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Zhang J, Lv G. Knockdown of LINC01138 protects human chondrocytes against IL-1β-induced damage by regulating the hsa-miR-1207-5p/KIAA0101 axis. Immun Inflamm Dis 2022; 11:e744. [PMID: 36705420 PMCID: PMC9753829 DOI: 10.1002/iid3.744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/19/2022] [Accepted: 11/06/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Long intergenic non-protein coding RNA 1138 (LINC01138) plays a vital role in human cancers. In this study, we aimed to investigate the effect of LINC01138 on the progression of osteoarthritis (OA) and explore its potential mechanism of action. METHODS The expression of LINC01138, hsa-miR-1207-5p, and KIAA0101 in OA tissues and normal tissues was analyzed using GSEA datasets and confirmed in human specimens. Human chondrocytes were treated with interleukin (IL)-1β to establish an OA cell model. Quantitative real time PCR(qRT-PCR), enzyme-linked immunosorbent assay, and western blotting analyses were performed to evaluate the role of LINC01138, hsa-miR-1207-5p, and KIAA0101 during extracellular matrix (ECM) protein degeneration and cellular inflammatory response. The target relationship was predicted using DIANA-TarBase and TargetScan. The binding effects were verified by dual-luciferase reporter assay. RESULTS LINC01138 expression was higher in OA tissues than in normal controls. LINC01138 levels increased in chondrocytes treated with IL-1β. Silencing of LINC01138 attenuated the IL-1β-induced decrease in Col2α1, aggrecan, and sulphated glycosaminoglycan (sGAG), and inhibited the IL-1β-induced increase in matrix metalloproteinase (MMP)-13, IL-6, and tumor necrosis factor (TNF)-α. miR-1207-5p is weakly expressed in OA tissues and cell models. The inhibition of hsa-miR-1207-5p, a target of LINC01138, attenuated the effects of LINC01138 silencing on chondrocyte ECM degeneration and inflammatory responses. Silencing KIAA0101, a target of hsa-miR-1207-5p, alleviated the effect of hsa-miR-1207-5p on chondrocyte ECM degeneration and inflammatory responses. Furthermore, silencing of KIAA0101 inhibited the JAK/STAT and Wnt signaling pathways. CONCLUSION Silencing LINC01138 protected chondrocytes from IL-1β-induced damage, possibly by regulating the hsa-miR-1207-5p/KIAA0101 axis.
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Affiliation(s)
- Jiangtao Zhang
- Three Departments of Knee Injury, Luoyang Orthopedic Hospital of Henan ProvinceOrthopedic Hospital of Henan ProvinceLuoyangHenanP. R. China
| | - Genbing Lv
- Department of Orthopedics, Sun Si Miao Hospital of Beijing University of Chinese MedicineTongchuan Traditional Chinese Medicine HospitalTongchuanShanxiP. R. China
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Gupta P, Chattopadhyay T, Mallick B. miRNome-transcriptome analysis unveils the key regulatory pathways involved in the tumorigenesis of tongue squamous cell carcinoma. Brief Funct Genomics 2022; 21:466-477. [PMID: 36255066 DOI: 10.1093/bfgp/elac031] [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: 05/23/2022] [Revised: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022] Open
Abstract
Tongue squamous cell carcinoma (TSCC) is considered the most common malignant tumor among the oral squamous cell carcinomas with a poor prognosis. Understanding the underlying molecular mechanisms that underpin TSCC and its treatments is the focus of the research. Deregulated expression of microRNAs (miRNAs) has recently been implicated in various biological processes linked to cancer. Therefore, in this study, we attempted to investigate miRNAs and their targets expressed in TSCC, which could be involved in its oncogenesis. We performed next-generation sequencing of small RNAs and transcriptomes in H357 TSCC cell line and human oral keratinocytes as a control to find miRNAs and mRNAs that are differentially expressed (DE), which were then supplemented with additional expression datasets from databases, yielding 269 DE miRNAs and 2094 DE genes. The target prediction followed by pathway and disease function analysis revealed that the DE targets were significantly associated with the key processes and pathways, such as apoptosis, epithelial-mesenchymal transition, endocytosis and vascular endothelial growth factor signaling pathways. Furthermore, the top 12 DE targets were chosen based on their involvement in more than one cancer-related pathway, of which 6 genes are targeted by miR-128-3p. Real-time quantitative PCR validation of this miRNA and its targets in H357 and SCC9 TSCC cells confirmed their possible targeting from their reciprocal expression, with MAP2K7 being a critical target that might be involved in oncogenesis and progression of TSCC by acting as a tumor suppressor. Further research is underway to understand how miR-128-3p regulates oncogenesis in TSCC via MAP2K7 and associated pathways.
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Affiliation(s)
- Pooja Gupta
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
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Chattopadhyay T, Gupta P, Nayak R, Mallick B. Genome-wide profiling of dysregulated piRNAs and their target genes implicated in oncogenicity of Tongue Squamous Cell Carcinoma. Gene 2022; 849:146919. [PMID: 36179965 DOI: 10.1016/j.gene.2022.146919] [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: 06/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are single-stranded, 23-36 nucleotide long RNAs that regulate gene expression in the germline but are also detected in some cancers. However, there are no reports yet on piRNA expression in tongue squamous cell carcinoma (TSCC), the most common oral cancer (80-90% percent of all oral cancers). We performed small RNA and whole transcriptome sequencing in H357 tongue cancer and HOK cells (GEO database accession numbers: GSE196674 and GSE196688). We also examined nine published sets of gene expression array data of TSCC tissues from the GEO database to decode piRNAs and their putative targets that may be involved in tumorigenesis. We identified a pool of 16058 and 25677 piRNAs in H357 and HOK, respectively, among which 406 are differentially expressed. We also found that 2094 protein-coding genes are differentially expressed in either TSCC tissues or cell lines. We performed target predictions for these piRNA, pathway and disease function (DF) analyses, as well as qRT-PCR validation of piRNA-target pairs. These experiments revealed one up-regulated (FDFT1) and four down-regulated (OGA, BDH1, TAT, HYAL4) target genes that are enriched in 11 canonical pathways (CPs), with postulated roles in the initiation and progression of TSCC. Downregulation of piR-33422 is predicted to upregulate the FDFT1 gene, which encodes a mevalonate/cholesterol-pathway related farnesyl-diphosphate farnesyltransferase. The FDFT1 appears to be involved in the largest number of oncogenesis-related processes and is interacting with statins, which is a classical cancer drug. This study provides the first evidence of the piRNome of TSCC, which could be investigated further to decode piRNA-mediated gene regulations in malignancy and potential drug targets, such as FDFT1.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Pooja Gupta
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rojalin Nayak
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Hatmal MM, Al-Hatamleh MAI, Olaimat AN, Alshaer W, Hasan H, Albakri KA, Alkhafaji E, Issa NN, Al-Holy MA, Abderrahman SM, Abdallah AM, Mohamud R. Immunomodulatory Properties of Human Breast Milk: MicroRNA Contents and Potential Epigenetic Effects. Biomedicines 2022; 10:biomedicines10061219. [PMID: 35740242 PMCID: PMC9219990 DOI: 10.3390/biomedicines10061219] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Infants who are exclusively breastfed in the first six months of age receive adequate nutrients, achieving optimal immune protection and growth. In addition to the known nutritional components of human breast milk (HBM), i.e., water, carbohydrates, fats and proteins, it is also a rich source of microRNAs, which impact epigenetic mechanisms. This comprehensive work presents an up-to-date overview of the immunomodulatory constituents of HBM, highlighting its content of circulating microRNAs. The epigenetic effects of HBM are discussed, especially those regulated by miRNAs. HBM contains more than 1400 microRNAs. The majority of these microRNAs originate from the lactating gland and are based on the remodeling of cells in the gland during breastfeeding. These miRNAs can affect epigenetic patterns by several mechanisms, including DNA methylation, histone modifications and RNA regulation, which could ultimately result in alterations in gene expressions. Therefore, the unique microRNA profile of HBM, including exosomal microRNAs, is implicated in the regulation of the genes responsible for a variety of immunological and physiological functions, such as FTO, INS, IGF1, NRF2, GLUT1 and FOXP3 genes. Hence, studying the HBM miRNA composition is important for improving the nutritional approaches for pregnancy and infant's early life and preventing diseases that could occur in the future. Interestingly, the composition of miRNAs in HBM is affected by multiple factors, including diet, environmental and genetic factors.
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Affiliation(s)
- Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
- Correspondence: (M.M.H.); (R.M.)
| | - Mohammad A. I. Al-Hatamleh
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Walhan Alshaer
- Cell Therapy Center (CTC), The University of Jordan, Amman 11942, Jordan;
| | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Khaled A. Albakri
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Enas Alkhafaji
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan;
| | - Nada N. Issa
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Murad A. Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (A.N.O.); (M.A.A.-H.)
| | - Salim M. Abderrahman
- Department of Biology and Biotechnology, Faculty of Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Atiyeh M. Abdallah
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar;
| | - Rohimah Mohamud
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
- Correspondence: (M.M.H.); (R.M.)
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Liu LJ, Liao JM, Zhu F. Proliferating cell nuclear antigen clamp associated factor, a potential proto-oncogene with increased expression in malignant gastrointestinal tumors. World J Gastrointest Oncol 2021; 13:1425-1439. [PMID: 34721775 PMCID: PMC8529917 DOI: 10.4251/wjgo.v13.i10.1425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers, including malignancies in the gastrointestinal tract and accessory organs of digestion, represent the leading cause of death worldwide due to the poor prognosis of most GI cancers. An investigation into the potential molecular targets of prediction, diagnosis, prognosis, and therapy in GI cancers is urgently required. Proliferating cell nuclear antigen (PCNA) clamp associated factor (PCLAF), which plays an essential role in cell proliferation, apoptosis, and cell cycle regulation by binding to PCNA, is a potential molecular target of GI cancers as it contributes to a series of malignant properties, including tumorigenesis, epithelial-mesenchymal transition, migration, and invasion. Furthermore, PCLAF is an underlying plasma prediction target in colorectal cancer and liver cancer. In addition to GI cancers, PCLAF is also involved in other types of cancers and autoimmune diseases. Several pivotal pathways, including the Rb/E2F pathway, NF-κB pathway, and p53-p21 cascade, are implicated in PCLAF-mediated diseases. PCLAF also contributes to some diseases through dysregulation of the p53 pathway, WNT signal pathway, MEK/ERK pathway, and PI3K/AKT/mTOR signal cascade. This review mainly describes in detail the role of PCLAF in physiological status and GI cancers. The signaling pathways involved in PCLAF are also summarized. Suppression of the interaction of PCLAF/PCNA or the expression of PCLAF might be potential biological therapeutic strategies for GI cancers.
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Affiliation(s)
- Li-Juan Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Jian-Ming Liao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
- Department of Neurosurgery, Renmin Hospital, Wuhan University, Wuhan 430060, Hubei Province, China
| | - Fan Zhu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy & Immunology, Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan 430071, Hubei Province, China
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Zhang Y, Yao H, Li Y, Yang L, Zhang L, Chen J, Wang Y, Li X. Circular RNA TADA2A promotes proliferation and migration via modulating of miR‑638/KIAA0101 signal in non‑small cell lung cancer. Oncol Rep 2021; 46:201. [PMID: 34296306 PMCID: PMC8317161 DOI: 10.3892/or.2021.8152] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/12/2021] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence indicates that circular (circ)RNAs exhibit complex functions in diverse malignant tumors, including non-small cell lung cancer (NSCLC). The role of the circRNA transcription adaptor 2A (circTADA2A) in NSCLC remains unclear. The expression, function and mechanism of circTADA2A in NSCLC development were investigated in the present study. The results revealed that circTADA2A was upregulated in NSCLC, and that knockdown of circTADA2A inhibited cell proliferation and migration in the NSCLC cell lines A549 and H1299. Functional assays demonstrated that circTADA2A promoted proliferation and migration via interacting with microRNA (miR)-638. Bioinformatics and reverse transcription-quantitative PCR assay confirmed that miR-638 was expressed at low levels in NSCLC. In addition, it was found that miR-638 served a tumor-suppressive role and suppressed proliferation and migration via PCNA clamp associated factor (KIAA0101) inhibition in A549 and H1299 cells. Lastly, it was verified that circTADA2A promoted cell proliferation and migration, at least partially, via miR-638/KIAA0101 signaling in A549 and H1299 cells. In summary, the present study showed that circTADA2A promoted NSCLC cell proliferation and migration via modulating miR-638/KIAA0101 signaling.
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Affiliation(s)
- Ye Zhang
- Department of Radiation Oncology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Hongmin Yao
- Department of Radiation Oncology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Ying Li
- Department of Radiation Oncology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Lu Yang
- First Department of Gastroenterology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Liang Zhang
- Department of Breast Internal Medicine, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Jinxin Chen
- Department of Gynecological Oncology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
| | - Yong Wang
- Central Laboratory, Central Hospital Affiliated to Shenyang Medical College, Dadong, Shenyang, Liaoning 110024, P.R. China
| | - Xia Li
- Department of Radiation Oncology, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Dadong, Shenyang, Liaoning 110042, P.R. China
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Lee HY, Son SW, Moeng S, Choi SY, Park JK. The Role of Noncoding RNAs in the Regulation of Anoikis and Anchorage-Independent Growth in Cancer. Int J Mol Sci 2021; 22:ijms22020627. [PMID: 33435156 PMCID: PMC7827914 DOI: 10.3390/ijms22020627] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/02/2021] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer is a global health concern, and the prognosis of patients with cancer is associated with metastasis. Multistep processes are involved in cancer metastasis. Accumulating evidence has shown that cancer cells acquire the capacity of anoikis resistance and anchorage-independent cell growth, which are critical prerequisite features of metastatic cancer cells. Multiple cellular factors and events, such as apoptosis, survival factors, cell cycle, EMT, stemness, autophagy, and integrins influence the anoikis resistance and anchorage-independent cell growth in cancer. Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are dysregulated in cancer. They regulate cellular signaling pathways and events, eventually contributing to cancer aggressiveness. This review presents the role of miRNAs and lncRNAs in modulating anoikis resistance and anchorage-independent cell growth. We also discuss the feasibility of ncRNA-based therapy and the natural features of ncRNAs that need to be contemplated for more beneficial therapeutic strategies against cancer.
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Huang R, Zeng Z, Yan P, Yin H, Zhu X, Hu P, Zhuang J, Li J, Li S, Song D, Meng T, Huang Z. Targeting Lymphotoxin Beta and Paired Box 5: a potential therapeutic strategy for soft tissue sarcoma metastasis. Cancer Cell Int 2021; 21:3. [PMID: 33397394 PMCID: PMC7784354 DOI: 10.1186/s12935-020-01632-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 10/29/2020] [Indexed: 11/10/2022] Open
Abstract
Background Soft tissue sarcomas (STS) has a high rate of early metastasis. In this study, we aimed to uncover the potential metastasis mechanisms and related signaling pathways in STS with differentially expressed genes and tumor-infiltrating cells. Methods RNA-sequencing (RNA-seq) of 261 STS samples downloaded from the Cancer Genome Atlas (TCGA) database were used to identify metastasis-related differentially expressed immune genes and transcription factors (TFs), whose relationship was constructed by Pearson correlation analysis. Metastasis-related prediction model was established based on the most significant immune genes. CIBERSORT algorithm was performed to identify significant immune cells co-expressed with key immune genes. The GSVA and GSEA were performed to identify prognosis-related KEGG pathways. Ultimately, we used the Pearson correlation analysis to explore the relationship among immune genes, immune cells, and KEGG pathways. Additionally, key genes and regulatory mechanisms were validated by single-cell RNA sequencing and ChIP sequencing data. Results A total of 204 immune genes and 12 TFs, were identified. The prediction model achieved a satisfactory effectiveness in distant metastasis with the Area Under Curve (AUC) of 0.808. LTB was significantly correlated with PAX5 (P < 0.001, R = 0.829) and hematopoietic cell lineage pathway (P < 0.001, R = 0.375). The transcriptional regulatory pattern between PAX5 and LTB was validated by ChIP sequencing data. Conclusions We hypothesized that down-regulated LTB (immune gene) modulated by PAX5 (TF) in STSs may have the capability of inducing cancer cell metastasis in patients with STS.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China.,Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
| | - Zhiwei Zeng
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Huabin Yin
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Juanwei Zhuang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Jiaju Li
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China
| | - Siqi Li
- Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China
| | - Dianwen Song
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China.
| | - Tong Meng
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China. .,Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China.
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450052, China.
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孙 瑞, 于 德. [Inhibitory effect of miR-429 on expressions of ZO-1, Occludin, and Claudin-5 proteins to improve the permeability of blood spinal cord barrier in vitro]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2020; 34:1163-1169. [PMID: 32929911 PMCID: PMC8171720 DOI: 10.7507/1002-1892.202001097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/18/2020] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To explore the feasibility and mechanism of inhibiting miR-429 to improve the permeability of the blood spinal cord barrier (BSCB) in vitro, and provide a new gene therapy target for enhancing the spinal cord microenvironment. METHODS First, the immortalized human brain microvascular endothelial cell line (hCMEC/D3) was transfected with the anti-miR-429 antagonist (antagomiR-429) and its negative control (antagomiR-429-NC), respectively. The miR-429 expression of hCMEC/D3 cells was observed by fluorescence microscopy and real-time fluorescence quantitative PCR to verify the transfection efficiency of antagomiR-429. Then the effect of miR-429 on BSCB permeability was observed in vitro. The experiment was divided into 4 groups. The blank control group (group A) was constructed of normal hCMEC/D3 cells and Ha-sc cells to prepare the BSCB model, the hypoxia-induced group (group B), the hypoxia-induced+antagomiR-429-NC group (group C), and the hypoxia-induced+antagomiR-429 group (group D) were constructed of normal, antagomiR-429-NC transfected, and antagomiR-429 transfected hCMEC/D3 cells and Ha-sc cells to prepare the BSCB models and hypoxia treatment for 12 hours. The permeability of BSCB in vitro was measured by horseradish peroxidase (HRP) permeability. Real-time fluorescence quantitative PCR, Western blot, and immunofluorescence staining were used to observe the expressions of ZO-1, Occludin, and Claudin-5. RESULTS The antagomiR-429 and antagomiR-429-NC were successfully transfected into hCMEC/D3 cells under a fluorescence microscope, and the transfection efficiency was about 90%. Real-time fluorescence quantitative PCR results showed that the relative expression of miR-429 in antagomiR-429 group was 0.109±0.013, which was significantly lower than that of antagomiR-429-NC group (0.956±0.004, P<0.05). HRP permeability measurement, real-time fluorescence quantitative PCR, and Western blot results showed that the HRP permeability of groups B and C were significantly higher than those of groups A and D ( P<0.05), and the relative expressions of ZO-1, Occludin, and Claudin-5 proteins and mRNAs were significantly lower in groups B and C than in groups A and D ( P<0.05) and in group D than in group A ( P<0.05); there was no significant difference between groups B and C ( P>0.05). Immunofluorescence staining showed that the immunofluorescence of ZO-1, Occudin, and Claudin-5 at the cell membrane boundary in group D were stronger than those in groups B and C, but not as strong as that in group A. CONCLUSION Inhibition of miR-429 expression can promote the expressions of ZO-1, Occludin, and Claudin-5 proteins in microvascular endothelial cells, thereby improving the increased permeability of BSCB due to hypoxia.
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Affiliation(s)
- 瑞 孙
- 锦州医科大学附属第一医院骨创伤科(辽宁锦州 121000)Department of Orthopedics, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou Liaoning, 121000, P.R.China
- 辽宁省健康产业集团阜新矿业集团总医院骨科(辽宁阜新 123000)Department of Orthopedics, General Hospital of Fuxin Mining Group, Liaoning Health Industry Group, Fuxin Liaoning, 123000, P.R.China
| | - 德水 于
- 锦州医科大学附属第一医院骨创伤科(辽宁锦州 121000)Department of Orthopedics, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou Liaoning, 121000, P.R.China
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MiR-429 regulates blood−spinal cord barrier permeability by targeting Krüppel-like factor 6. Biochem Biophys Res Commun 2020; 525:740-746. [DOI: 10.1016/j.bbrc.2020.02.138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/22/2020] [Indexed: 11/17/2022]
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Jain N, Das B, Mallick B. Restoration of microRNA-197 expression suppresses oncogenicity in fibrosarcoma through negative regulation of RAN. IUBMB Life 2020; 72:1034-1044. [PMID: 32027089 DOI: 10.1002/iub.2240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/23/2020] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) act as crucial regulators of biological pathways/processes by reinforcing transcriptional programs and moderating transcripts. Emerging evidences have shown the involvement of dysregulated miRNAs in pathophysiology of human diseases including several cancer types. Recently, miR-197-3p has been reported to play different roles in different cancers; however, its role in fibrosarcoma, a highly aggressive and malignant soft tissue sarcoma originated from the mesenchymal tissues, has not yet been studied. Therefore, this study aims to investigate the possible regulatory roles of miR-197-3p in the oncogenicity of fibrosarcoma. For this, we initially performed qRT-PCR of miR-197-3p, which we found to be downregulated in HT1080 human fibrosarcoma cells compared with IMR90-tert normal fibroblast cells. Subsequently, we performed gain-of-function study by employing several methods such as MTT assay, clonogenic assay, wound healing, flow cytometry cell cycle analysis, and acridine orange staining after transfecting HT1080 cells with miR-197-3p mimic. From these assays, we observed that miR-197-3p significantly inhibits viability, colony forming, and migration ability as well as triggers G2/M phase cell cycle arrest and autophagy in fibrosarcoma cells. To understand the mechanism through which miRNA performs these functions, we predicted its targets using TargetScan and performed pathway enrichment analysis after screening them by their expression in fibrosarcoma. Among the enriched targets, we found RAN (ras-related nuclear protein) to be a crucial target through which miR-197-3p represses tumorigenesis by binding to its 3´ UTR, validated by luciferase reporter assay. The tumor suppressive role of the miRNA was further confirmed by transfecting its mimic in RAN-overexpressed cells which showed significant attenuation in tumorigenic effect of RAN in fibrosarcoma as seen in different assays. Taken together, our study unveiled that miR-197-3p acts as an oncosuppressor in fibrosarcoma through G2/M phase arrest and induction of autophagy, and raises the possibility to act as a novel therapeutic intervention for the malignancy.
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Affiliation(s)
- Neha Jain
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Basudeb Das
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
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Das B, Jain N, Mallick B. piR‐39980 promotes cell proliferation, migration and invasion, and inhibits apoptosis via repression of SERPINB1 in human osteosarcoma. Biol Cell 2020; 112:73-91. [DOI: 10.1111/boc.201900063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Basudeb Das
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Neha Jain
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Bibekanand Mallick
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
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Wang Z, Zhu Z, Lin Z, Luo Y, Liang Z, Zhang C, Chen J, Peng P. miR-429 suppresses cell proliferation, migration and invasion in nasopharyngeal carcinoma by downregulation of TLN1. Cancer Cell Int 2019; 19:115. [PMID: 31068760 PMCID: PMC6492405 DOI: 10.1186/s12935-019-0831-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/20/2019] [Indexed: 02/06/2023] Open
Abstract
Background miR-429 and TLN1 have been shown to affect the biological behaviours of many carcinomas. However, their effects in nasopharyngeal carcinoma (NPC) are not yet clear. Here, we investigated their regulatory relationships and effects on NPC cells. Methods TargetScan was used to predict the regulatory relationships of miR-429 and TLN1 in NPC cells. Then, Western blotting and quantitative real-time PCR (qPCR) were performed to examine TLN1 levels, and qPCR was used to determine miR-429 levels in NPC cell lines with different metastatic characteristics (5-8F, CNE-2, CNE-1, 6-10B and NP69), to investigate whether TLN1 and miR-429 are correlated with the metastatic characteristics of these cells. Next, we upregulated or downregulated miR-429 in 5-8F and 6-10B cells, which have different tumourigenicity and transferability, and examined TLN1 expression by western blotting and qPCR after transfection. QPCR was also performed to confirm successful transfection of miR-429 mimic into 5-8F and 6-10B cells. Dual luciferase reporter gene assay was performed to investigate whether miR-429 regulates TLN1 by binding to its 3′UTR. After transfection, Cell Counting Kit-8 (CCK8) and IncuCyte were used to examine the proliferation of these cells, and wound-healing assay, Transwell migration assay, and invasion assays were performed to investigate the changes in migration and invasion after transfection. Results Western blotting and qPCR analyses showed that the protein level of TLN1 was negatively correlated with miR-429 in NPC cell lines (P < 0.05), while the mRNA level showed no relation with miR429 expression (P > 0.05). In addition, cells with high transferability showed high TLN1 expression at the protein level, while miR429 expression showed the opposite trend (P < 0.05), but there were no differences at the mRNA level between the different cell lines. Overexpression of miR429 in 5-8F and 6-10B cells was accompanied by downregulation of TLN1 at the protein level (P < 0.05), while there were no significant differences at the mRNA level (P > 0.05). In addition, transferability, proliferation, and invasion were downregulated by miR429 overexpression (P < 0.05). However, dual-luciferase reporter gene assay indicated that TLN1 was not a direct target of miR-429. Conclusion This study showed that miR-429 functions as a tumour suppressor in NPC by downregulation of TLN1, although the relationship is not direct.
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Affiliation(s)
- Zhihui Wang
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Zhiquan Zhu
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Zhong Lin
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Youli Luo
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Zibin Liang
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Caibin Zhang
- 2Department of Neurology, The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Jianxu Chen
- 3Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
| | - Peijian Peng
- 1Department of Thoracic Oncology, The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, Guangdong China
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Jain N, Roy J, Das B, Mallick B. miR-197-5p inhibits sarcomagenesis and induces cellular senescence via repression of KIAA0101. Mol Carcinog 2019; 58:1376-1388. [PMID: 31001891 DOI: 10.1002/mc.23021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022]
Abstract
The abnormal expressions of microRNAs (miRNAs) are known to be associated with various pathophysiological processes that lead to the development of a plethora of diseases including cancer. Among several miRNAs studied so far, miR-197 has been reported to play a vital role either as an oncogene or tumor suppressor in different cancers. However, its role in carcinogenesis of fibrosarcoma has not yet been elucidated. Therefore, the current study investigated the role of miR-197-5p, which is significantly downregulated in HT1080 fibrosarcoma cells compared to IMR90-tert fibroblast cells. The transient overexpression of miR-197-5p causes a significant decrease in viability and proliferation of fibrosarcoma cells in both concentration- and time-dependent manners. Interestingly, we did not observe any significant changes in cell cycle pattern or apoptotic cell populations, but rather noticed cellular senescence of fibrosarcoma cells upon overexpression of miR-197-5p. Further, this miRNA suppresses the metastatic properties, such as migration, invasion, and anchorage-independent growth of fibrosarcoma possibly through targeting KIAA0101, which is a proliferating cell nuclear antigen-associated factor and overexpressed in the malignancy. In nutshell, our result revealed that miR-197-5p acts as an oncosuppressor miRNA in fibrosarcoma through target regulation of KIAA0101, which can be exploited for developing RNA-based therapeutic strategies for the cure of this malignancy.
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Affiliation(s)
- Neha Jain
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Jyoti Roy
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Basudeb Das
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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Das B, Roy J, Jain N, Mallick B. Tumor suppressive activity of PIWI-interacting RNA in human fibrosarcoma mediated through repression of RRM2. Mol Carcinog 2018; 58:344-357. [DOI: 10.1002/mc.22932] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Basudeb Das
- RNAi and Functional Genomics Lab; Department of Life Science; National Institute of Technology; Rourkela Odisha India
| | - Jyoti Roy
- RNAi and Functional Genomics Lab; Department of Life Science; National Institute of Technology; Rourkela Odisha India
| | - Neha Jain
- RNAi and Functional Genomics Lab; Department of Life Science; National Institute of Technology; Rourkela Odisha India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab; Department of Life Science; National Institute of Technology; Rourkela Odisha India
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Jin C, Liu Z, Li Y, Bu H, Wang Y, Xu Y, Qiu C, Yan S, Yuan C, Li R, Diao N, Zhang Z, Wang X, Liu L, Kong B. PCNA-associated factor P15PAF, targeted by FOXM1, predicts poor prognosis in high-grade serous ovarian cancer patients. Int J Cancer 2018; 143:2973-2984. [PMID: 30129654 DOI: 10.1002/ijc.31800] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/24/2018] [Accepted: 08/01/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Chengjuan Jin
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
- Department of Obstetrics and Gynecology; Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University; 650 XinSongjiang Road, Shanghai People's Republic of China
| | - Zhaojian Liu
- Department of Cell Biology; Shandong University School of Medicine; 44 Wenhua Xi Road, Jinan China
| | - Yingwei Li
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Hualei Bu
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Yu Wang
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Ying Xu
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Chunping Qiu
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Shi Yan
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Rongrong Li
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Nannan Diao
- Institute of Diagnostics, School of Medicine; Shandong University; 44 Wenhua Xi Road, Jinan China
| | - Zhiwei Zhang
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Xiangxiang Wang
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Lidong Liu
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
| | - Beihua Kong
- Department of Obstetrics and Gynecology; Qilu Hospital, Shandong University; 107 Wenhua Xi Road, Jinan China
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Deciphering synergistic regulatory networks of microRNAs in hESCs and fibroblasts. Int J Biol Macromol 2018; 113:1279-1286. [DOI: 10.1016/j.ijbiomac.2018.03.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/06/2018] [Accepted: 03/11/2018] [Indexed: 12/14/2022]
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Swain AC, Mallick B. miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers. Mol Oncol 2018; 12:855-868. [PMID: 29603582 PMCID: PMC5983123 DOI: 10.1002/1878-0261.12198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
Competing endogenous RNA (ceRNA) are transcripts that cross‐regulate each other at the post‐transcriptional level by competing for shared microRNA response elements (MREs). These have been implicated in various biological processes impacting cell‐fate decisions and diseases including cancer. There are several studies that predict possible ceRNA pairs by adopting various machine‐learning and mathematical approaches; however, there is no method that enables us to gauge as well as compare the propensity of the ceRNA of a gene and precisely envisages which among a pair exerts a stronger pull on the shared miRNA pool. In this study, we developed a method that uses the ‘tug of war of genes’ concept to predict and quantify ceRNA potential of a gene for the shared miRNA pool in cancers based on a score represented by SoCeR (score of competing endogenous RNA). The method was executed on the RNA‐Seq transcriptional profiles of genes and miRNA available at TCGA along with CLIP‐supported miRNA‐target sites to predict ceRNA in 32 cancer types which were validated with already reported cases. The proposed method can be used to determine the sequestering capability of the gene of interest as well as in ranking the probable ceRNA candidates of a gene. Finally, we developed standalone applications (SoCeR tool) to aid researchers in easier implementation of the method in analysing different data sets or diseases.
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Affiliation(s)
- Arpit Chandan Swain
- Department of Mathematics, National Institute of Technology, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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Roy J, Mallick B. Investigating piwi-interacting RNA regulome in human neuroblastoma. Genes Chromosomes Cancer 2018. [PMID: 29516567 DOI: 10.1002/gcc.22535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Remarkable attempts have been exercised in recent years using high-throughput technologies to identify and decipher the functions of piRNAs in various abnormalities like cancer. However, piRNAs in the oncogenesis of neuroblastoma (NB) has not been reported yet even after their illustrated roles in neurological processes. Therefore, we investigated the piRNA transcriptome in IMR-32 and SH-SY-5Y NB cell lines by employing high-throughput next-generation sequencing after confirming the expression of three associated PIWILs both at mRNAs and protein level by qRT-PCR and immunofluroscence, respectively. We identified a common pool of 525 piRNAs of 26-32 nts long expressed in both the cell lines. The possible functions of these piRNAs were charted by predicting their targeting on retrotransposon-containing 1769 mRNAs differentially expressed in 39 NB cell lines followed by network and pathway analysis. The analysis revealed that majority of the target binding sites in NB fall within retrotransposons residing within the 3'UTR of target mRNA transcripts like miRNA-targets. Further, we validated the expression of key piRNAs and their target genes enriched in cancer-related networks, pathways and biological processes which are hypothesized to play crucial roles in neoplastic events of NB. We believe that the evidence of piRNAs in human NB and their possible contribution to its pathogenesis reported in this work will open up new exciting possibilities for piRNA-mediated therapeutics for this malignancy.
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Affiliation(s)
- Jyoti Roy
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.,Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-Zentrum Für Molekulare Biologie Der Universität Heidelberg (ZMBH) Alliance, Heidelberg, 69120, Germany
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
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Singh G, Roy J, Rout P, Mallick B. Genome-wide profiling of the PIWI-interacting RNA-mRNA regulatory networks in epithelial ovarian cancers. PLoS One 2018; 13:e0190485. [PMID: 29320577 PMCID: PMC5761873 DOI: 10.1371/journal.pone.0190485] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/17/2017] [Indexed: 12/27/2022] Open
Abstract
PIWI-interacting (piRNAs), ~23–36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing. We detected 219, 256 and 234 piRNAs in normal ovary, endometrioid and serous ovarian cancer samples respectively. We observed piRNAs are encoded from various genomic regions, among which introns harbor the majority of them. Surprisingly, piRNAs originated from different genomic contexts showed the varied level of conservations across vertebrates. The functional analysis of predicted targets of differentially expressed piRNAs revealed these could modulate key processes and pathways involved in ovarian oncogenesis. Our study provides the first comprehensive piRNA landscape in these samples and a useful resource for further functional studies to decipher new mechanistic views of piRNA-mediated gene regulatory networks affecting ovarian oncogenesis. The RNA-seq data is submitted to GEO database (GSE83794).
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Affiliation(s)
- Garima Singh
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Jyoti Roy
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Pratiti Rout
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
- * E-mail: ,
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