, hsa-mir-145 and hsa-let-7c, respectively. However, further validation of these data is required.
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Affiliation(s)
- Ming Yan
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Maomin Song
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Rixing Bai
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Shi Cheng
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Wenmao Yan
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
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31
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Fu L, Shi YB. The Sox transcriptional factors: Functions during intestinal development in vertebrates. Semin Cell Dev Biol 2016; 63:58-67. [PMID: 27567710 DOI: 10.1016/j.semcdb.2016.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022]
Abstract
The intestine has long been studied as a model for adult stem cells due to the life-long self-renewal of the intestinal epithelium through the proliferation of the adult intestinal stem cells. Recent evidence suggests that the formation of adult intestinal stem cells in mammals takes place during the thyroid hormone-dependent neonatal period, also known as postembryonic development, which resembles intestinal remodeling during frog metamorphosis. Studies on the metamorphosis in Xenopus laevis have revealed that many members of the Sox family, a large family of DNA binding transcription factors, are upregulated in the intestinal epithelium during the formation and/or proliferation of the intestinal stem cells. Similarly, a number of Sox genes have been implicated in intestinal development and pathogenesis in mammals. Futures studies are needed to determine the expression and potential involvement of this important gene family in the development of the adult intestinal stem cells. These include the analyses of the expression and regulation of these and other Sox genes during postembryonic development in mammals as well as functional investigations in both mammals and amphibians by using the recently developed gene knockout technologies.
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Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD, 20892, United States
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), 18 Library Dr., Bethesda, MD, 20892, United States.
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Liu Y, Cui L, Huang J, Ji EH, Chen W, Messadi D, Hu S. SOX4 Promotes Progression in OLP-Associated Squamous Cell Carcinoma. J Cancer 2016; 7:1534-40. [PMID: 27471569 PMCID: PMC4964137 DOI: 10.7150/jca.15689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/01/2016] [Indexed: 01/06/2023] Open
Abstract
Background: The development of oral squamous cell carcinoma (OSCC) is a multistep process that involves in both genetic alterations and epigenetic modifications. Previous studies suggest SOX4 might function as an oncogene or a tumor suppressor in different types of cancers. However, whether SOX4 involves in promoting the progression of oral precancer to cancer is unknown. Methods: Liquid chromatography with tandem mass spectrometry (LC-MS/MS) was used to identify the proteins that may be differentially expressed between oral lichen planus (OLP) and OLP-associated OSCC (OLP-OSCC) formalin-fixed paraffin-embedded (FFPE) tissues. Immunohistochemistry (IHC) and Western blotting were performed to evaluate SOX4 expression between OLP and OLP-OSCC tissues and among oral cancer cell lines and normal human oral keratinocytes (NHOKs). SOX4 siRNA was used to knock down the expression of SOX4 in UM1 oral cancer cells. MTT, cell counting, migration and Matrigel invasion assays were utilized to examine the effect of SOX4 down-regulation on proliferation, migration and invasion capacity of UM1 cells. Results: LC-MS/MS analysis showed that 88 proteins including SOX4 were only identified in OLP-OSCC FFPE tissues when compared to OLP FFPE tissues. IHC confirmed that SOX4 expression was significantly higher in OLP-OSCC than OLP and Western blot analysis indicated that SOX4 was over-expressed in UM1/UM2 cells when compared to NHOKs. Knockdown of SOX4 significantly inhibited the proliferation, migration and invasion of UM1 cells (P<0.01). Conclusions: Our study indicated that SOX4 is significantly upregulated in OLP-OSCC versus OLP tissues. In addition, down-regulation of SOX4 led to significantly reduced proliferation, migration and invasion capability of oral cancer cells. These findings suggest that SOX4 might be actively involved in the progression of OLP to OSCC.
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Affiliation(s)
- Yi Liu
- 1. Department of Oral Medicine, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Affiliated Hospital to University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China.; 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Li Cui
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Junwei Huang
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Eoon Hye Ji
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Wei Chen
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Diana Messadi
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
| | - Shen Hu
- 2. UCLA School of Dentistry and Jonsson Comprehensive Cancer Center, 10833 Le Conte Ave, Los Angeles, CA 90095, USA
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Fryland T, Christensen JH, Pallesen J, Mattheisen M, Palmfeldt J, Bak M, Grove J, Demontis D, Blechingberg J, Ooi HS, Nyegaard M, Hauberg ME, Tommerup N, Gregersen N, Mors O, Corydon TJ, Nielsen AL, Børglum AD. Identification of the BRD1 interaction network and its impact on mental disorder risk. Genome Med 2016; 8:53. [PMID: 27142060 PMCID: PMC4855718 DOI: 10.1186/s13073-016-0308-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/15/2016] [Indexed: 01/23/2023] Open
Abstract
Background The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development, and susceptibility to schizophrenia and bipolar disorder. To advance the understanding of BRD1 and its role in mental disorders, we characterized the protein and chromatin interactions of the BRD1 isoforms, BRD1-S and BRD1-L. Methods Stable human cell lines expressing epitope tagged BRD1-S and BRD1-L were generated and used as discovery systems for identifying protein and chromatin interactions. Protein-protein interactions were identified using co-immunoprecipitation followed by mass spectrometry and chromatin interactions were identified using chromatin immunoprecipitation followed by next generation sequencing. Gene expression profiles and differentially expressed genes were identified after upregulating and downregulating BRD1 expression using microarrays. The presented functional molecular data were integrated with human genomic and transcriptomic data using available GWAS, exome-sequencing datasets as well as spatiotemporal transcriptomic datasets from the human brain. Results We present several novel protein interactions of BRD1, including isoform-specific interactions as well as proteins previously implicated with mental disorders. By BRD1-S and BRD1-L chromatin immunoprecipitation followed by next generation sequencing we identified binding to promoter regions of 1540 and 823 genes, respectively, and showed correlation between BRD1-S and BRD1-L binding and regulation of gene expression. The identified BRD1 interaction network was found to be predominantly co-expressed with BRD1 mRNA in the human brain and enriched for pathways involved in gene expression and brain function. By interrogation of large datasets from genome-wide association studies, we further demonstrate that the BRD1 interaction network is enriched for schizophrenia risk. Conclusion Our results show that BRD1 interacts with chromatin remodeling proteins, e.g. PBRM1, as well as histone modifiers, e.g. MYST2 and SUV420H1. We find that BRD1 primarily binds in close proximity to transcription start sites and regulates expression of numerous genes, many of which are involved with brain development and susceptibility to mental disorders. Our findings indicate that BRD1 acts as a regulatory hub in a comprehensive schizophrenia risk network which plays a role in many brain regions throughout life, implicating e.g. striatum, hippocampus, and amygdala at mid-fetal stages. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0308-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tue Fryland
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jane H Christensen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jonatan Pallesen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University Hospital, 8200, Skejby, Denmark
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark.,Bioinformatics Research Centre (BiRC, Aarhus University, 8000, Aarhus C, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Jenny Blechingberg
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark
| | - Hong Sain Ooi
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Mads E Hauberg
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Niels Gregersen
- Research Unit for Molecular Medicine, Aarhus University Hospital, 8200, Skejby, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark.,Research Department P, Aarhus University Hospital, 8240, Risskov, Denmark
| | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Building 1242, Bartholins Allé 6, 8000, Aarhus C, Denmark. .,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000 Aarhus C, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000, Aarhus C, Denmark. .,Research Department P, Aarhus University Hospital, 8240, Risskov, Denmark.
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Hu F, Min J, Cao X, Liu L, Ge Z, Hu J, Li X. MiR-363-3p inhibits the epithelial-to-mesenchymal transition and suppresses metastasis in colorectal cancer by targeting Sox4. Biochem Biophys Res Commun 2016; 474:35-42. [DOI: 10.1016/j.bbrc.2016.04.055] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/12/2016] [Indexed: 12/18/2022]
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Kooi IE, Mol BM, Massink MPG, de Jong MC, de Graaf P, van der Valk P, Meijers-Heijboer H, Kaspers GJL, Moll AC, te Riele H, Cloos J, Dorsman JC. A Meta-Analysis of Retinoblastoma Copy Numbers Refines the List of Possible Driver Genes Involved in Tumor Progression. PLoS One 2016; 11:e0153323. [PMID: 27115612 PMCID: PMC4846005 DOI: 10.1371/journal.pone.0153323] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND While RB1 loss initiates retinoblastoma development, additional somatic copy number alterations (SCNAs) can drive tumor progression. Although SCNAs have been identified with good concordance between studies at a cytoband resolution, accurate identification of single genes for all recurrent SCNAs is still challenging. This study presents a comprehensive meta-analysis of genome-wide SCNAs integrated with gene expression profiling data, narrowing down the list of plausible retinoblastoma driver genes. METHODS We performed SCNA profiling of 45 primary retinoblastoma samples and eight retinoblastoma cell lines by high-resolution microarrays. We combined our data with genomic, clinical and histopathological data of ten published genome-wide SCNA studies, which strongly enhanced the power of our analyses (N = 310). RESULTS Comprehensive recurrence analysis of SCNAs in all studies integrated with gene expression data allowed us to reduce candidate gene lists for 1q, 2p, 6p, 7q and 13q to a limited gene set. Besides the well-established driver genes RB1 (13q-loss) and MYCN (2p-gain) we identified CRB1 and NEK7 (1q-gain), SOX4 (6p-gain) and NUP205 (7q-gain) as novel retinoblastoma driver candidates. Depending on the sample subset and algorithms used, alternative candidates were identified including MIR181 (1q-gain) and DEK (6p gain). Remarkably, our study showed that copy number gains rarely exceeded change of one copy, even in pure tumor samples with 100% homozygosity at the RB1 locus (N = 34), which is indicative for intra-tumor heterogeneity. In addition, profound between-tumor variability was observed that was associated with age at diagnosis and differentiation grades. INTERPRETATION Since focal alterations at commonly altered chromosome regions were rare except for 2p24.3 (MYCN), further functional validation of the oncogenic potential of the described candidate genes is now required. For further investigations, our study provides a refined and revised set of candidate retinoblastoma driver genes.
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Affiliation(s)
- Irsan E. Kooi
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Berber M. Mol
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Maarten P. G. Massink
- Department of Bio-medical Genetics, University Medical center Utrecht, Utrecht, The Netherlands
| | - Marcus C. de Jong
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - Pim de Graaf
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - Paul van der Valk
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Gertjan J. L. Kaspers
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Annette C. Moll
- Department of Ophthalmology, VU University Medical Center, Amsterdam, the Netherlands
| | - Hein te Riele
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josephine C. Dorsman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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Roisman A, Huamán Garaicoa F, Metrebian F, Narbaitz M, Kohan D, García Rivello H, Fernandez I, Pavlovsky A, Pavlovsky M, Hernández L, Slavutsky I. SOXC and MiR17-92 gene expression profiling defines two subgroups with different clinical outcome in mantle cell lymphoma. Genes Chromosomes Cancer 2016; 55:531-40. [PMID: 26998831 DOI: 10.1002/gcc.22355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Mantle cell lymphoma (MCL) is a heterogeneous B-cell lymphoid malignancy where most patients follow an aggressive clinical course whereas others are associated with an indolent performance. SOX4, SOX11, and SOX12 belong to SOXC family of transcription factors involved in embryonic neurogenesis and tissue remodeling. Among them, SOX11 has been found aberrantly expressed in most aggressive MCL patients, being considered a reliable biomarker in the pathology. Several studies have revealed that microRNAs (miRs) from the miR-17-92 cluster are among the most deregulated miRNAs in human cancers, still little is known about this cluster in MCL. In this study we screened the transcriptional profiles of 70 MCL patients for SOXC cluster and miR17, miR18a, miR19b and miR92a, from the miR-17-92 cluster. Gene expression analysis showed higher SOX11 and SOX12 levels compared to SOX4 (P ≤ 0.0026). Moreover we found a negative correlation between the expression of SOX11 and SOX4 (P < 0.0001). miR17-92 cluster analysis showed that miR19b and miR92a exhibited higher levels than miR17 and miR18a (P < 0.0001). Unsupervised hierarchical clustering revealed two subgroups with significant differences in relation to aggressive MCL features, such as blastoid morphological variant (P = 0.0412), nodal presentation (P = 0.0492), CD5(+) (P = 0.0004) and shorter overall survival (P < 0.0001). Together, our findings show for the first time an association between the differential expression profiles of SOXC and miR17-92 clusters in MCL and also relate them to different clinical subtypes of the disease adding new biological information that may contribute to a better understanding of this pathology. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alejandro Roisman
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina
| | - Fuad Huamán Garaicoa
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina.,FUNDALEU, Buenos Aires, Argentina
| | - Fernanda Metrebian
- División Patología, Instituto de Investigaciones Hematológicas, ANM, Buenos Aires, Argentina
| | - Marina Narbaitz
- FUNDALEU, Buenos Aires, Argentina.,División Patología, Instituto de Investigaciones Hematológicas, ANM, Buenos Aires, Argentina
| | - Dana Kohan
- Servicio de Patología, Hospital Italiano, Buenos Aires, Argentina
| | | | | | | | | | - Luis Hernández
- Patología Molecular, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, España
| | - Irma Slavutsky
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina
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Zhao Y, Liu ZG, Tang J, Zou RF, Chen XY, Jiang GM, Qiu YF, Wang H. High expression of Sox10 correlates with tumor aggressiveness and poor prognosis in human nasopharyngeal carcinoma. Onco Targets Ther 2016; 9:1671-7. [PMID: 27051302 PMCID: PMC4807932 DOI: 10.2147/ott.s101344] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose The aim of the study was to detect the expression of Sox10 in human nasopharyngeal carcinoma (NPC) and investigate the relationship between its expression and the clinicopathological characteristics of NPC patients. Patients and methods Tumor specimens (n=105) were retrospectively collected from patients with NPC diagnosed between 2004 and 2005 who presented at Hunan Cancer Hospital. Immunohistochemistry analyses were performed to characterize the expression of Sox10 in NPC. Kaplan–Meier survival and Cox regression analyses were employed to evaluate the prognosis of 105 NPC patients. Results The results showed that Sox10 was markedly overexpressed in human NPC tissues. Analysis of clinicopathological parameters showed that high Sox10 expression was significantly correlated with the clinical stage (P=0.032), T classification (P=0.034), and lymph node metastasis (P=0.03). Cox regression analyses further showed that Sox10 expression was an independent prognostic factor for overall survival (P=0.005). This is the first time Sox10 has shown its importance in predicting NPC progressiveness and survival outcomes. Conclusion Sox10 serves as a potential biomarker for NPC patients. It may hopefully become a novel therapeutic target for NPC patients.
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Affiliation(s)
- Yu Zhao
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
| | - Zhi-Gang Liu
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
| | - Jiao Tang
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
| | - Ren-Fang Zou
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
| | - Xiao-Yan Chen
- Department of Pathology, Central South University, Changsha, Hunan, People's Republic of China
| | - Guan-Min Jiang
- Department of Clinical Laboratory, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, People's Republic of China
| | - Yan-Fang Qiu
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
| | - Hui Wang
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Changsha, Hunan, People's Republic of China
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Markus MA, Yang YHJ, Morris BJ. Transcriptome-wide targets of alternative splicing by RBM4 and possible role in cancer. Genomics 2016; 107:138-44. [PMID: 26898347 DOI: 10.1016/j.ygeno.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/22/2016] [Accepted: 02/16/2016] [Indexed: 10/25/2022]
Abstract
This study determined transcriptome-wide targets of the splicing factor RBM4 using Affymetrix GeneChip(®) Human Exon 1.0 ST Arrays and HeLa cells treated with RBM4-specific siRNA. This revealed 238 transcripts that were targeted for alternative splicing. Cross-linking and immunoprecipitation experiments identified 945 RBM4 targets in mouse HEK293 cells, 39% of which were ascribed to "alternative splicing" by in silico pathway analysis. Mouse embryonic stem cells transfected with Rbm4 siRNA hairpins exhibited reduced colony numbers and size consistent with involvement of RBM4 in cell proliferation. RBM4 cDNA probing of a cancer cDNA array involving 18 different tumor types from 13 different tissues and matching normal tissue found overexpression of RBM4 mRNA (p<0.01) in cervical, breast, lung, colon, ovarian and rectal cancers. Many RBM4 targets we identified have been implicated in these cancers. In conclusion, our findings reveal transcriptome-wide targets of RBM4 and point to potential cancer-related targets and mechanisms that may involve RBM4.
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Affiliation(s)
- M Andrea Markus
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, New South Wales, Australia.
| | - Yee Hwa J Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia.
| | - Brian J Morris
- Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, New South Wales, Australia.
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Marcker Espersen ML, Linnemann D, Christensen IJ, Alamili M, Troelsen JT, Høgdall E. SOX9 expression predicts relapse of stage II colon cancer patients. Hum Pathol 2016; 52:38-46. [PMID: 26980019 DOI: 10.1016/j.humpath.2015.12.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/13/2015] [Accepted: 12/19/2015] [Indexed: 01/05/2023]
Abstract
The aim of this study was to investigate if the protein expression of sex-determining region y-box 9 (SOX9) in primary tumors could predict relapse of stage II colon cancer patients. One hundred forty-four patients with stage II primary colon cancer were retrospectively enrolled in the study. SOX9 expression was evaluated by immunohistochemistry, and mismatch repair status was assessed by both immunohistochemistry and promoter hypermethylation assay. High SOX9 expression at the invasive front was significantly associated with lower risk of relapse when including the SOX9 expression as a continuous variable (from low to high expression) in univariate (hazard ratio [HR], 0.73; 95% confidence interval [CI], 0.56-0.94; P = .01) and multivariate Cox proportional hazards analyses (HR, 0.75; 95% CI, 0.58-0.96; P = .02), adjusting for mismatch repair deficiency and histopathologic risk factors. Conversely, low SOX9 expression at the invasive front was significantly associated with high risk of relapse, when including SOX9 expression as a dichotomous variable, in univariate (HR, 2.32; 95% CI, 1.14-4.69; P = .02) and multivariate analyses (HR, 2.32; 95% CI, 1.14-4.69; P = .02), adjusting for histopathologic risk factors and mismatch repair deficiency. In conclusion, high levels of SOX9 of primary stage II colon tumors predict low risk of relapse, whereas low levels of SOX9 predict high risk of relapse. SOX9 may have an important value as a biomarker when evaluating risk of relapse for personalized treatment.
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Affiliation(s)
- Maiken Lise Marcker Espersen
- Department of Pathology, Herlev University Hospital, DK-2730 Herlev, Denmark; Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde, Denmark.
| | - Dorte Linnemann
- Department of Pathology, Herlev University Hospital, DK-2730 Herlev, Denmark.
| | | | - Mahdi Alamili
- Department of Surgery, Køge University Hospital, DK-4600 Køge, Denmark.
| | - Jesper T Troelsen
- Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde, Denmark.
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, DK-2730 Herlev, Denmark.
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Epigenomic regulation of oncogenesis by chromatin remodeling. Oncogene 2016; 35:4423-36. [PMID: 26804164 DOI: 10.1038/onc.2015.513] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023]
Abstract
Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy.
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41
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Wang B, Li Y, Tan F, Xiao Z. Increased expression of SOX4 is associated with colorectal cancer progression. Tumour Biol 2016; 37:9131-7. [PMID: 26768610 DOI: 10.1007/s13277-015-4756-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/29/2015] [Indexed: 11/29/2022] Open
Abstract
Sex-determining region Y-related high-mobility group box 4 (SOX4) has been proven to serve as a critical role in cancer progression. However, the pathological role of SOX4 in colorectal cancer (CRC) remains unknown. The aim of this study was to investigate the role of SOX4 in CRC. In this study, we investigated the expression of SOX4 in CRC tissues by immunohistochemistry, quantitative reverse transcription polymerase chain reaction (qRT-PCR), and Western blot. We also evaluated the effect of SOX4 on cell proliferation and invasion by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) and transwell assay. The SOX4 messenger RNA (mRNA) and protein expression were markedly higher in CRC tissues compared with adjacent normal mucosa tissues. Inhibition of SOX4 could suppress CRC cell proliferation, and invasion in vitro. Our findings indicate that targeting SOX4 might provide a new therapeutic modality for the treatment of CRC patients.
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Affiliation(s)
- Baochun Wang
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, Hunan, 410008, China.,Department of General Surgery, Hainan Province People's Hospital, Haikou, 570311, China
| | - Yixiong Li
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, Hunan, 410008, China.
| | - Fengbo Tan
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87 Xiangya Road, Changsha, Hunan, 410008, China
| | - Zhanxiang Xiao
- Department of General Surgery, Hainan Province People's Hospital, Haikou, 570311, China
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Kaller M, Hermeking H. Interplay Between Transcription Factors and MicroRNAs Regulating Epithelial-Mesenchymal Transitions in Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 937:71-92. [DOI: 10.1007/978-3-319-42059-2_4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Chen J, Ju HL, Yuan XY, Wang TJ, Lai BQ. SOX4 is a potential prognostic factor in human cancers: a systematic review and meta-analysis. Clin Transl Oncol 2015; 18:65-72. [PMID: 26250764 DOI: 10.1007/s12094-015-1337-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/20/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The aim of the this study was to analyze the status of sex-determining region Y-related high-mobility group box 4 (SOX4) expression in varied human cancers and its correlation with overall survival in patients with human cancers. METHODS To observe initially the expression status of SOX4 in twenty kinds of human cancers at protein database (The Human Protein Atlas). We systematically and carefully searched the studies from electronic databases and seriously identified according to eligibility criteria. The correlation between SOX4 expression and overall survival in human cancers was evaluated through Review Manager. RESULTS We found that SOX4 expression was significantly positive in most types of human cancer tissues, and the positive rate of SOX4 expression was about 78 % in overall cancer tissues. Furthermore, a total of 10 studies which included 1348 cancer patients were included in the final analysis. Meta-analysis showed that SOX4 overexpression was correlated with a poor overall survival and the pooled hazard ratio (HR), and corresponding 95 % confidence interval (CI) was 1.67 (95 % CI 1.01-2.78). From subgroup analyses, we present evidence that SOX4 overexpression was an unfavorable prognostic factor for colorectal cancer patients' recurrence-free survival and gastric cancer patients' overall survival, and the pooled HRs (95 % CI) were 1.73 (95 % CI 1.04-2.88) and 3.74 (95 % CI 1.04-13.45), respectively. CONCLUSIONS In summary, SOX4 is a potential prognostic biomarker in human cancers.
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Affiliation(s)
- J Chen
- Department of Anaesthesiology and Surgery, The Tumor Hospital of Shanxi Province, Xi'an, 710061, Shanxi, China
| | - H L Ju
- Department of Anaesthesiology and Surgery, The Tumor Hospital of Shanxi Province, Xi'an, 710061, Shanxi, China
| | - X Y Yuan
- Department of Stomatology, The Jiaotong Hospital of Shanxi Province, Xi'an, 710068, Shanxi, China
| | - T J Wang
- Department of Anaesthesiology and Surgery, The Tumor Hospital of Shanxi Province, Xi'an, 710061, Shanxi, China
| | - B Q Lai
- Intensive Care Unit, The Tumor Hospital of Shanxi Province, No. 309 Yanta Road West, Xi'an, 710061, Shanxi, China.
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Espersen MLM, Olsen J, Linnemann D, Høgdall E, Troelsen JT. Clinical Implications of Intestinal Stem Cell Markers in Colorectal Cancer. Clin Colorectal Cancer 2015; 14:63-71. [DOI: 10.1016/j.clcc.2014.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 12/16/2022]
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Song GD, Sun Y, Shen H, Li W. SOX4 overexpression is a novel biomarker of malignant status and poor prognosis in breast cancer patients. Tumour Biol 2015; 36:4167-73. [PMID: 25592378 DOI: 10.1007/s13277-015-3051-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/02/2015] [Indexed: 12/22/2022] Open
Abstract
Sex-determining region Y-related high mobility group box 4 (SOX4) has been proven to serve as a critical role in cancer development and progression. However, little is known about the pathological role of SOX4 in breast cancer patients. The purpose of this study is to measure the expression of SOX4 in breast cancer patients and to explore the clinical significance of SOX4. Using RT-PCR and Western blot, messenger RNA (mRNA) and protein expression of SOX4 were measured in breast cancer tissues and adjacent normal mammary tissues. The relationship of SOX4 expression with clinical characteristics of 148 breast cancer patients was analyzed by immunohistochemistry. In the present study, our results indicated that SOX4 mRNA and protein were highly expressed in breast cancer tissues compared with adjacent normal mammary tissues and positively correlated with clinical stage (I-II vs. III-IV; P = 0.008), T classification (T1-T2 vs. T3-T4; P = 0.013), N classification (N0-N1 vs. N2-N3; P < 0.001), M classification (M0 vs. M1; P = 0.001), estrogen receptor (negative vs. positive; P = 0.029), progesterone receptor (negative vs. positive; P = 0.004), and histological grade (G1 vs. G2-G3; P = 0.033) in breast cancer patients. Furthermore, we also found that SOX4 protein overexpression was an unfavorable prognostic factor in breast cancer patients (P < 0.001), regardless of clinical stage, tumor size, lymph node metastasis, and distant metastasis. Finally, high SOX4 expression was an independent poor prognostic factor for pancreatic patients through multivariate analysis (P = 0.033). In conclusion, SOX4 overexpression serves as an unfavorable prognostic biomarker in breast cancer patients.
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Affiliation(s)
- Guo-Dong Song
- Department of Surgery, The Second Hospital of Tianjin Medical University, No.23 Pingjiang Avenue, Xihe District, Tianjin, 300211, China,
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Increased expression of SOX4 is a biomarker for malignant status and poor prognosis in patients with non-small cell lung cancer. Mol Cell Biochem 2015; 402:75-82. [PMID: 25567207 DOI: 10.1007/s11010-014-2315-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/20/2014] [Indexed: 12/22/2022]
Abstract
The aim of the present study was to analyze the expression of sex-determining region Y-related high mobility group box 4 (SOX4) in non-small cell lung cancer (NSCLC) and its correlation with clinicopathologic characteristics, including the survival of NSCLC patients. To observe initially the expression status of SOX4 in lung squamous cell carcinoma and adenocarcinoma at gene expression omnibus. The expression of SOX4 mRNA and protein was examined in NSCLC tissues and normal lung tissues through real-time PCR and immunohistochemistry. Meanwhile, the relationship of SOX4 expression levels with clinical characteristics of 168 NSCLC patients was analyzed by immunohistochemistry. Univariate and multivariate analyses were performed to determine the association between SOX4 expression and prognosis of NSCLC patients. In our results, SOX4 expression was increased in NSCLC tissues compared with paired normal lung tissues in microarray data (GSE3268). SOX4 mRNA and protein expression were markedly higher in NSCLC tissues than in normal lung tissues (P = 0.001 and P = 0.001, respectively). Using immunohistochemistry, high levels of SOX4 protein were positively correlated with status of differentiated degree (high vs. middle, P = 0.004; high vs. low, P < 0.001), clinical stage (I-II vs. III-IV, P < 0.001), T classification (T1-T2 vs. T3-T4, P = 0.004), N classification (N0-N1 vs. N2-N3, P = 0.002), and M classification (M0 vs. M1, P = 0.011) in NSCLC. Moreover, the higher level of SOX4 expression was markedly correlated with poor overall survival in NSCLC patients (P < 0.001). Multivariate analysis suggested that increased SOX4 expression was a poor independent prognostic predictor for NSCLC patients (P = 0.002). In conclusion, SOX4 plays an important role on NSCLC progression and prognosis and may serve as a convictive prognostic biomarker for NSCLC patients.
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Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E. An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol 2015; 14:R96. [PMID: 24025402 PMCID: PMC4053835 DOI: 10.1186/gb-2013-14-9-r96] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/06/2013] [Indexed: 12/28/2022] Open
Abstract
Background We have used a sensitized ENU mutagenesis screen to produce mouse lines that carry mutations in genes required for epigenetic regulation. We call these lines Modifiers of murine metastable epialleles (Mommes). Results We report a basic molecular and phenotypic characterization for twenty of the Momme mouse lines, and in each case we also identify the causative mutation. Three of the lines carry a mutation in a novel epigenetic modifier, Rearranged L-myc fusion (Rlf), and one gene, Rap-interacting factor 1 (Rif1), has not previously been reported to be involved in transcriptional regulation in mammals. Many of the other lines are novel alleles of known epigenetic regulators. For two genes, Rlf and Widely-interspaced zinc finger (Wiz), we describe the first mouse mutants. All of the Momme mutants show some degree of homozygous embryonic lethality, emphasizing the importance of epigenetic processes. The penetrance of lethality is incomplete in a number of cases. Similarly, abnormalities in phenotype seen in the heterozygous individuals of some lines occur with incomplete penetrance. Conclusions Recent advances in sequencing enhance the power of sensitized mutagenesis screens to identify the function of previously uncharacterized factors and to discover additional functions for previously characterized proteins. The observation of incomplete penetrance of phenotypes in these inbred mutant mice, at various stages of development, is of interest. Overall, the Momme collection of mouse mutants provides a valuable resource for researchers across many disciplines.
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Zhang J, Jiang H, Shao J, Mao R, Liu J, Ma Y, Fang X, Zhao N, Zheng S, Lin B. SOX4 inhibits GBM cell growth and induces G0/G1 cell cycle arrest through Akt-p53 axis. BMC Neurol 2014; 14:207. [PMID: 25366337 PMCID: PMC4233052 DOI: 10.1186/s12883-014-0207-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/06/2014] [Indexed: 01/16/2023] Open
Abstract
Background SOX4 is a transcription factor required for tissue development and differentiation in vertebrates. Overexpression of SOX4 has been reported in many cancers including glioblastoma multiforme (GBM), however, the underlying mechanism of actions has not been studied. In this study, we investigated the role of SOX4 in GBM. Methods Kaplan-Meier analysis was performed to assess the association between SOX4 expression levels and survival times in primary GBM samples. Cre/lox P system was used to generate gain or loss of SOX4 in GBM cells, and microarray analysis uncovered the regulation network of SOX4 in GBM cells. Results High SOX4 expression was significantly associated with good prognosis of primary GBMs. SOX4 inhibited the growth of GBM cell line LN229, A172G and U87MG, partly via the activation of p53-p21 signaling and down-regulation of phosphorylated AKT1. Gene expression profiling and subsequent gene ontology analysis showed that SOX4 influenced several key pathways including the Wnt/ beta-catenin and TGF-beta signaling pathways. Conclusions Our study found that SOX4 acts as a tumor suppressor in GBM cells by induce cell cycle arrest and inhibiting cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12883-014-0207-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, P R China. .,Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Huawei Jiang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, P R China. .,Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Jiaofang Shao
- Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu Province, P R China.
| | - Ruifang Mao
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Jie Liu
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Yingying Ma
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Xuefeng Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Na Zhao
- Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, P R China.
| | - Biaoyang Lin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, P R China. .,Systems Biology Division and Propriumbio Research Center, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Province, P R China. .,Department of Urology, University of Washington, Seattle, WA, 98195, USA.
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Pampaloni B, Mavilia C, Fabbri S, Romani A, Ieri F, Tanini A, Tonelli F, Brandi ML. In Vitro Effects of Extracts of Extra Virgin Olive Oil on Human Colon Cancer Cells. Nutr Cancer 2014; 66:1228-36. [DOI: 10.1080/01635581.2014.951727] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Wang W, Zhang J, Zhan X, Lin T, Yang M, Hu J, Han B, Hu S. SOX4 is associated with poor prognosis in cholangiocarcinoma. Biochem Biophys Res Commun 2014; 452:614-21. [PMID: 25181339 DOI: 10.1016/j.bbrc.2014.08.124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 08/23/2014] [Indexed: 02/08/2023]
Abstract
Overexpressions of EGFR and HER2 are thought to be prognostic factors of cholangiocarcinoma (CCA). The SOX4 transcription factor is involved in the development and cell fate decision. Although up-regulation of SOX4 has been described in multiple human malignancies, the prognostic value of SOX4 and its relationship to EGFR/HER2 in CCA remain unclear. In the current study, we showed that SOX4 and EGFR were overexpressed in 17 (29.3%), and 13 (22.4%) of the 58 intrahepatic cholangiocarcinomas (IHCCs), as well as 28 (29.8%), and 33 (35.1%) of the 94 extrahepatic cholangiocarcinomas (EHCCs), respectively. Overexpression of HER2 was exclusively identified in EHCCs, with the rate being 4.4% (4/90). In all, amplification of EGFR was identified in 1.8% (1/52) of IHCC cases, and in 2% (3/82) of EHCC cases. By contrast, HER2 amplification was present only in 3.5% (3/94) of the EHCC cases. Notably, Kaplan-Meier survival analysis suggested that SOX4 expression is a significant prognostic factor for poor prognosis in IHCC patients. Importantly, our findings suggested significant association of SOX4 and EGFR expression both in IHCC (P<0.001) and EHCC (P=0.014). SOX4 may modulate expression of EGFR, and SOX4+/EGFR+ defines a subset of CCA patients with poor prognosis. Finally, in vitro data indicated that SOX4 inhibits cellular migratory capacity and promotes epithelial-mesenchymal transition (EMT) process of CCA cells. Collectively, our results define an important role for SOX4 in CCA by orchestrating EMT and modulation on EGFR expression. SOX4 expression may serve as a prognostic marker for patients with IHCC.
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Affiliation(s)
- Weishan Wang
- Department of General Surgery, Shandong University Qilu Hospital, Jinan, China; Department of General Surgery, Yishui Central Hospital, Linyi, China
| | - Jing Zhang
- Department of Pharmacy, Shandong Provincial Hospital, Jinan, China
| | - Xuemei Zhan
- Department of Pathology, Linyi People's Hospital, Linyi, China
| | - Tao Lin
- Department of Surgery, Jinan Central Hospital, Jinan, China
| | - Muyi Yang
- Department of Pathology, Shandong University Medical School, Jinan, China
| | - Jing Hu
- Department of Pathology, Shandong University Medical School, Jinan, China
| | - Bo Han
- Department of Pathology, Shandong University Medical School, Jinan, China; Department of Pathology, Shandong University Qilu Hospital, Jinan, China.
| | - Sanyuan Hu
- Department of General Surgery, Shandong University Qilu Hospital, Jinan, China.
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