1
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Mahajan A, Hong J, Krukovets I, Shin J, Tkachenko S, Espinosa-Diez C, Owens GK, Cherepanova OA. Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions. Front Genet 2024; 15:1356558. [PMID: 38660676 PMCID: PMC11039880 DOI: 10.3389/fgene.2024.1356558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Objectives: We previously found that the pluripotency factor OCT4 is reactivated in smooth muscle cells (SMC) in human and mouse atherosclerotic plaques and plays an atheroprotective role. Loss of OCT4 in SMC in vitro was associated with decreases in SMC migration. However, molecular mechanisms responsible for atheroprotective SMC-OCT4-dependent effects remain unknown. Methods: Since studies in embryonic stem cells demonstrated that OCT4 regulates long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), making them candidates for OCT4 effect mediators, we applied an in vitro approach to investigate the interactions between OCT4-regulated lncRNAs, mRNAs, and miRNAs in SMC. We used OCT4 deficient mouse aortic SMC (MASMC) treated with the pro-atherogenic oxidized phospholipid POVPC, which, as we previously demonstrated, suppresses SMC contractile markers and induces SMC migration. Differential expression of lncRNAs, mRNAs, and miRNAs was obtained by lncRNA/mRNA expression array and small-RNA microarray. Long non-coding RNA to mRNA associations were predicted based on their genomic proximity and association with vascular diseases. Given a recently discovered crosstalk between miRNA and lncRNA, we also investigated the association of miRNAs with upregulated/downregulated lncRNA-mRNA pairs. Results: POVPC treatment in SMC resulted in upregulating genes related to the axon guidance and focal adhesion pathways. Knockdown of Oct4 resulted in differential regulation of pathways associated with phagocytosis. Importantly, these results were consistent with our data showing that OCT4 deficiency attenuated POVPC-induced SMC migration and led to increased phagocytosis. Next, we identified several up- or downregulated lncRNA associated with upregulation of the specific mRNA unique for the OCT4 deficient SMC, including upregulation of ENSMUST00000140952-Hoxb5/6 and ENSMUST00000155531-Zfp652 along with downregulation of ENSMUST00000173605-Parp9 and, ENSMUST00000137236-Zmym1. Finally, we found that many of the downregulated miRNAs were associated with cell migration, including miR-196a-1 and miR-10a, targets of upregulated ENSMUST00000140952, and miR-155 and miR-122, targets of upregulated ENSMUST00000155531. Oppositely, the upregulated miRNAs were anti-migratory and pro-phagocytic, such as miR-10a/b and miR-15a/b, targets of downregulated ENSMUST00000173605, and miR-146a/b and miR-15b targets of ENSMUST00000137236. Conclusion: Our integrative analyses of the lncRNA-miRNA-mRNA interactions in SMC indicated novel potential OCT4-dependent mechanisms that may play a role in SMC phenotypic transitions.
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Affiliation(s)
- Aatish Mahajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junyoung Hong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Irene Krukovets
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junchul Shin
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Cristina Espinosa-Diez
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Gary K. Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, United States
| | - Olga A. Cherepanova
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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2
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Hu D, Ma A, Lu H, Gao Z, Yu Y, Fan J, Liu S, Wang Y, Zhang M. LINC00963 Promotes Cisplatin Resistance in Esophageal Squamous Cell Carcinoma by Interacting with miR-10a to Upregulate SKA1 Expression. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04897-4. [PMID: 38507172 DOI: 10.1007/s12010-024-04897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Long non-coding RNA (lncRNA) is associated with a large number of tumor cellular functions together with chemotherapy resistance in a variety of tumors. LINC00963 was identified to regulate the malignant progression of various cancers. However, whether LINC00963 affects drug resistence in esophageal squamous cell carcinoma (ESCC) and the relevant molecular mechanisms have never been reported. This study aims to investigate the effect of LINC00963 on cisplatin resistance in ESCC. After detecting the level of LINC00963 in human esophageal squamous epithelial cells (HET-1 A), ESCC cells (TE-1) and cisplatin resistant cells of ESCC (TE-1/DDP), TE-1/DDP cell line and nude mouse model that interfered with LINC00963 expression were established. Then, the interaction among LINC00963, miR-10a, and SKA1 was clarified by double luciferase and RNA immunoprecipitation (RIP) assays. Meanwhile, the biological behavior changes of TE-1/DDP cells with miR-10a overexpression or SKA1 silencing were observed by CCK-8, flow cytometry, scratch, Transwell, and colony formation tests. Finally, the biological function of the LINC00963/SKA1 axis was elucidated by rescue experiments. LINC00963 was upregulated in TE-1 and TE-1/DDP cell lines. LINC00963 knockdown inhibited SKA1 expression of both cells and impaired tumorigenicity. Moreover, LINC00963 has a target relationship with miR-10a, and SKA1 is a target gene of miR-10a. MiR-10a overexpression or SKA1 silencing decreased the biological activity of TE-1/DDP cells and the expression of SKA1. Furthermore, SKA1 overexpression reverses the promoting effect of LINC00963 on cisplatin resistance of ESCC. LINC00963 regulates TE-1/DDP cells bioactivity and mediates cisplatin resistance through interacting with miR-10a and upregulating SKA1 expression.
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Affiliation(s)
- Dongxin Hu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Anqun Ma
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Hongda Lu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Zhen Gao
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Yue Yu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Jiaming Fan
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Shang Liu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Yancheng Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Mingyan Zhang
- Department of Gastroenterology and Hepatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jing Wu Road, Huaiyin District, Jinan, Shandong, 250021, China.
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3
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Singh R, Ha SE, Park HS, Debnath S, Cho H, Baek G, Yu TY, Ro S. Sustained Effectiveness and Safety of Therapeutic miR-10a/b in Alleviating Diabetes and Gastrointestinal Dysmotility without Inducing Cancer or Inflammation in Murine Liver and Colon. Int J Mol Sci 2024; 25:2266. [PMID: 38396943 PMCID: PMC10888952 DOI: 10.3390/ijms25042266] [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: 01/01/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
microRNAs (miRNAs) are key regulators of both physiological and pathophysiological mechanisms in diabetes and gastrointestinal (GI) dysmotility. Our previous studies have demonstrated the therapeutic potential of miR-10a-5p mimic and miR-10b-5p mimic (miR-10a/b mimics) in rescuing diabetes and GI dysmotility in murine models of diabetes. In this study, we elucidated the safety profile of a long-term treatment with miR-10a/b mimics in diabetic mice. Male C57BL/6 mice were fed a high-fat, high-sucrose diet (HFHSD) to induce diabetes and treated by five subcutaneous injections of miR-10a/b mimics for a 5 month period. We examined the long-term effects of the miRNA mimics on diabetes and GI dysmotility, including an assessment of potential risks for cancer and inflammation in the liver and colon using biomarkers. HFHSD-induced diabetic mice subcutaneously injected with miR-10a/b mimics on a monthly basis for 5 consecutive months exhibited a marked reduction in fasting blood glucose levels with restoration of insulin and significant weight loss, improved glucose and insulin intolerance, and restored GI transit time. In addition, the miR-10a/b mimic-treated diabetic mice showed no indication of risk for cancer development or inflammation induction in the liver, colon, and blood for 5 months post-injections. This longitudinal study demonstrates that miR-10a/b mimics, when subcutaneously administered in diabetic mice, effectively alleviate diabetes and GI dysmotility for 5 months with no discernible risk for cancer or inflammation in the liver and colon. The sustained efficacy and favorable safety profiles position miR-10a/b mimics as promising candidates in miRNA-based therapeutics for diabetes and GI dysmotility.
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Affiliation(s)
- Rajan Singh
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Se Eun Ha
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Han Sung Park
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Sushmita Debnath
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Hayeong Cho
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Gain Baek
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Tae Yang Yu
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Seungil Ro
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
- RosVivo Therapeutics, Applied Research Facility, 1664 N. Virginia St., Reno, NV 89557, USA
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4
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Jin Z, Wang M, Tang C, Zheng X, Zhang W, Sha X, An S. Predicting miRNA-disease association via graph attention learning and multiplex adaptive modality fusion. Comput Biol Med 2024; 169:107904. [PMID: 38181611 DOI: 10.1016/j.compbiomed.2023.107904] [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: 08/01/2023] [Revised: 12/12/2023] [Accepted: 12/23/2023] [Indexed: 01/07/2024]
Abstract
miRNAs are a class of small non-coding RNA molecules that play important roles in gene regulation. They are crucial for maintaining normal cellular functions, and dysregulation or dysfunction of miRNAs which are linked to the onset and advancement of multiple human diseases. Research on miRNAs has unveiled novel avenues in the realm of the diagnosis, treatment, and prevention of human diseases. However, clinical trials pose challenges and drawbacks, such as complexity and time-consuming processes, which create obstacles for many researchers. Graph Attention Network (GAT) has shown excellent performance in handling graph-structured data for tasks such as link prediction. Some studies have successfully applied GAT to miRNA-disease association prediction. However, there are several drawbacks to existing methods. Firstly, most of the previous models rely solely on concatenation operations to merge features of miRNAs and diseases, which results in the deprivation of significant modality-specific information and even the inclusion of redundant information. Secondly, as the number of layers in GAT increases, there is a possibility of excessive smoothing in the feature extraction process, which significantly affects the prediction accuracy. To address these issues and effectively complete miRNA disease prediction tasks, we propose an innovative model called Multiplex Adaptive Modality Fusion Graph Attention Network (MAMFGAT). MAMFGAT utilizes GAT as the main structure for feature aggregation and incorporates a multi-modal adaptive fusion module to extract features from three interconnected networks: the miRNA-disease association network, the miRNA similarity network, and the disease similarity network. It employs adaptive learning and cross-modality contrastive learning to fuse more effective miRNA and disease feature embeddings as well as incorporates multi-modal residual feature fusion to tackle the problem of excessive feature smoothing in GATs. Finally, we employ a Multi-Layer Perceptron (MLP) model that takes the embeddings of miRNA and disease features as input to anticipate the presence of potential miRNA-disease associations. Extensive experimental results provide evidence of the superior performance of MAMFGAT in comparison to other state-of-the-art methods. To validate the significance of various modalities and assess the efficacy of the designed modules, we performed an ablation analysis. Furthermore, MAMFGAT shows outstanding performance in three cancer case studies, indicating that it is a reliable method for studying the association between miRNA and diseases. The implementation of MAMFGAT can be accessed at the following GitHub repository: https://github.com/zixiaojin66/MAMFGAT-master.
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Affiliation(s)
- Zixiao Jin
- School of Computer, China University of Geosciences, Wuhan, 430074, China.
| | - Minhui Wang
- Department of Pharmacy, Lianshui People's Hospital of Kangda College Affiliated to Nanjing Medical University, Huai'an 223300, China.
| | - Chang Tang
- School of Computer, China University of Geosciences, Wuhan, 430074, China.
| | - Xiao Zheng
- School of Computer, National University of Defense Technology, Changsha, 410073, China.
| | - Wen Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaofeng Sha
- Department of Oncology, Huai'an Hongze District People's Hospital, Huai'an, 223100, China.
| | - Shan An
- JD Health International Inc., China.
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5
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Gao F, Wu Q, Lu D. MicroRNA-10a-5p-mediated downregulation of GATA6 inhibits tumor progression in ovarian cancer. Hum Cell 2024; 37:271-284. [PMID: 37768544 DOI: 10.1007/s13577-023-00987-3] [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: 04/18/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Ovarian cancer is the common cause of cancer-related death in women and is considered the most deadly gynecological cancer. It has been established that GATA-binding protein 6 (GATA6) is abnormally expressed in several types of malignant tumors and acts as an oncogenic protein or a tumor suppressor. However, the underlying mechanism of GATA6 in ovarian cancer progression has not been elucidated. Data in the present study revealed that GATA6 expression was negatively correlated to microRNA-10a-5p (miR-10a-5p) in ovarian cancer tissue and cells and that GATA6 is directly targeted by miR-10a-5p. Notably, upregulated miR-10a-5p dramatically inhibited ovarian cancer cell proliferation, tumorigenic ability, migration, and invasion by targeting GATA6. In vitro and in vivo experiments confirmed that miR-10a-5p-mediated downregulation of GATA6 suppressed Akt pathway activation. Overall, our findings suggest that miR-10a-5p could be a novel therapeutic target for ovarian cancer, and targeting the miR-10a-5p/GATA6/Akt axis could improve outcomes in this patient population.
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Affiliation(s)
- Feiying Gao
- Medical College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Integrative Medicine in Geriatrics Control of Jiangsu Province, Yangzhou, 225009, China
- Yangzhou Jiangdu Binjiang City People's Hospital, Yangzhou, 225211, China
| | - Qiang Wu
- Key Laboratory of Integrative Medicine in Geriatrics Control of Jiangsu Province, Yangzhou, 225009, China
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Northern Jiangsu People's Hospital, Yangzhou, 225001, China
| | - Dan Lu
- Medical College of Yangzhou University, Yangzhou, 225009, China.
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6
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Chang YH, Huang YL, Tsai HC, Chang AC, Ko CY, Fong YC, Tang CH. Chemokine Ligand 2 Promotes Migration in Osteosarcoma by Regulating the miR-3659/MMP-3 Axis. Biomedicines 2023; 11:2768. [PMID: 37893141 PMCID: PMC10604484 DOI: 10.3390/biomedicines11102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma is a common malignant tumor in children and adolescents, known for its aggressive invasion and distant metastasis, leading to a poor prognosis. Matrix metalloproteinases (MMPs) can degrade the extracellular matrix and basement membranes through their proteolytic activity, thereby promoting osteosarcoma metastasis. Chemokine ligand 2 (CCL2) is a well-studied chemokine that plays a significant role in the cell motility of many cancers. However, its specific involvement in osteosarcoma metastasis is not fully understood. The aim of this study is to examine the role of miRNAs in CCL2-mediated MMP expression and cell motility in human osteosarcoma. The analysis of immunohistochemistry data and databases associated a positive correlation between CCL2 or MMP-3 levels with the metastasis of osteosarcoma patients. The in vivo lung metastatic osteosarcoma model also demonstrated similar effects, showing higher levels of CCL2 and MMP-3 in lung metastatic osteosarcoma tissues. The stimulation of osteosarcoma cells with CCL2 enhanced migration and invasion abilities through the upregulation of MMP-3 synthesis. Our results also indicate that CCL2 enhances MMP-3-dependent cell motility by inhibiting miR-3659 synthesis. Therefore, CCL2 represents a promising therapeutic target for treating metastasis in osteosarcoma.
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Affiliation(s)
- Yu-Hsiang Chang
- Program for Cancer Biology and Drug Discovery, China Medical University, Taichung 404328, Taiwan;
| | - Yuan-Li Huang
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan;
| | - Hsiao-Chi Tsai
- Department of Medical Education and Research, China Medical University Beigang Hospital, Yunlin 651012, Taiwan;
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital, Taichung 404327, Taiwan
| | - An-Chen Chang
- Translational Medicine Center, Shin-Kong Wu Ho-Su Memorial Hospital, Taipei 111045, Taiwan;
| | - Chih-Yuan Ko
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404328, Taiwan;
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung 404327, Taiwan
| | - Yi-Chin Fong
- Department of Orthopedic Surgery, China Medical University Hospital, Taichung 404327, Taiwan
- Department of Sports Medicine, College of Health Care, China Medical University, Taichung 404328, Taiwan
- Department of Orthopedic Surgery, China Medical University Beigang Hospital, Yunlin 651012, Taiwan
| | - Chih-Hsin Tang
- Program for Cancer Biology and Drug Discovery, China Medical University, Taichung 404328, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan;
- Department of Pharmacology, School of Medicine, China Medical University, Taichung 404328, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung 404328, Taiwan
- Department of Medical Research, China Medical University Hsinchu Hospital, Hsinchu 302056, Taiwan
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7
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Ghionescu AV, Sorop A, Dima SO. The pivotal role of EMT-related noncoding RNAs regulatory axes in hepatocellular carcinoma. Front Pharmacol 2023; 14:1270425. [PMID: 37767397 PMCID: PMC10520284 DOI: 10.3389/fphar.2023.1270425] [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: 07/31/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains a major health problem worldwide, being the leading cause of cancer-related deaths, with limited treatment options, especially in its advanced stages. Tumor resistance is closely associated with the activation of the EMT phenomenon and its reversal, being modulated by different molecules, including noncoding RNAs (ncRNAs). Noncoding RNAs have the potential to function as both tumor suppressors and oncogenic molecules, controlling the malignant potential of HCC cells. Basically, these molecules circulate in the tumor microenvironment, encapsulated in exosomes. Their impact on cell biology is more significant than originally expected, which makes related research rather complex. The temporal and spatial expression patterns, precise roles and mechanisms of specific ncRNAs encapsulated in exosomes remain primarily unknown in different stages of the disease. This review aims to highlight the recent advances in ncRNAs related to EMT and classifies the described mechanism as direct and indirect, for a better summarization. Moreover, we provide an overview of current research on the role of ncRNAs in several drug resistance-related pathways, including the emergence of resistance to sorafenib, doxorubicin, cisplatin and paclitaxel therapy. Nevertheless, we comprehensively discuss the underlying regulatory mechanisms of exosomal ncRNAs in EMT-HCC via intercellular communication pathways.
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Affiliation(s)
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Olimpia Dima
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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Dżaman K, Czerwaty K, Reichert TE, Szczepański MJ, Ludwig N. Expression and Regulatory Mechanisms of MicroRNA in Cholesteatoma: A Systematic Review. Int J Mol Sci 2023; 24:12277. [PMID: 37569652 PMCID: PMC10418341 DOI: 10.3390/ijms241512277] [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: 07/08/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Cholesteatoma is a temporal bone disease characterized by dysfunctions of keratinocytes. MicroRNAs (miRNAs) are evolutionary conserved noncoding RNAs that regulate mRNA expression. They can be packaged into exosomes and transported to target cells that can be used in the future therapy of cholesteatoma. This study aimed to collect knowledge on the role of miRNAs and exosomal miRNAs in cholesteatoma and was conducted according to the PRISMA guidelines for systematic reviews. Four databases were screened: Pubmed/MEDLINE, Web of Science, Scopus, and the Cochrane Library. The last search was run on the 6th of June 2023. We included full-text original studies written in English, which examined miRNAs in cholesteatoma. The risk of bias was assessed using the Office of Health Assessment and Translation (OHAT) Risk of Bias Rating Tool, modified for the needs of this review. We identified 118 records and included 18 articles. Analyses revealed the downregulation of exosomal miR-17 as well as miR-10a-5p, miR-125b, miR-142-5p, miR34a, miR-203a, and miR-152-5p and the overexpression of exosomal miR-106b-5p as well as miR-1297, miR-26a-5p, miR-199a, miR-508-3p, miR-21-3p, miR-584-5p, and miR-16-1-3p in cholesteatoma. The role of differentially expressed miRNAs in cholesteatoma, including cell proliferation, apoptosis, the cell cycle, differentiation, bone resorption, and the remodeling process, was confirmed, making them a potential therapeutic target in this disease.
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Affiliation(s)
- Karolina Dżaman
- Department of Otolaryngology, The Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland; (K.D.); (K.C.)
| | - Katarzyna Czerwaty
- Department of Otolaryngology, The Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland; (K.D.); (K.C.)
| | - Torsten E. Reichert
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany; (T.E.R.); (N.L.)
| | - Mirosław J. Szczepański
- Department of Otolaryngology, The Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland; (K.D.); (K.C.)
- Department of Biochemistry, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Nils Ludwig
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany; (T.E.R.); (N.L.)
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9
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Pandey P, Suyal G, Pasbola K, Sharma R. NGS-based profiling identifies miRNAs and pathways dysregulated in cisplatin-resistant esophageal cancer cells. Funct Integr Genomics 2023; 23:111. [PMID: 36995552 DOI: 10.1007/s10142-023-01041-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Esophageal cancer (EC) incidence remains to be on a global rise supported by an unchanged recurrence and 5-year survival rate owing to the development of chemoresistance. Resistance to cisplatin, one of the majorly used chemotherapeutic drugs in EC, is a major nuisance. This study sheds light on miRNA dysregulation and its inverse relation with dysregulated mRNAs to guide pathways into the manifestation of cisplatin resistance in EC. A cisplatin-resistant version of an EC cell line was established and comparative profiling by NGS with the parental cell line was employed to identify dysregulation in miRNA and mRNA levels. Protein-protein interaction network analysis was done using Cytoscape, followed by Funrich pathway analysis. Furthermore, selective significant miRNAs were validated using qRT-PCR. miRNA-mRNA integrated analysis was carried out using the Ingenuity Pathway Analysis (IPA) tool. Expression of various established resistance markers supported the successful establishment of cisplatin-resistant cell line. Whole-cell small RNA sequencing and transcriptome sequencing identified 261 miRNAs and 1892 genes to be significantly differentially expressed (DE), respectively. Pathway analysis indicated enrichment of EMT signaling, supported by NOTCH, mTOR, TNF receptor, and PI3K-mediated AKT signaling pathways, in chemoresistant cells. Validation by qRT-PCR confirmed upregulation of miR-10a-5p, miR-618, miR-99a-5p, and miR-935 and downregulation of miR-335-3p, miR-205-5p, miR-944, miR-130a-3p, and miR-429 in resistant cells. Pathway analysis that followed IPA analysis indicated that the dysregulation of these miRNAs and their target genes may be instrumental in the development and regulation of chemoresistance via p53 signaling, xenobiotic metabolism, and NRF2-mediated oxidative stress. This study concludes the interplay between miRNA and mRNA as an important aspect and occurrence in guiding the regulation, acquisition, and maintenance of chemoresistance in esophageal cancer in vitro.
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Affiliation(s)
- Prerna Pandey
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Geetika Suyal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
- Zonal Technology Management & Business Planning and Development Unit (ZTM & BPD Unit), Indian Council of Agricultural Research- Indian Agricultural Research Institute (ICAR-IARI), Pusa, New Delhi, India
| | - Kiran Pasbola
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Rinu Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India.
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Selvakumar SC, Auxzilia Preethi K, Veeraiyan DN, Sekar D. The role of microRNAs on the pathogenesis, diagnosis and management of portal hypertension in patients with chronic liver disease. Expert Rev Gastroenterol Hepatol 2022; 16:941-951. [PMID: 36315408 DOI: 10.1080/17474124.2022.2142562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Portal hypertension (PH) is the elevated pressure in the portal vein, which results in poor functioning of the liver and is influenced by various factors like liver cirrhosis, nonalcoholic fatty liver disease, schistosomiasis, thrombosis, and angiogenesis. Though the diagnosis and treatment have been advanced, early diagnosis of the disease remains a challenge, and the diagnosis methods are often invasive. Hence, the clear understanding of the molecular mechanisms of PH can give rise to the development of novel biomarkers which can pave way for early diagnosis in noninvasive methods, and also the identification of target genes can elucidate an efficient therapeutic target. AREAS COVERED PubMed and Embase database was used to search articles with search terms 'Portal Hypertension' or 'pathophysiology' and 'diagnosis' and 'treatment' or "role of miRNAs in portal hypertension. EXPERT OPINION Interestingly, biomarkers like microRNAs (miRNAs) have been studied for their potential role in various diseases including hypertension. In recent years, miRNAs have been proved to be an efficient biomarker and therapeutic target and few studies have assessed the roles of miRNAs in PH. The present paper highlights the potential roles of miRNAs in PH.
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Affiliation(s)
- Sushmaa Chandralekha Selvakumar
- Centre for Cellular and Molecular Research, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - K Auxzilia Preethi
- Centre for Cellular and Molecular Research, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Deepak Nallaswamy Veeraiyan
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Durairaj Sekar
- Centre for Cellular and Molecular Research, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha University, Chennai, India
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Yang Y, Shang J, Sun Y, Li F, Zhang Y, Kong XZ, Li S, Liu JX. TLNPMD: Prediction of miRNA-Disease Associations Based on miRNA-Drug-Disease Three-Layer Heterogeneous Network. Molecules 2022; 27:4371. [PMID: 35889243 PMCID: PMC9324587 DOI: 10.3390/molecules27144371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
Many microRNAs (miRNAs) have been confirmed to be associated with the generation of human diseases. Capturing miRNA-disease associations (M-DAs) provides an effective way to understand the etiology of diseases. Many models for predicting M-DAs have been constructed; nevertheless, there are still several limitations, such as generally considering direct information between miRNAs and diseases, usually ignoring potential knowledge hidden in isolated miRNAs or diseases. To overcome these limitations, in this study a novel method for predicting M-DAs was developed named TLNPMD, highlights of which are the introduction of drug heuristic information and a bipartite network reconstruction strategy. Specifically, three bipartite networks, including drug-miRNA, drug-disease, and miRNA-disease, were reconstructed as weighted ones using such reconstruction strategy. Based on these weighted bipartite networks, as well as three corresponding similarity networks of drugs, miRNAs and diseases, the miRNA-drug-disease three-layer heterogeneous network was constructed. Then, this heterogeneous network was converted into three two-layer heterogeneous networks, for each of which the network path computational model was employed to predict association scores. Finally, both direct and indirect miRNA-disease paths were used to predict M-DAs. Comparative experiments of TLNPMD and other four models were performed and evaluated by five-fold and global leave-one-out cross validations, results of which show that TLNPMD has the highest AUC values among those of compared methods. In addition, case studies of two common diseases were carried out to validate the effectiveness of the TLNPMD. These experiments demonstrate that the TLNPMD may serve as a promising alternative to existing methods for predicting M-DAs.
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Affiliation(s)
- Yi Yang
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Junliang Shang
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Yan Sun
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Feng Li
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Yuanyuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao 266520, China;
| | - Xiang-Zhen Kong
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Shengjun Li
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao 276826, China; (Y.Y.); (Y.S.); (F.L.); (X.-Z.K.); (S.L.); (J.-X.L.)
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