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Patowary P, Bhattacharyya DK, Barah P. SNMRS: An advanced measure for Co-expression network analysis. Comput Biol Med 2022; 143:105222. [PMID: 35121360 DOI: 10.1016/j.compbiomed.2022.105222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 11/17/2022]
Abstract
The challenge of identifying modules in a gene interaction network is important for a better understanding of the overall network architecture. In this work, we develop a novel similarity measure called Scaling-and-Shifting Normalized Mean Residue Similarity (SNMRS), based on the existing NMRS technique [1]. SNMRS yields correlation values in the range of 0 to +1 corresponding to negative and positive dependency. To study the performance of our measure, internal validation of extracted clusters resulting from different methods is carried out. Based on the performance, we choose hierarchical clustering and apply the same using the corresponding dissimilarity (distance) values of SNMRS scores, and utilize a dynamic tree cut method for extracting dense modules. The modules are validated using a literature search, KEGG pathway analysis, and gene-ontology analyses on the genes that make up the modules. Moreover, our measure can handle absolute, shifting, scaling, and shifting-and-scaling correlations and provides better performance than several other measures in terms of cluster-validity indices. Also, SNMRS based module detection method results in interesting biologically relevant patterns from gene microarray and RNA-seq dataset. A set of crucial genes having high relevance with the ESCC are also identified.
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Affiliation(s)
- Pallabi Patowary
- Department of Computer Science and Engineering, Tezpur University, Assam, India.
| | | | - Pankaj Barah
- Dept. of Molecular Biology and Biotechnology Tezpur University, Assam, India.
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Yue M, Liu Y, Zuo T, Jiang Y, Pan J, Zhang S, Shen X. Circ_0006948 Contributes to Cell Growth, Migration, Invasion and Epithelial-Mesenchymal Transition in Esophageal Carcinoma. Dig Dis Sci 2022; 67:492-503. [PMID: 33630215 DOI: 10.1007/s10620-021-06894-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) can act as promoters or inhibitors in cancer progression. Has_circ_0006948 (circ_0006948) was reported to aggravate the malignant behaviors of esophageal carcinoma (EC). AIMS This study focused on investigating the molecular mechanism of circ_0006948 in EC progression. METHODS The quantitative real-time polymerase chain reaction was performed to detect the expression of circ_0006948, microRNA-4262 (miR-4262) and fibronectin type III domain containing 3B (FNDC3B). Cell growth analysis was conducted by Cell Counting Kit-8 and colony formation assays. Cell migration and invasion were assessed by transwell assay. Epithelial-mesenchymal transition (EMT)-associated proteins and FNDC3B protein expression were assayed using western blot. Dual-luciferase reporter and RNA pull-down assays were performed to validate the target combination. Xenograft tumor assay was used for investigating the role of circ_0006948 in vivo. RESULTS Circ_0006948 was upregulated in EC tissues and cells. Downregulating the expression of circ_0006948 or FNDC3B repressed cell growth, migration, invasion and EMT in EC cells. Target analysis indicated that miR-4262 was a target for circ_0006948 and FNDC3B was a downstream gene for miR-4262. Moreover, circ_0006948 could affect the expression of FNDC3B via sponging miR-4262. The effects of si-circ_0006948#1 on EC cells were partly restored by miR-4262 inhibition or FNDC3B overexpression. In addition, circ_0006948 also facilitated EC tumorigenesis in vivo by targeting the miR-4262/FNDC3B axis. CONCLUSION Taken together, circ_0006948 functioned as an oncogenic factor in EC by the miR-4262-mediated FNDC3B expression regulation.
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Affiliation(s)
- Meng Yue
- Department of Gastroenterology, Jinan Central Hospital Affiliated to Shandong First Medical University, No.105 Jiefang Road, Lixia District, Jinan, 250013, Shandong Province, China.
| | - Yanxia Liu
- Department of Oncology, Shengli Oil Central Hospital, Dongying City, Shandong Province, China
| | - Taiyang Zuo
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan City, Shandong Province, China
| | - Yakun Jiang
- Department of Gastroenterology, Jinan Central Hospital Affiliated to Shandong First Medical University, No.105 Jiefang Road, Lixia District, Jinan, 250013, Shandong Province, China
| | - Jianmei Pan
- Department of Gastroenterology, Jinan Central Hospital Affiliated to Shandong First Medical University, No.105 Jiefang Road, Lixia District, Jinan, 250013, Shandong Province, China
| | - Shuhong Zhang
- Department of Gastroenterology, Jinan Central Hospital Affiliated to Shandong First Medical University, No.105 Jiefang Road, Lixia District, Jinan, 250013, Shandong Province, China
| | - Xingjie Shen
- Department of Gastroenterology, Jinan Central Hospital Affiliated to Shandong First Medical University, No.105 Jiefang Road, Lixia District, Jinan, 250013, Shandong Province, China
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Askari N, Hadizadeh M. Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2022; 15:232-240. [PMID: 36311956 PMCID: PMC9589132 DOI: 10.22037/ghfbb.v15i3.2465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/10/2022] [Indexed: 11/16/2022]
Abstract
Aim The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. Background The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown. Methods Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs. Results KEGG pathway analysis indicated that the p53 signaling pathway, ECM-receptor interaction, and AGE-RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen-containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched. Conclusion Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future.
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Affiliation(s)
- Nahid Askari
- Department of Biotechnology, Institute of Sciences and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
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Gga-miR-181a modulates ANP32A expression and inhibits MDCC-MSB-1 cell. In Vitro Cell Dev Biol Anim 2021; 57:272-279. [PMID: 33686586 DOI: 10.1007/s11626-021-00550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Marek's disease (MD), a highly contagious T cell lymphoid neoplasia disease of chickens, causes huge economic losses to the poultry industry. It is the only one tumor disease which can be prevented by vaccine in chickens; therefore, MD is considered to be an excellent model to study the pathogenesis of virus-induced cancer. Recently, abundant evidences have verified that miRNAs are regulators in the process of neoplastic transformation. In our previous study on miRNome analysis of MDV-induced lymphoma in chicken, we found that gga-miR-181a was downregulated drastically in MDV-infected spleens. To further investigate the role of gga-miR-181a in MDV-induced lymphomagenesis, we performed cell migration assay, and the results suggested that gga-miR-181a suppressed the migration of MDV-transformed lymphoid cell (MSB-1). Subsequently, luciferase reporter gene assay revealed that acidic nuclear phosphoprotein 32A (ANP32A) was a functional target gene of gga-miR181a. Real-time PCR and western blot assay showed that the mRNA and protein levels of ANP32A were downregulated in gga-miR-181a mimic group at 48-h and 96-h post-transfection, respectively, indicating that ANP32A was modulated by gga-miR-181a. All the results suggested that gga-miR-181a was an inhibitor in MSB-1 cell migration. ANP32A was a direct target gene of gga-miR-181a and they were implicated in MD lymphoma tumorigenesis.
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He Z, Chen J, Chen X, Wang H, Tang L, Han C. microRNA-377 acts as a suppressor in esophageal squamous cell carcinoma through CBX3-dependent P53/P21 pathway. J Cell Physiol 2020; 236:107-120. [PMID: 33459391 DOI: 10.1002/jcp.29631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Abstract
Stem cells play pivotal roles in esophageal squamous cell carcinoma (ESCC) recurrence and metastasis. The self-renewal ability of stem cells was associated with specific microRNAs (miRs). Herein, we identified the effects of miR-377 on ESCC stem cell activities. First, the expression of miR-377 in ESCC and adjacent normal tissues was determined. The relationship between miR-377 and chromobox protein homolog 3 (CBX3) was assessed by a dual-luciferase reporter gene assay. miR-377 was overexpressed or inhibited in ESCC stem cells to explore its role in ESCC. To further investigate the mechanism of miR-377 in ESCC, cells were introduced with short hairpin RNA against CBX3 or pifithrin-α (inhibitor of P53 pathway). Besides, the expression of P21, P53, CD133, CD13, Nanog, sex determining region Y-Box 2 (Sox2), and octamer-binding transcription factor 4 (Oct4), cell sphere formation, colony formation, and proliferation were evaluated respectively. Finally, limiting dilution assay in vivo and tumor xenograft in nude mice were conducted to confirm the roles of miR-377 in vivo. miR-377 was poorly expressed in ESCC. Overexpression of miR-377 could suppress the stem-like trait of ESCC as well as the tumor growth in vivo. miR-377 targeted CBX3 to activate the P53/P21 pathway. Besides, the expression of stem-like markers including CD133, CD13, Oct4, Sox2, and Nanog was decreased, and the abilities of cell sphere formation, colony formation, proliferation, and tumorigenicity were significantly reduced by overexpressing miR-377 or silencing CBX3. The results were reversed after inactivating the P53/P21 pathway. In summary, upregulation of miR-377 inhibits the self-renewal of ESCC stem cells by inhibiting CBX3 expression and promoting activation of the P53/P21 pathway.
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Affiliation(s)
- Zhisheng He
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Junjing Chen
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Xiaoliang Chen
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Huanyuan Wang
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Lang Tang
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Chunbin Han
- Department of Thoracic Surgery Oncology, Jiangxi Cancer Hospital, Nanchang, China
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Esophageal Cancer Development: Crucial Clues Arising from the Extracellular Matrix. Cells 2020; 9:cells9020455. [PMID: 32079295 PMCID: PMC7072790 DOI: 10.3390/cells9020455] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
In the last years, the extracellular matrix (ECM) has been reported as playing a relevant role in esophageal cancer (EC) development, with this compartment being related to several aspects of EC genesis and progression. This sounds very interesting due to the complexity of this highly incident and lethal tumor, which takes the sixth position in mortality among all tumor types worldwide. The well-established increase in ECM stiffness, which is able to trigger mechanotransduction signaling, is capable of regulating several malignant behaviors by converting alteration in ECM mechanics into cytoplasmatic biochemical signals. In this sense, it has been shown that some molecules play a key role in these events, particularly the different collagen isoforms, as well as enzymes related to its turnover, such as lysyl oxidase (LOX) and matrix metalloproteinases (MMPs). In fact, MMPs are not only involved in ECM stiffness, but also in other events related to ECM homeostasis, which includes ECM remodeling. Therefore, the crucial role of distinct MMPs isoform has already been reported, especially MMP-2, -3, -7, and -9, along EC development, thus strongly associating these proteins with the control of important cellular events during tumor progression, particularly in the process of invasion during metastasis establishment. In addition, by distinct mechanisms, a vast diversity of glycoproteins and proteoglycans, such as laminin, fibronectin, tenascin C, galectin, dermatan sulfate, and hyaluronic acid exert remarkable effects in esophageal malignant cells due to the activation of oncogenic signaling pathways mainly involved in cytoskeleton alterations during adhesion and migration processes. Finally, the wide spectrum of interactions potentially mediated by ECM may represent a singular intervention scenario in esophageal carcinogenesis natural history and, due to the scarce knowledge on the cellular and molecular mechanisms involved in EC development, the growing body of evidence on ECM’s role along esophageal carcinogenesis might provide a solid base to improve its management in the future.
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Yin L, Li W, Xu A, Shi H, Wang K, Yang H, Wang R, Peng B. SH3BGRL2 inhibits growth and metastasis in clear cell renal cell carcinoma via activating hippo/TEAD1-Twist1 pathway. EBioMedicine 2020; 51:102596. [PMID: 31911271 PMCID: PMC7000347 DOI: 10.1016/j.ebiom.2019.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignancies in the world, and tumor metastasis is still the main reason for disease progression. Accumulating evidence shows that SH3BGRL2 may play a key role in tumor progression and metastasis. However, the role of SH3BGRL2 in ccRCC has not been systematically investigated and remains elusive. Methods The clinical significance of SH3BGRL2 was evaluated by bioinformatic analysis and tissue microarray (TMA) samples. SH3BGRL2 expression was determined by RT-PCR, western blot and immunohistochemistry staining. Tumor suppressive effect of SH3BGRL2 was determined by both in vitro and in vivo studies. Western blot, chromatin immunoprecipitation assay and luciferase report assay were applied for mechanism dissection. Findings SH3BGRL2 was crucial for epithelial-mesenchymal transition (EMT) progression and metastasis in ccRCC. Clinically, SH3BGRL2 was identified as an independent prognostic factor for ccRCC patients. Gain- and loss-of-function results suggested that SH3BGRL2 played a critical role in cell proliferation, migration and invasion. Mechanistically, we found that SH3BGRL2 acted as a tumor suppressor through Hippo/TEAD1 signaling, then TEAD1 altered Twist1 expression at the transcriptional level via directly binding to its promoter region. Interpretation Our findings established that SH3BGRL2 performed as a tumor suppressor and modulator via Hippo/TEAD1-Twist1 signaling in ccRCC, and the alteration of SH3BGRL2 could serve as a functional response biomarker of tumor progression and metastasis in ccRCC.
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Affiliation(s)
- Lei Yin
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Wenjia Li
- Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Aiming Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Shi
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ronghao Wang
- School of basic medical sciences, Southwest Medical University, Luzhou, China.
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China.
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Cui XW, Qian ZL, Li C, Cui SC. Identification of miRNA and mRNA expression profiles by PCR microarray in hepatitis B virus‑associated hepatocellular carcinoma. Mol Med Rep 2018; 18:5123-5132. [PMID: 30272372 DOI: 10.3892/mmr.2018.9516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to identify differentially expressed microRNAs (miRNAs) and mRNAs in hepatitis B virus‑associated hepatocellular carcinoma (HCC). A total of five HCC tissues and paired adjacent non‑tumor tissues were screened to identify the differentially expressed miRNAs and target mRNAs using polymerase chain reaction microarrays. The interaction between differential miRNA and mRNA expression was concurrently analyzed using bioinformatics methods. A total of 32 differentially expressed miRNAs (four upregulated miRNAs and 28 downregulated miRNAs) and 16 differentially expressed mRNAs (11 upregulated mRNAs and five downregulated mRNAs) were identified. Among these, upregulated hsa‑miRNA (miR)‑96‑5p and hsa‑miR‑18b‑5p suppressed their target mRNAs forkhead box O1 and MET transcriptional regulator MACC1 (MACC1). Downregulation of hsa‑miR‑199a‑5p led to upregulation of its target mRNAs, cyclin dependent kinase 4 and insulin like growth factor 2 (IGF2). The high‑level expression of IGF2 mRNA and cyclin E1 mRNA was due to the low‑level expression of hsa‑miR‑145‑5p, hsa‑miR‑181a‑5p, hsa‑miR‑199a‑5p and hsa‑miR‑223a‑3p, and hsa‑miR‑26a‑5p and hsa‑miR‑26b‑5p, respectively. The low‑level expression of coronin 1A mRNA and MACC1 mRNA was due to overexpression of hsa‑miR‑517a‑3p and hsa‑miR‑18a‑5p, and hsa‑miR‑18b‑5p, respectively. Numerous gene ontology terms were associated with oncogenesis. The most enriched pathways targeted by the dysregulated miRNAs and mRNAs were associated with cancer and oncogenesis pathways. The present data suggested that differential miRNA and mRNA expression is present in HCC. Thus, interactions between certain miRNAs and mRNAs may be involved in the pathogenesis of HCC.
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Affiliation(s)
- Xiong-Wei Cui
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Zhi-Ling Qian
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Cong Li
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Shi-Chang Cui
- Interventional Center for Oncology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P.R. China
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Lin CH, Lin YW, Chen YC, Liao CC, Jou YS, Hsu MT, Chen CF. FNDC3B promotes cell migration and tumor metastasis in hepatocellular carcinoma. Oncotarget 2018; 7:49498-49508. [PMID: 27385217 PMCID: PMC5226524 DOI: 10.18632/oncotarget.10374] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/13/2016] [Indexed: 01/07/2023] Open
Abstract
Recurrence and metastasis are common in hepatocellular carcinoma (HCC) and correlate with poor prognosis. We investigated the role of fibronectin type III domain containing 3B (FNDC3B) in HCC metastasis. Overexpression of FNDC3B in HCC cell lines enhanced cell migration and invasion. On the other hand, knockdown of FNDC3B using short-hairpin RNA reduced tumor nodule formation in both intra- and extra-hepatic metastasis. High levels of FNDC3B were observed in metastatic HCCs and correlated with poor patient survival and shorter recurrence time. Mutagenesis and LC-MS/MS analyses showed that FNDC3B promotes cell migration by cooperating with annexin A2 (ANXA2). Furthermore, FNDC3B and ANXA2 expression correlated negatively with patient survival. Our results indicate that FNDC3B behaves like an oncogene by promoting cell migration. This suggests FNDC3B could serve as a biomarker and therapeutic target for HCC metastasis.
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Affiliation(s)
- Chin-Hui Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yao-Wen Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Ying-Chun Chen
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yuh-Shan Jou
- Institutes of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Ta Hsu
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Chian-Feng Chen
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
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Yang L, Song X, Zhu J, Li M, Ji Y, Wu F, Chen Y, Cui X, Hu J, Wang L, Cao Y, Wei Y, Zhang W, Li F. Tumor suppressor microRNA-34a inhibits cell migration and invasion by targeting MMP-2/MMP-9/FNDC3B in esophageal squamous cell carcinoma. Int J Oncol 2017; 51:378-388. [PMID: 28534990 DOI: 10.3892/ijo.2017.4015] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/12/2017] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are a large family of small, non-coding RNAs that play a pivotal role in tumorigenesis. miR‑34a, which is a member of the miR-34 family, is a downstream target of p53. Increasing evidence shows that miR-34a dysregulation may contribute to tumor development and progression in numerous cancers, including esophageal squamous cell carcinoma (ESCC). However, the mechanism of miR-34a in the regulation of ESCC cells need to be further elucidated because of the complex regulative network of miRNAs. The miR-34a expression in ESCC samples has been confirmed using quantitative reverse transcription polymerase chain reaction. The effects of miR-34a on cell migration and invasion were examined in ESCC cell lines using wound healing and Transwell assays, respectively. The effects of miR-34a on matrix metalloproteinase (MMP)-2 and -9 and fibronectin type III domain containing 3B (FNDC3B) expression levels were detected by luciferase reporter assays and western blot analysis. Quantitative polymerase chain reaction revealed that the miR‑34a expression is significantly downregulated in the ESCC tissues compared to that in the adjacent normal tissues. miR-34a overexpression was significantly suppressed migration and invasion in the ESCC cells and simultaneously inhibited the MMP-2, MMP-9 and FNDC3B expression levels by targeting the coding and 3'-untranslated regions, respectively. The findings indicated that microRNA‑34a suppresses cell migration and invasion by targeting MMP-2, MMP-9, and FNDC3B in ESCC.
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Affiliation(s)
- Lan Yang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Xiaoyue Song
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Jianbo Zhu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Mei Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Yu Ji
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Fei Wu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Yunzhao Chen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Xiaobin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Jianming Hu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Lianghai Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Yuwen Cao
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Yutao Wei
- The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Wenjie Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
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Feng S, Han M, Zhou L, Wang Q, Li Z, Li Y, Lu H, Liu T, Ma Y, Liu S, Cheng J. NS5ABP37 inhibits liver cancer by impeding lipogenesis and cholesterogenesis. Cancer Sci 2017; 108:12-22. [PMID: 27862769 PMCID: PMC5276832 DOI: 10.1111/cas.13117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/27/2016] [Accepted: 10/30/2016] [Indexed: 12/12/2022] Open
Abstract
The molecular mechanism underlying non‐alcoholic fatty liver disease progression to hepatocellular carcinoma (HCC) remains unknown. In this study, immunohistochemistry staining results showed that NS5ABP37 protein, which is in a state of lower expression in tumor tissues, decreased with increasing degree of HCC malignancy. Two cell models, HepG2 and L02, were used to analyze the mechanism between NS5ABP37 and HCC. In agreement, NS5ABP37 protein overexpression significantly suppressed cell proliferation, caused G1/S cell cycle arrest, and induced apoptosis by increasing caspase‐3/7 activity and cleaved caspase‐3 levels. In addition, NS5ABP37 overexpression resulted in decreased intracellular triglyceride and total cholesterol contents, with level reduction in sterol regulatory element‐binding proteins (SREBPs) and downstream effectors. Furthermore, NS5ABP37 overexpression decreased SREBP1c and SREBP2 levels by reducing their respective promoters. Finally, reactive oxygen species levels and endoplasmic reticulum stress were both induced by NS5ABP37 overexpression. These findings together indicate that NS5ABP37 inhibits cancer cell proliferation and promotes apoptosis, by altering SREBP‐dependent lipogenesis and cholesterogenesis in HepG2 and L02 cells and inducing oxidative stress and endoplasmic reticulum stress.
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Affiliation(s)
- Shenghu Feng
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China
| | - Ming Han
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China
| | - Li Zhou
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China
| | - Qi Wang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhongshu Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yaru Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hongping Lu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ting Liu
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China
| | - Yanhua Ma
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China
| | - Shunai Liu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jun Cheng
- Beijing Ditan Hospital, Peking University Teaching Hospital, Beijing, China.,Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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Cao Y, Mitchell EB, Gorski JL, Hollinger C, Hoppman NL. Two cases with de novo 3q26.31 microdeletion suggest a role forFNDC3Bin human craniofacial development. Am J Med Genet A 2016; 170:3276-3281. [DOI: 10.1002/ajmg.a.37892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/31/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Yang Cao
- Cytogenetics Laboratory; Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Elyse B. Mitchell
- Cytogenetics Laboratory; Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - Jerome L. Gorski
- Departments of Child Health and Pathology and Anatomical Sciences; University of Missouri School of Medicine; Columbia Missouri
| | - Cassandra Hollinger
- Department of Child Health; University of Missouri School of Medicine; Columbia Missouri
| | - Nicole L. Hoppman
- Cytogenetics Laboratory; Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
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Identification of More Feasible MicroRNA-mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction. Int J Mol Sci 2016; 17:ijms17050696. [PMID: 27171078 PMCID: PMC4881522 DOI: 10.3390/ijms17050696] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/13/2016] [Accepted: 04/27/2016] [Indexed: 12/28/2022] Open
Abstract
MicroRNA(miRNA)–mRNA interactions are important for understanding many biological processes, including development, differentiation and disease progression, but their identification is highly context-dependent. When computationally derived from sequence information alone, the identification should be verified by integrated analyses of mRNA and miRNA expression. The drawback of this strategy is the vast number of identified interactions, which prevents an experimental or detailed investigation of each pair. In this paper, we overcome this difficulty by the recently proposed principal component analysis (PCA)-based unsupervised feature extraction (FE), which reduces the number of identified miRNA–mRNA interactions that properly discriminate between patients and healthy controls without losing biological feasibility. The approach is applied to six cancers: hepatocellular carcinoma, non-small cell lung cancer, esophageal squamous cell carcinoma, prostate cancer, colorectal/colon cancer and breast cancer. In PCA-based unsupervised FE, the significance does not depend on the number of samples (as in the standard case) but on the number of features, which approximates the number of miRNAs/mRNAs. To our knowledge, we have newly identified miRNA–mRNA interactions in multiple cancers based on a single common (universal) criterion. Moreover, the number of identified interactions was sufficiently small to be sequentially curated by literature searches.
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Sand M, Bechara FG, Sand D, Gambichler T, Hahn SA, Bromba M, Stockfleth E, Hessam S. Circular RNA expression in basal cell carcinoma. Epigenomics 2016; 8:619-32. [DOI: 10.2217/epi-2015-0019] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: Circular RNAs (circRNAs), are nonprotein coding RNAs consisting of a circular loop with multiple miRNA, binding sites called miRNA response elements (MREs), functioning as miRNA sponges. This study was performed to identify differentially expressed circRNAs and their MREs in basal cell carcinoma (BCC). Materials & methods: Microarray circRNA expression profiles were acquired from BCC and control followed by qRT-PCR validation. Bioinformatical target prediction revealed multiple MREs. Sequence analysis was performed concerning MRE interaction potential with the BCC miRNome. Results: We identified 23 upregulated and 48 downregulated circRNAs with 354 miRNA response elements capable of sequestering miRNA target sequences of the BCC miRNome. Conclusion: The present study describes a variety of circRNAs that are potentially involved in the molecular pathogenesis of BCC.
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Affiliation(s)
- Michael Sand
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
- Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany
| | - Falk G Bechara
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Daniel Sand
- University of Michigan Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Thilo Gambichler
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Stephan A Hahn
- Department of Internal Medicine, Knappschaftskrankenhaus University of Bochum, Zentrum für Klinische Forschung, Labor für Molekulare Gastroenterologische Onkologie, 44780 Bochum, Germany
| | - Michael Bromba
- Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany
| | - Eggert Stockfleth
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Schapoor Hessam
- Dermatologic Surgery Unit, Department of Dermatology, Venereology & Allergology, Ruhr-University Bochum, 44791 Bochum, Germany
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