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Ali A, Mahla SB, Reza V, Hossein A, Bahareh K, Mohammad H, Fatemeh S, Mostafa AB, Leili R. MicroRNAs: Potential prognostic and theranostic biomarkers in chronic lymphocytic leukemia. EJHAEM 2024; 5:191-205. [PMID: 38406506 PMCID: PMC10887358 DOI: 10.1002/jha2.849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 02/27/2024]
Abstract
Small noncoding ribonucleic acids called microRNAs coordinate numerous critical physiological and biological processes such as cell division, proliferation, and death. These regulatory molecules interfere with the function of many genes by binding the 3'-UTR region of target mRNAs to inhibit their translation or even degrade them. Given that a large proportion of miRNAs behave as either tumor suppressors or oncogenes, any genetic or epigenetic aberration changeing their structure and/or function could initiate tumor formation and development. An example of such cancers is chronic lymphocytic leukemia (CLL), the most prevalent adult leukemia in Western nations, which is caused by unregulated growth and buildup of defective cells in the peripheral blood and lymphoid organs. Genetic alterations at cellular and molecular levels play an important role in the occurrence and development of CLL. In this vein, it was noted that the development of this disease is noticeably affected by changes in the expression and function of miRNAs. Many studies on miRNAs have shown that these molecules are pivotal in the prognosis of different cancers, including CLL, and their epigenetic alterations (e.g., methylation) can predict disease progression and response to treatment. Furthermore, miRNAs are involved in the development of drug resistance in CLL, and targeting these molecules can be considered a new therapeutic approach for the treatment of this disease. MiRNA screening can offer important information on the etiology and development of CLL. Considering the importance of miRNAs in gene expression regulation, their application in the diagnosis, prognosis, and treatment of CLL is reviewed in this paper.
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Affiliation(s)
- Afgar Ali
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Sattarzadeh Bardsiri Mahla
- Stem Cells and Regenerative Medicine Innovation CenterKerman University of Medical SciencesKermanIran
- Department of Hematology and Laboratory Sciences, Faculty of Allied Medical SciencesKerman University of Medical SciencesKermanIran
| | - Vahidi Reza
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Arezoomand Hossein
- Department of Hematology and Laboratory Sciences, Faculty of Allied Medical SciencesKerman University of Medical SciencesKermanIran
| | - Kashani Bahareh
- Department of Medical Genetics, School of MedicineTehran University of Medical SciencesTehranIran
| | - Hosseininaveh Mohammad
- Research Center for Hydatid Disease in IranKerman University of Medical SciencesKermanIran
| | - Sharifi Fatemeh
- Research Center of Tropical and Infectious DiseasesKerman University of Medical SciencesKermanIran
| | - Amopour Bahnamiry Mostafa
- Department of Research and Development, Production and Research ComplexPasteur Institute of IranTehranIran
| | - Rouhi Leili
- Student Research CommitteeKerman University of Medical SciencesKermanIran
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Iqbal S, Pal D. microRNA Isolation, Expression Profiling, and Target Identification for Neuroprotection in Alzheimer's Disease. Methods Mol Biol 2024; 2761:277-290. [PMID: 38427244 DOI: 10.1007/978-1-0716-3662-6_20] [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] [Indexed: 03/02/2024]
Abstract
Millions of people throughout the world are affected by neurodegenerative disorders like Alzheimer's disease (AD), making them a major public health concern. To create successful medicines, early diagnosis and illness monitoring are required. Emerging as possible diagnostic and treatment tools for neurodegenerative illnesses are biomarkers such as microRNAs (miRNAs). In the realm of neuroscience, miRNAs have been discovered to function as essential regulators of gene expression, with roles spanning development, differentiation, and illness. Several neurodegenerative diseases, including AD, have been linked to miRNA dysregulation. As high-throughput methods have been developed for monitoring miRNA expression and identifying miRNA targets, miRNAs have become a prime candidate for use in diagnostics and therapy. The techniques for isolating miRNAs and the most up-to-date computational methods for finding miRNA target transcripts are both described in this chapter. This chapter will be a helpful reference for anyone investigating the role of miRNAs in AD and related neurodegenerative illnesses.
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Affiliation(s)
- Saleem Iqbal
- Axe Molecular Endocrinology and Nephrology, CHUL Research Center and Laval University, Quebec City, QC, Canada
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India.
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Wang S, Pan C, Sheng H, Yang M, Yang C, Feng X, Hu C, Ma Y. Construction of a molecular regulatory network related to fat deposition by multi-tissue transcriptome sequencing of Jiaxian red cattle. iScience 2023; 26:108346. [PMID: 38026203 PMCID: PMC10665818 DOI: 10.1016/j.isci.2023.108346] [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: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Intramuscular fat (IMF) refers to the fat that accumulates between muscle bundles or within muscle cells, whose content significantly impacts the taste, tenderness, and flavor of meat products, making it a crucial economic characteristic in livestock production. However, the intricate mechanisms governing IMF deposition, involving non-coding RNAs (ncRNAs), genes, and complex regulatory networks, remain largely enigmatic. Identifying adipose tissue-specific genes and ncRNAs is paramount to unravel these molecular mysteries. This study, conducted on Jiaxian red cattle, harnessed whole transcriptome sequencing to unearth the nuances of circRNAs and miRNAs across seven distinct tissues. The interplay of these ncRNAs was assessed through differential expression analysis and network analysis. These findings are not only pivotal in unveiling the intricacies of fat deposition mechanisms but also lay a robust foundation for future research, setting the stage for enhancing IMF content in Jiaxian red cattle breeding.
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Affiliation(s)
- Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Mengli Yang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chaoyun Yang
- Xichang College, Liangshan Prefecture, Sichuan Province, China
| | - Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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Koh HB, Kim HJ, Kang SW, Yoo TH. Exosome-Based Drug Delivery: Translation from Bench to Clinic. Pharmaceutics 2023; 15:2042. [PMID: 37631256 PMCID: PMC10459753 DOI: 10.3390/pharmaceutics15082042] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Exosome-based drug delivery is emerging as a promising field with the potential to revolutionize therapeutic interventions. Exosomes, which are small extracellular vesicles released by various cell types, have attracted significant attention due to their unique properties and natural ability to transport bioactive molecules. These nano-sized vesicles, ranging in size from 30 to 150 nm, can effectively transport a variety of cargoes, including proteins, nucleic acids, and lipids. Compared to traditional drug delivery systems, exosomes exhibit unique biocompatibility, low immunogenicity, and reduced toxicity. In addition, exosomes can be designed and tailored to improve targeting efficiency, cargo loading capacity, and stability, paving the way for personalized medicine and precision therapy. However, despite the promising potential of exosome-based drug delivery, its clinical application remains challenging due to limitations in exosome isolation and purification, low loading efficiency of therapeutic cargoes, insufficient targeted delivery, and rapid elimination in circulation. This comprehensive review focuses on the transition of exosome-based drug delivery from the bench to clinic, highlighting key aspects, such as exosome structure and biogenesis, cargo loading methods, surface engineering techniques, and clinical applications. It also discusses challenges and prospects in this emerging field.
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Affiliation(s)
- Hee Byung Koh
- Division of Nephrology, Department of Internal Medicine, International Saint Mary’s Hospital, College of Medicine, Catholic Kwandong University, Seo-gu, Incheon 22711, Republic of Korea;
| | - Hyo Jeong Kim
- Division of Nephrology, Department of Internal Medicine, Gangnam Severance Hospital, College of Medicine, Yonsei University, Gangnam-gu, Seoul 06273, Republic of Korea;
| | - Shin-Wook Kang
- Department of Internal Medicine, Institute of Kidney Disease Research, College of Medicine, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Tae-Hyun Yoo
- Department of Internal Medicine, Institute of Kidney Disease Research, College of Medicine, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
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Wong L, Wang L, You ZH, Yuan CA, Huang YA, Cao MY. GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm. BMC Bioinformatics 2023; 24:188. [PMID: 37158823 PMCID: PMC10169329 DOI: 10.1186/s12859-023-05309-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND The limited knowledge of miRNA-lncRNA interactions is considered as an obstruction of revealing the regulatory mechanism. Accumulating evidence on Human diseases indicates that the modulation of gene expression has a great relationship with the interactions between miRNAs and lncRNAs. However, such interaction validation via crosslinking-immunoprecipitation and high-throughput sequencing (CLIP-seq) experiments that inevitably costs too much money and time but with unsatisfactory results. Therefore, more and more computational prediction tools have been developed to offer many reliable candidates for a better design of further bio-experiments. METHODS In this work, we proposed a novel link prediction model based on Gaussian kernel-based method and linear optimization algorithm for inferring miRNA-lncRNA interactions (GKLOMLI). Given an observed miRNA-lncRNA interaction network, the Gaussian kernel-based method was employed to output two similarity matrixes of miRNAs and lncRNAs. Based on the integrated matrix combined with similarity matrixes and the observed interaction network, a linear optimization-based link prediction model was trained for inferring miRNA-lncRNA interactions. RESULTS To evaluate the performance of our proposed method, k-fold cross-validation (CV) and leave-one-out CV were implemented, in which each CV experiment was carried out 100 times on a training set generated randomly. The high area under the curves (AUCs) at 0.8623 ± 0.0027 (2-fold CV), 0.9053 ± 0.0017 (5-fold CV), 0.9151 ± 0.0013 (10-fold CV), and 0.9236 (LOO-CV), illustrated the precision and reliability of our proposed method. CONCLUSION GKLOMLI with high performance is anticipated to be used to reveal underlying interactions between miRNA and their target lncRNAs, and deciphers the potential mechanisms of the complex diseases.
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Affiliation(s)
- Leon Wong
- Guangxi Key Lab of Human-machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, 200092, Shanghai, China
| | - Lei Wang
- Guangxi Key Lab of Human-machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China.
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China.
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710139, China.
| | - Chang-An Yuan
- Guangxi Key Lab of Human-machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Yu-An Huang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710139, China
| | - Mei-Yuan Cao
- School of Electrical and Electronic Engineering, Guangdong Technology College, Zhaoqing, 526100, China
- Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
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Dharavath B, Butle A, Pal A, Desai S, Upadhyay P, Rane A, Khandelwal R, Manavalan S, Thorat R, Sonawane K, Vaish R, Gera P, Bal M, D'Cruz AK, Nair S, Dutt A. Role of miR-944/MMP10/AXL- axis in lymph node metastasis in tongue cancer. Commun Biol 2023; 6:57. [PMID: 36650344 PMCID: PMC9845355 DOI: 10.1038/s42003-023-04437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Occult lymph-node metastasis is a crucial predictor of tongue cancer mortality, with an unmet need to understand the underlying mechanism. Our immunohistochemical and real-time PCR analysis of 208 tongue tumors show overexpression of Matrix Metalloproteinase, MMP10, in 86% of node-positive tongue tumors (n = 79; p < 0.00001). Additionally, global profiling for non-coding RNAs associated with node-positive tumors reveals that of the 11 significantly de-regulated miRNAs, miR-944 negatively regulates MMP10 by targeting its 3'-UTR. We demonstrate that proliferation, migration, and invasion of tongue cancer cells are suppressed by MMP10 knockdown or miR-944 overexpression. Further, we show that depletion of MMP10 prevents nodal metastases using an orthotopic tongue cancer mice model. In contrast, overexpression of MMP10 leads to opposite effects upregulating epithelial-mesenchymal-transition, mediated by a tyrosine kinase gene, AXL, to promote nodal and distant metastasis in vivo. Strikingly, AXL expression is essential and sufficient to mediate the functional consequence of MMP10 overexpression. Consistent with our findings, TCGA-HNSC data suggests overexpression of MMP10 or AXL positively correlates with poor survival of the patients. In conclusion, our results establish that the miR-944/MMP10/AXL- axis underlies lymph node metastases with potential therapeutic intervention and prediction of nodal metastases in tongue cancer patients.
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Affiliation(s)
- Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Ankita Pal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Pawan Upadhyay
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Risha Khandelwal
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Sujith Manavalan
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Rahul Thorat
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Kavita Sonawane
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Richa Vaish
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Poonam Gera
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Tissue Biorepository, Advanced Centre for Treatment Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
| | - Munita Bal
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
| | - Anil K D'Cruz
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India
- Apollo Cancer Center, Apollo Hospitals, CBD Belapur, Navi Mumbai, 400614, India
| | - Sudhir Nair
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, India.
| | - Amit Dutt
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
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Zhang X, Tan J, Chen Y, Ma S, Bai W, Peng Y, Shi G. Identification of serum MiRNAs as candidate biomarkers for non-small cell lung cancer diagnosis. BMC Pulm Med 2022; 22:479. [PMID: 36522766 PMCID: PMC9756610 DOI: 10.1186/s12890-022-02267-6] [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: 07/26/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lung cancer is one of the most common solid tumors worldwide and the leading cause of cancer-associated death. Non-small cell lung cancer (NSCLC) is accounts for approximately 85% of all the lung cancers and lung squamous carcinoma (SCC) and adenocarcinoma (ADC) are the main subtypes of NSCLC. Early diagnose using serum biomarkers could improve the overall survival of patients. In this study, we aimed to identify miRNAs from serum with clinical utility in the diagnosis of NSCLC. METHODS Ten patients with SCC, ten patients with ADC and five noncancerous individuals were enrolled in the screening cohort. miRNA expression levels in serum were measured by microarray analysis. Candidate miRNAs were validated by real-time quantitative polymerase chain reaction analysis in a validation cohort of 78 NSCLC patients and 44 noncancerous individuals. Receiver operating characteristic curves were used to assess the diagnostic performance of serum miRNAs for NSCLC. Logistic regression was used to evaluate the diagnostic value of the combination of markers. RESULTS Six candidate miRNAs were differentially expressed between NSCLC patients and noncancerous individuals in the screening set (fold change > 2, p < 0.05). Among them, expression levels of miR-3149 and miR-4769.3p were confirmed to be significantly increased in tumor serum in the validation set. The area under the curve values of miR-3149 and miR-4769.3p in distinguishing NSCLC patients from noncancerous controls were 0.830 and 0.735, respectively. When combined with tumor markers CEA and Cyfra21-1, the joint diagnostic model increased the area under the curve to 0.898. CONCLUSION Serum miRNAs miR-3149 and miR-4769.3p were up-regulated in NSCLC and may be potential biomarkers for early diagnosis of lung cancer.
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Affiliation(s)
- Xintong Zhang
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Jinjing Tan
- Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China ,grid.414341.70000 0004 1757 0026Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yan Chen
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Shang Ma
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Wanqiu Bai
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
| | - Yanjing Peng
- Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China ,grid.414341.70000 0004 1757 0026Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Guangli Shi
- grid.414341.70000 0004 1757 0026Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, China ,Beijing Tuberculosis Thoracic Tumor Institute, Beijing, 101149 China
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Alswailem R, Alqahtani FY, Aleanizy FS, Alrfaei BM, Badran M, Alqahtani QH, Abdelhady HG, Alsarra I. MicroRNA-219 loaded chitosan nanoparticles for treatment of glioblastoma. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2022; 50:198-207. [PMID: 35762105 DOI: 10.1080/21691401.2022.2092123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Recent evidence has implicated microRNA-219 (miR-219) in regulation of gene contributed in glioblastoma (GBM) pathogenesis. This study aimed to prepare miR-219 in chitosan (CS) nanoparticles (NPs), characterize and investigate their efficacy on human GBM cell line (U87 MG). NPs were prepared using ionic gelation method. The influence of process parameters on physicochemical characteristics of NPs was investigated. Apoptotic effect of miR-219 was examined on U87 MG cells. Formulated NPs showed particle size of 109 ± 2.18 nm, with poly dispersity index equal to 0.2 ± 0.05, and zeta potential of +20.5 ± 0.7 mV. Entrapment efficiency of miR-219 in loaded NP has reached 95%. The in vitro release study demonstrated sustained release pattern of miR-219 from CS-NPs. Gel retardation assay has confirmed the integrity of miR-219 after production process. The fabricated NPs reduced the survival of U87 MG cells to 78% after 24 h of post-transfection, and into 67.5% after 48 h. However, fibroblasts were not affected by the NPs, revealing their specificity for GBM cells. Given the tumour suppressing function of miR-219, and advantage of CS-NPs for gene delivery to the central nervous system, the presented NPs have a great potential for treatment of GBM.
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Affiliation(s)
- Rawan Alswailem
- Drug sector, Saudi Food and Drug Authority, Riyadh, Saudi Arabia.,Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fulwah Yahya Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fadilah Sfouq Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bahauddeen M Alrfaei
- Department of Cellular Therapy and Cancer Research, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health, Riyadh, Saudi Arabia
| | - Mohammad Badran
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Qamraa Hamad Alqahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | | | - Ibrahim Alsarra
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Mostafa SA, Mohammad MHS, Negm WA, Batiha GES, Alotaibi SS, Albogami SM, Waard MD, Tawfik NZ, Abdallah HY. Circulating microRNA203 and its target genes' role in psoriasis pathogenesis. Front Med (Lausanne) 2022; 9:988962. [DOI: 10.3389/fmed.2022.988962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous microRNAs (miRNAs) have been found to have an aberrant expression in the peripheral blood or psoriasis patients' lesions. Psoriasis was shown to have the abnormal expression of microRNA-203 (miR-203). It is a skin-specific signal that governs cellular proliferation in a protein kinase C-dependent manner and is mostly generated by keratinocytes. This work evaluated the expression levels of the circulating miR-203 target genes SOCS3, SOCS6, TP63, TNF-, IL8, and IL24 in psoriasis patients. Using a relative quantitation PCR technique, we determined the expression levels of miR-203 and its target genes (SOCS3, SOCS6, TP63, TNF-, IL8, and IL24) in the plasma of 120 psoriatic patients and matched healthy controls. The disease characteristics of the patients were then correlated with the expression results. We also conducted numerous enrichment analyses for the diseases, functions, and pathways connected to the under-researched biomarkers. Compared to healthy controls, psoriatic patients had significantly increased levels of miR-203 expression; 7.1 (4.4–9.9). In contrast, psoriatic patients had significantly lower expression of all the examined genes compared to healthy controls. Regarding all the study biomarkers, the receiver operating characteristic (ROC) curve analysis demonstrated significant sensitivity and specificity for differentiating between psoriatic patients and healthy controls. According to the results of the disease matching score generated by miR-203 and its target genes, psoriasis was ranked first with a score of 4.45. The third-place finisher with a value of 3.98, it also demonstrated that miR-203 and its target genes are connected to various skin disorders. Our results show that miR-203 contributes to psoriasis pathogenesis not only locally in skin lesions but also in circulation, indicating that it may contribute to the systemic symptoms of the illness. MiR-203 overexpression in psoriasis suggests that miR-203 may be involved in an anti-inflammatory response because it targets both SOCS gene family members and pro-inflammatory cytokines.
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10
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Xie Y, Cao Y, Guo CJ, Guo XY, He YF, Xu QY, Shen F, Pan Q. Profile analysis and functional modeling identify circular RNAs in nonalcoholic fatty liver disease as regulators of hepatic lipid metabolism. Front Genet 2022; 13:884037. [PMID: 36186461 PMCID: PMC9520628 DOI: 10.3389/fgene.2022.884037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease, associated with an outcome of hepatic fibrosis/cirrhosis and hepatocellular carcinoma. However, limited exploration of the underlying mechanisms hinders its prevention and treatment. To investigate the mechanisms of epigenetic regulation in NAFLD, the expression profile of circular RNA (circRNA) of rodents in which NAFLD was induced by a high-fat, high-cholesterol (HFHC) diet was studied. Modeling of the circRNA-microRNA (miRNA) -mRNA regulatory network revealed the functional characteristics of NAFLD-specific circRNAs. The targets and effects in the liver of such NAFLD-specific circRNAs were further assessed. Our results uncovered that the downregulation of 28 annotated circRNAs characterizes HFHC diet-induced NAFLD. Among the downregulated circRNAs, long intergenic non-protein coding RNA, P53 induced transcript (LNCPINT) -derived circRNAs (circ_0001452, circ_0001453, and circ_0001454) targeted both miR-466i-3p and miR-669c-3p. Their deficiency in NAFLD abrogated the circRNA-based inhibitory effect on both miRNAs, which further inactivated the AMPK signaling pathway via AMPK-α1 suppression. Inhibition of the AMPK signaling pathway promotes hepatic steatosis, depending on the transcriptional and translational upregulation of lipogenic genes, such as those encoding sterol regulatory element-binding protein 1 (SREBP1) and fatty acid synthase (FASN) in hepatocytes. The levels of LNCPINT-derived circRNAs displayed a negative association with hepatic triglyceride (TG) concentration. These findings suggest that loss of LNCPINT-derived circRNAs may underlie NAFLD via miR-466i-3p- and miR-669c-3p-dependent inactivation of the AMPK signaling pathway.
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Affiliation(s)
- Yang Xie
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Cao
- Department of Pediatric Digestion and Nutrition, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Can-Jie Guo
- Department of Gastroenterology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Ya Guo
- Department of Gastroenterology, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ya-Fang He
- Department of Pediatric Respiratory, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing-Yang Xu
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Shen
- Endoscopy Center, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Feng Shen, ; Qin Pan,
| | - Qin Pan
- Department of Gastroenterology, School of Medicine, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, China
- Research Center, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- *Correspondence: Feng Shen, ; Qin Pan,
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11
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Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
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12
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Hu R, Xu Y, Han B, Chen Y, Li W, Guan G, Hu P, Zhou Y, Xu Q, Chen L. MiR-202-3p determines embryo viability during mid-blastula transition. Front Cell Dev Biol 2022; 10:897826. [PMID: 36003151 PMCID: PMC9393261 DOI: 10.3389/fcell.2022.897826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Developmental growth is an intricate process involving the coordinated regulation of the expression of various genes, and microRNAs (miRNAs) play crucial roles in diverse processes throughout animal development. The mid-blastula transition (MBT) is a developmental milestone when maternal RNAs are cleared and the zygotic genome programmed asynchronous cell division begins to drive embryogenesis. While mechanisms underlying MBT have been intensively revealed, factors regulating cell proliferation at the transition remain largely unknown. We report here a microRNA, miR-202-3p to be a key factor that determines embryonic fate during MBT in zebrafish. A miR-202-3p antagomir specifically terminated embryo development at the mid-blastula stage. In vivo deletion of the miR-202 locus recapitulated the fatal phenotypes, which were rescued only by miR-202-3p or its precursor. Transcriptome comparison revealed >250 RNAs including both maternal and zygotic origins were dysregulated at MBT in the miR-202−/− embryos, corresponding with arrays of homeostatic disorders leading to massive apoptosis. A trio of genes: nfkbiaa, perp and mgll, known to be intimately involved with cell proliferation and survival, were identified as direct targets of miR-202-3p. Importantly, over- or under-expression of any of the trio led to developmental delay or termination at the blastula or gastrula stages. Furthermore, nfkbiaa and perp were shown to inter-regulate each other. Thus, miR-202-3p mediates a regulatory network whose components interact closely during MBT to determine embryonic viability and development.
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Affiliation(s)
- Ruiqin Hu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yanna Xu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Bingshe Han
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yi Chen
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Guijun Guan
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Peng Hu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yan Zhou
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, College of Marine Science, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Joint Research Centre for Marine Biosciences (Ministry of Science and Technology), College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Centre for Marine Biosciences, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- *Correspondence: Liangbiao Chen,
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13
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Zhao Y, Qin F, Han S, Li S, Zhao Y, Wang H, Tian J, Cen X. MicroRNAs in drug addiction: Current status and future perspectives. Pharmacol Ther 2022; 236:108215. [DOI: 10.1016/j.pharmthera.2022.108215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/21/2022]
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14
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Peng J, Liang Q, Xu Z, Cai Y, Peng B, Li J, Zhang W, Kang F, Hong Q, Yan Y, Zhang M. Current Understanding of Exosomal MicroRNAs in Glioma Immune Regulation and Therapeutic Responses. Front Immunol 2022; 12:813747. [PMID: 35095909 PMCID: PMC8796999 DOI: 10.3389/fimmu.2021.813747] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Exosomes, the small extracellular vesicles, are released by multiple cell types, including tumor cells, and represent a novel avenue for intercellular communication via transferring diverse biomolecules. Recently, microRNAs (miRNAs) were demonstrated to be enclosed in exosomes and therefore was protected from degradation. Such exosomal miRNAs can be transmitted to recipient cells where they could regulate multiple cancer-associated biological processes. Accumulative evidence suggests that exosomal miRNAs serve essential roles in modifying the glioma immune microenvironment and potentially affecting the malignant behaviors and therapeutic responses. As exosomal miRNAs are detectable in almost all kinds of biofluids and correlated with clinicopathological characteristics of glioma, they might be served as promising biomarkers for gliomas. We reviewed the novel findings regarding the biological functions of exosomal miRNAs during glioma pathogenesis and immune regulation. Furthermore, we elaborated on their potential clinical applications as biomarkers in glioma diagnosis, prognosis and treatment response prediction. Finally, we summarized the accessible databases that can be employed for exosome-associated miRNAs identification and functional exploration of cancers, including glioma.
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Affiliation(s)
- Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, Xiangya Changde Hospital, Changde, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianbo Li
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Wenqin Zhang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Fanhua Kang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Qianhui Hong
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mingyu Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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15
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Saçar Demirci MD. Computational Detection of Pre-microRNAs. Methods Mol Biol 2022; 2257:167-174. [PMID: 34432278 DOI: 10.1007/978-1-0716-1170-8_8] [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] [Indexed: 06/13/2023]
Abstract
MicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs is a vital element for investigating miRNA mediated posttranscriptional gene regulation machineries. Furthermore, experimental methods have challenging inadequacies in their capability to detect rare miRNAs, and are also limited to the state of the organism under examination (e.g., tissue type, developmental stage, stress-disease conditions). These issues have initiated the creation of high-level computational methodologies endeavoring to distinguish potential miRNAs in silico. On the other hand, most of these tools suffer from high numbers of false positives and/or false negatives and as a result they do not provide enough confidence for validating all their predictions experimentally. In this chapter, computational difficulties in detection of pre-miRNAs are discussed and a machine learning based approach that has been designed to address these issues is reviewed.
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16
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Machine Learning Based Methods and Best Practices of microRNA-Target Prediction and Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:109-131. [DOI: 10.1007/978-3-031-08356-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Cerro-Herreros E, González-Martínez I, Moreno N, Espinosa-Espinosa J, Fernández-Costa JM, Colom-Rodrigo A, Overby SJ, Seoane-Miraz D, Poyatos-García J, Vilchez JJ, López de Munain A, Varela MA, Wood MJ, Pérez-Alonso M, Llamusí B, Artero R. Preclinical characterization of antagomiR-218 as a potential treatment for myotonic dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:174-191. [PMID: 34513303 PMCID: PMC8413838 DOI: 10.1016/j.omtn.2021.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 07/17/2021] [Indexed: 12/13/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by expansion of unstable CTG repeats in a non-coding region of the DMPK gene. CUG expansions in mutant DMPK transcripts sequester MBNL1 proteins in ribonuclear foci. Depletion of this protein is a primary contributor to disease symptoms such as muscle weakness and atrophy and myotonia, yet upregulation of endogenous MBNL1 levels may compensate for this sequestration. Having previously demonstrated that antisense oligonucleotides against miR-218 boost MBNL1 expression and rescue phenotypes in disease models, here we provide preclinical characterization of an antagomiR-218 molecule using the HSALR mouse model and patient-derived myotubes. In HSALR, antagomiR-218 reached 40–60 pM 2 weeks after injection, rescued molecular and functional phenotypes in a dose- and time-dependent manner, and showed a good toxicity profile after a single subcutaneous administration. In muscle tissue, antagomiR rescued the normal subcellular distribution of Mbnl1 and did not alter the proportion of myonuclei containing CUG foci. In patient-derived cells, antagomiR-218 improved defective fusion and differentiation and rescued up to 34% of the gene expression alterations found in the transcriptome of patient cells. Importantly, miR-218 was found to be upregulated in DM1 muscle biopsies, pinpointing this microRNA (miRNA) as a relevant therapeutic target.
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Affiliation(s)
- Estefanía Cerro-Herreros
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Irene González-Martínez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Nerea Moreno
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Juan M Fernández-Costa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Anna Colom-Rodrigo
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Sarah J Overby
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - David Seoane-Miraz
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.,MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Javier Poyatos-García
- The IISLAFE Health Research Institute, Avenida Fernando Abril Martorell, 106 Torre A 7 planta, 46026 Valencia, Spain.,Neuromuscular Reference Centre ERN EURO-NMD and Neuromuscular Pathology and Ataxia Research Group, Hospital La Fe Health Research Institute, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan J Vilchez
- The IISLAFE Health Research Institute, Avenida Fernando Abril Martorell, 106 Torre A 7 planta, 46026 Valencia, Spain.,Neuromuscular Reference Centre ERN EURO-NMD and Neuromuscular Pathology and Ataxia Research Group, Hospital La Fe Health Research Institute, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Adolfo López de Munain
- Biodonostia Health Research Institute, P° Dr. Beguiristain s/n, 20014 Donostia-San Sebastián, Spain.,Hospital Universitario Donostia-Osakidetza-Departamento de Neurociencias-Universidad del Pais Vasco-CIBERNED
| | - Miguel A Varela
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.,MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Matthew J Wood
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.,MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Manuel Pérez-Alonso
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Beatriz Llamusí
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.,Incliva Biomedical Research Institute, Avenida Menéndez Pelayo 4 acc, 46010 Valencia, Spain
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18
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Coletta S, Lonardi S, Sensi F, D’Angelo E, Fassan M, Pucciarelli S, Valzelli A, Biccari A, Vermi W, Della Bella C, Barizza A, D’Elios MM, de Bernard M, Agostini M, Codolo G. Tumor Cells and the Extracellular Matrix Dictate the Pro-Tumoral Profile of Macrophages in CRC. Cancers (Basel) 2021; 13:cancers13205199. [PMID: 34680345 PMCID: PMC8533926 DOI: 10.3390/cancers13205199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
Tumor-associated macrophages (TAMs) are major components of the tumor microenvironment. In colorectal cancer (CRC), a strong infiltration of TAMs is accompanied by a decrease in effector T cells and an increase in the metastatic potential of CRC. We investigated the functional profile of TAMs infiltrating CRC tissue by immunohistochemistry, flow cytometry, ELISA, and qRT-PCR and their involvement in impairing the activation of effector T cells. In CRC biopsies, we evidenced a high percentage of macrophages with low expression of the antigen-presenting complex MHC-II and high expression of CD206. Monocytes co-cultured with tumor cells or a decellularized tumor matrix differentiated toward a pro-tumoral macrophage phenotype characterized by decreased expression of MHC-II and CD86 and increased expression of CD206 and an abundant release of pro-tumoral cytokines and chemokines. We demonstrated that the hampered expression of MHC-II in macrophages is due to the downregulation of the MHC-II transactivator CIITA and that this effect relies on increased expression of miRNAs targeting CIITA. As a result, macrophages become unable to present antigens to CD4 T lymphocytes. Our data suggest that the tumor microenvironment contributes to defining a pro-tumoral profile of macrophages infiltrating CRC tissue with impaired capacity to activate T cell effector functions.
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Affiliation(s)
- Sara Coletta
- Department of Biology, University of Padova, 35131 Padova, Italy; (S.C.); (A.B.); (M.d.B.)
| | - Silvia Lonardi
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (S.L.); (A.V.); (W.V.)
| | - Francesca Sensi
- Department of Molecular Sciences and Nanosystems, Cà Foscari University of Venice, 30172 Venice, Italy;
- Pediatric Research Institute, 35127 Padova, Italy
| | - Edoardo D’Angelo
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, 35124 Padova, Italy; (E.D.); (S.P.); (A.B.)
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Veneto Region, 35128 Padova, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology Unit, University of Padova, 35124 Padova, Italy;
- Veneto Institute of Oncology, IOV-IRCCS, 35100 Padova, Italy
| | - Salvatore Pucciarelli
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, 35124 Padova, Italy; (E.D.); (S.P.); (A.B.)
| | - Arianna Valzelli
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (S.L.); (A.V.); (W.V.)
| | - Andrea Biccari
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, 35124 Padova, Italy; (E.D.); (S.P.); (A.B.)
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Veneto Region, 35128 Padova, Italy
| | - William Vermi
- Section of Pathology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (S.L.); (A.V.); (W.V.)
| | - Chiara Della Bella
- Department of Experimental and Clinical Medicine, University of Firenze, 50121 Firenze, Italy; (C.D.B.); (M.M.D.)
| | - Annica Barizza
- Department of Biology, University of Padova, 35131 Padova, Italy; (S.C.); (A.B.); (M.d.B.)
| | - Mario Milco D’Elios
- Department of Experimental and Clinical Medicine, University of Firenze, 50121 Firenze, Italy; (C.D.B.); (M.M.D.)
| | - Marina de Bernard
- Department of Biology, University of Padova, 35131 Padova, Italy; (S.C.); (A.B.); (M.d.B.)
| | - Marco Agostini
- Pediatric Research Institute, 35127 Padova, Italy
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, 35124 Padova, Italy; (E.D.); (S.P.); (A.B.)
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Veneto Region, 35128 Padova, Italy
- Correspondence: (M.A.); (G.C.); Tel.: +39-049-964-0160 (M.A.); +39-049-827-6182 (G.C.)
| | - Gaia Codolo
- Department of Biology, University of Padova, 35131 Padova, Italy; (S.C.); (A.B.); (M.d.B.)
- Correspondence: (M.A.); (G.C.); Tel.: +39-049-964-0160 (M.A.); +39-049-827-6182 (G.C.)
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Mahjoubin-Tehran M, Rezaei S, Jalili A, Sahebkar A, Aghaee-Bakhtiari SH. A comprehensive review of online resources for microRNA-diseases associations: the state of the art. Brief Bioinform 2021; 23:6376589. [PMID: 34571538 DOI: 10.1093/bib/bbab381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/07/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) as small 19- to 24-nucleotide noncoding RNAs regulate several mRNA targets and signaling pathways. Therefore, miRNAs are considered key regulators in cellular pathways as well as various pathologies. There is substantial interest in the relationship between disease and miRNAs, which made that one of the important research topics. Interestingly, miRNAs emerged as an attractive approach for clinical application, not only as biomarkers for diagnosis and prognosis or in the prediction of therapy response but also as therapeutic tools. For these purposes, the identification of crucial miRNAs in disease is very important. Databases provided valuable experimental and computational miRNAs-disease information in an accessible and comprehensive manner, such as miRNA target genes, miRNA related in signaling pathways and miRNA involvement in various diseases. In this review, we summarized miRNAs-disease databases in two main categories based on the general or specific diseases. In these databases, researchers could search diseases to identify critical miRNAs and developed that for clinical applications. In another way, by searching particular miRNAs, they could recognize in which disease these miRNAs would be dysregulated. Despite the significant development that has been done in these databases, there are still some limitations, such as not being updated and not providing uniform and detailed information that should be resolved in future databases. This survey can be helpful as a comprehensive reference for choosing a suitable database by researchers and as a guideline for comparing the features and limitations of the database by developer or designer. Short abstract We summarized miRNAs-disease databases that researchers could search disease to identify critical miRNAs and developed that for clinical applications. This survey can help choose a suitable database for researchers.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Jalili
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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20
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Quitian-Useche YF, Sánchez-Ortiz BL, Borges SF, Ramos B, de Souza GC, Batista MA, da Silva Hage Melim LI, Ferreira IM, Carvalho JCT, Borges RS. Fatty ethanolamide of Bertholletia excelsa triglycerides (Brazil nuts): anti-inflammatory action and acute toxicity evaluation in Zebrafish (Danio rerio). Inflammopharmacology 2021; 29:1519-1537. [PMID: 34498144 DOI: 10.1007/s10787-021-00867-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022]
Abstract
Fatty amides (N-alkylamides) are bioactive lipids that are widely distributed in microorganisms, animals, and plants. The low yield in the extraction process of spilantol, a fatty amide, which is mainly related to its diverse biological effects, compromises its application on a large scale. Thus, this study proposes an alternative method to synthesise fatty amides from Bertholletia excelsa (AGBe) oil, with a chemical structure similar to that of spilantol. Carrageenan-induced abdominal oedema in vivo models were used in zebrafish (Danio rerio). In in vivo studies, oral AGBe produced no signs of toxicity. In the histopathological study, AGBe did not cause significant changes in the main metabolising organs (liver, kidneys, and intestines). All doses of AGBe (100 mg/kg, 500 mg/kg, and 750 mg/kg) were effective in reducing oedema by 65%, 69%, and 95%, respectively, producing a dose-response effect compared to the control group, and spilantol-inhibited oedema by 48%. In the in silico study, with the use of molecular docking, it was observed that among the AGBe, the molecules 18:1, ω-7-ethanolamine, and 18:1, ω-9-ethanolamine stood out, with 21 interactions for COX-2 and 20 interactions for PLA2, respectively, surpassing the spilantol standard with 15 interactions for COX-2 and PLA2. The anti-inflammatory action hypothesis was confirmed in the in silico study, demonstrating the involvement of AGBe in the process of inhibiting the enzymes COX-2 and PLA2. Therefore, based on all the results obtained and the fact that until the dose of 1000 mg/kg was administered orally in zebrafish, it was not possible to determine the LD50; it can be said that AGBe is effective and safe for anti-inflammatory activity.
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Affiliation(s)
- Yesica Fernanda Quitian-Useche
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.,Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Brenda Lorena Sánchez-Ortiz
- Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Swanny Ferreira Borges
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.,Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Benilson Ramos
- Laboratório de Biocatálise e Síntese Orgânica Aplicada, Departamento de Ciências Exatas, Curso de Química, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Gisele Custódio de Souza
- Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Mateus Alves Batista
- Laboratório de Química Farmacêutica e Medicinal (PharMedChem), Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Lorane Izabel da Silva Hage Melim
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.,Laboratório de Química Farmacêutica e Medicinal (PharMedChem), Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Irlon Maciel Ferreira
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.,Laboratório de Biocatálise e Síntese Orgânica Aplicada, Departamento de Ciências Exatas, Curso de Química, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - José Carlos Tavares Carvalho
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.,Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil
| | - Raphaelle Sousa Borges
- Programa de Pós-Graduação em Ciências Farmacêuticas, Departamento de Ciências Biológicas e da Saúde, Curso de Farmácia, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil. .,Laboratório de Pesquisa em Fármacos, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Rod. JK, km 02, Macapá, Amapá, 68902-280, Brazil.
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21
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Ghafouri F, Bahrami A, Sadeghi M, Miraei-Ashtiani SR, Bakherad M, Barkema HW, Larose S. Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry. Front Genet 2021; 12:646297. [PMID: 34306005 PMCID: PMC8292821 DOI: 10.3389/fgene.2021.646297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid metabolism in poultry has a major impact on production and disease resistance traits. According to the high rate of interactions between lipid metabolism and its regulating properties, a holistic approach is necessary. To study omics multilayers of adipose tissue and identification of genes and miRNAs involved in fat metabolism, storage and endocrine signaling pathways in two groups of broiler chickens with high and low abdominal fat, as well as high-throughput techniques, were used. The gene–miRNA interacting bipartite and metabolic-signaling networks were reconstructed using their interactions. In the analysis of microarray and RNA-Seq data, 1,835 genes were detected by comparing the identified genes with significant expression differences (p.adjust < 0.01, fold change ≥ 2 and ≤ −2). Then, by comparing between different data sets, 34 genes and 19 miRNAs were detected as common and main nodes. A literature mining approach was used, and seven genes were identified and added to the common gene set. Module finding revealed three important and functional modules, which were involved in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, biosynthesis of unsaturated fatty acids, Alzheimer’s disease metabolic pathway, adipocytokine, insulin, PI3K–Akt, mTOR, and AMPK signaling pathway. This approach revealed a new insight to better understand the biological processes associated with adipose tissue.
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Affiliation(s)
- Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Maryam Bakherad
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Herman W Barkema
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada
| | - Samantha Larose
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
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22
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Mortazavi SS, Bahmanpour Z, Daneshmandpour Y, Roudbari F, Sheervalilou R, Kazeminasab S, Emamalizadeh B. An updated overview and classification of bioinformatics tools for MicroRNA analysis, which one to choose? Comput Biol Med 2021; 134:104544. [PMID: 34119921 DOI: 10.1016/j.compbiomed.2021.104544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 12/16/2022]
Abstract
The term 'MicroRNA' (miRNA) refers to a class of small endogenous non-coding RNAs (ncRNAs) regenerated from hairpin transcripts. Recent studies reveal miRNAs' regulatory involvement in essential biological processes through translational repression or mRNA degradation. Recently, there is a growing body of literature focusing on the importance of miRNAs and their functions. In this respect, several databases have been developed to manage the dispersed data produced. Therefore, it is necessary to know the parameters and characteristics of each database to benefit their data. Besides, selecting the correct database is of great importance to scientists who do not have enough experience in this field. A comprehensive classification along with an explanation of the information contained in each database leads to facilitating access to these resources. In this regard, we have classified relevant databases into several categories, including miRNA sequencing and annotation, validated/predicted miRNA targets, disease-related miRNA, SNP in miRNA sequence or target site, miRNA-related pathways, or gene ontology, and mRNA-miRNA interactions. Hence, this review introduces available miRNA databases and presents a convenient overview to inform researchers of different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant information rapidly.
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Affiliation(s)
| | - Zahra Bahmanpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Somayeh Kazeminasab
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Vice-Chancellor, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Emamalizadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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23
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Gaza A, Fritz V, Malek L, Wormser L, Treiber N, Danner J, Kremer AE, Thasler WE, Siebler J, Meister G, Neurath MF, Hellerbrand C, Bosserhoff AK, Dietrich P. Identification of novel targets of miR-622 in hepatocellular carcinoma reveals common regulation of cooperating genes and outlines the oncogenic role of zinc finger CCHC-type containing 11. Neoplasia 2021; 23:502-514. [PMID: 33901943 PMCID: PMC8099721 DOI: 10.1016/j.neo.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The poor prognosis of advanced hepatocellular carcinoma (HCC) is driven by diverse features including dysregulated microRNAs inducing drug resistance and stemness. Lin-28 homolog A (LIN28A) and its partner zinc finger CCHC-type containing 11 (ZCCHC11) cooperate in binding, oligouridylation and subsequent degradation of tumorsuppressive let-7 precursor microRNAs. Functionally, activation of LIN28A was recently shown to promote stemness and chemoresistance in HCC. However, the expression and regulation of LIN28A in HCC had been unclear. Moreover, the expression, regulation and function of ZCCHC11 in liver cancer remained elusive. In contrast to "one-microRNA-one-target" interactions, we identified common binding sites for miR-622 in both LIN28A and ZCCHC11, suggesting miR-622 to function as a superior pathway regulator. Applying comprehensive microRNA database screening, human hepatocytes and HCC cell lines, patient-derived tissue samples as well as "The Cancer Genome Atlas" (TCGA) patient cohorts, we demonstrated that loss of tumorsuppressive miR-622 mediates derepression and overexpression of LIN28A in HCC. Moreover, the cooperator of LIN28A, ZCCHC11, was newly identified as a prognostic and therapeutic target of miR-622 in liver cancer. Together, identification of novel miR-622 target genes revealed common regulation of cooperating genes and outlines the previously unknown oncogenic role of ZCCHC11 in liver cancer.
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Affiliation(s)
- Anne Gaza
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Valerie Fritz
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Lara Malek
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Laura Wormser
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Johannes Danner
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Andreas E Kremer
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang E Thasler
- Department of General and Visceral Surgery, Red Cross Hospital of Munich, Germany
| | - Jürgen Siebler
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Markus F Neurath
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Anja K Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany.
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24
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Das P, Shah D, Bhandari V. miR34a: a novel small molecule regulator with a big role in bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol 2021; 321:L228-L235. [PMID: 33825492 DOI: 10.1152/ajplung.00279.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Preterm infants with bronchopulmonary dysplasia (BPD), characterized by pulmonary inflammation leading to impaired alveolarization and vascular dysregulation, have an increased risk of abnormal lung function in infancy, childhood, and adulthood. These include a heightened risk of pulmonary hypertension, and respiratory illnesses. MicroRNAs (miRNAs) are known to disrupt normal lung development and function by interrupting alveolarization and vascularization resulting in the development of BPD. Among the various miRs involved in BPD, miR34a has been shown to have a significant role in BPD pathogenesis. Targeting miR34a or its downstream targets may be a promising therapeutic intervention for BPD. In this review, we summarize the data on cellular arrest, proliferation, differentiation, epithelial-mesenchymal transition, mitochondrial dysfunction, and apoptosis impacted by miR34a in the development of BPD pulmonary phenotypes while predicting the future perspective of miR34a in BPD.
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Affiliation(s)
- Pragnya Das
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper/Cooper University Health Care, Camden, New Jersey
| | - Dilip Shah
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper/Cooper University Health Care, Camden, New Jersey
| | - Vineet Bhandari
- Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper/Cooper University Health Care, Camden, New Jersey
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25
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Combined De-Repression of Chemoresistance Associated Mitogen-Activated Protein Kinase 14 and Activating Transcription Factor 2 by Loss of microRNA-622 in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13051183. [PMID: 33803354 PMCID: PMC7967205 DOI: 10.3390/cancers13051183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Chemoresistance is a major hallmark driving the progression and poor prognosis of hepatocellular carcinoma (HCC). Limited chemoresponse of HCC was demonstrated to be mediated by mitogen-activated protein kinase 14 (MAPK14) and activating transcription factor 2 (ATF2). Recently, we have demonstrated loss of control of RAS-RAF-ERK-signaling as a consequence of miR-622 downregulation in HCC. However, the majority of target genes of this potent tumorsuppressive microRNA had remained elusive. The MAPK14-ATF2-axis represents a collateral pathway ensuring persisting ERK-activation in the presence of sorafenib-mediated RAF-inhibition. In contrast to the function of the MAPK14-ATF2-axis, both the expression and regulation of MAPK14 and ATF2 in human HCC remained to be clarified. We found combined overexpression of MAPK14 and ATF2 in human HCC cells, tissues and in sorafenib resistant cell lines. High expression of MAPK14 and ATF2 was associated with reduced overall survival in HCC patients. Deciphering the molecular mechanism promoting combined upregulation of MAPK14 and ATF2 in HCC, we revealed that miR-622 directly targets both genes, resulting in combined de-repression of the MAPK14-ATF2-axis. Together, miR-622 represents a superior regulator of both RAS-RAF-ERK as well as MAPK14-ATF2-signaling pathways in liver cancer.
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26
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Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, Fehlmann T, Kahraman M, Rheinheimer S, Aparicio-Puerta E, Wagner S, Ludwig N, Backes C, Lenhof HP, von Briesen H, Hart M, Keller A, Meese E. Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Res 2021; 49:127-144. [PMID: 33305319 PMCID: PMC7797041 DOI: 10.1093/nar/gkaa1161] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 10/20/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Lena Krammes
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Karin Danz
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Caroline Diener
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Oliver Küchler
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain.,Instituto de Investigación Biosanitaria ibs. Granada, University of Granada, 18071 Granada, Spain
| | - Sylvia Wagner
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Nicole Ludwig
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.,Center of Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Hagen von Briesen
- Department of Bioprocessing & Bioanalytics, Fraunhofer Institute for Biomedical Engineering, 66280 Sulzbach, Germany
| | - Martin Hart
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421 Homburg, Germany
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27
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Liu D, Li B, Shi X, Zhang J, Chen AM, Xu J, Wang W, Huang K, Gao J, Zheng Z, Liu D, Wang H, Shi W, Chen L, Xu J. Cross-platform genomic identification and clinical validation of breast cancer diagnostic biomarkers. Aging (Albany NY) 2021; 13:4258-4273. [PMID: 33493140 PMCID: PMC7906147 DOI: 10.18632/aging.202388] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022]
Abstract
Introduction: Circulating non-coding RNA is an ideal source to discover novel biomarkers for non-invasive screening. However, studies for the discovery of universal miRNAs in serum and exosomes for breast cancer early diagnosis are limited. Methods: Based on bioinformatic analysis, in vitro and in vivo studies were performed to understand the role of identified hsa-miR-423-5p in cancer proliferation, migration, cancer stem cell properties. Next, global non-coding RNA expression profiles in blood serum and exosome were performed. hsa-miR-423-5p expression from a total of 356 peripheral blood samples was evaluated and the association of hsa-miR-423-5p expression with clinical characteristics, sensitivity and specificity for breast cancer diagnosis were assessed. Results: The expression of serum and exosomal hsa-miR-423-5p is abnormally increased in breast cancer. Suppression of hsa-miR-423-5p inhibited cell proliferation and invasion in both T47D and MDA-MB-231 breast cancer cell lines, and tumor growth in vivo. Compared with 113 healthy women, quantification analysis of hsa-miR-423-5p in 224 breast cancer samples confirmed the abnormal expression. Serum hsa-miR-423-5p was significantly associated with the clinical stage (P=0.001) and Ki-67 level (P=0.004). Conclusions: A translational bioinformatics analysis procedure and validation by in vitro, in vivo, and clinical samples reveal that hsa-miR-423-5p could be used as a non-invasive breast cancer biomarker.
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Affiliation(s)
- Dongdong Liu
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Beibei Li
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China.,Department of Laboratory Science, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan 528300, P.R. China
| | - Xiaoshun Shi
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jiexia Zhang
- Department of Respiratory, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, P.R. China
| | - Allen Menglin Chen
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou 510530, P.R. China
| | - Jiarui Xu
- Department of Laboratory Science, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518000, P.R. China
| | - Wan Wang
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Kailing Huang
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou 510530, P.R. China
| | - Jinwei Gao
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou 510530, P.R. China
| | - Zhouxia Zheng
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou 510530, P.R. China
| | - Dan Liu
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Huimin Wang
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Wen Shi
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Lin Chen
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, P.R. China
| | - Jianhua Xu
- Department of Laboratory Science, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan 528300, P.R. China
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Identifying Key MicroRNAs Targeted by Narenmandula in a Rodent Nephropathy Model. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9196379. [PMID: 33299464 PMCID: PMC7707998 DOI: 10.1155/2020/9196379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022]
Abstract
Background Untreated nephropathy can progress to renal failure. The traditional Mongolian remedy Narenmandula regulates the kidney “yang.” This study aimed to identify key microRNAs (miRNAs) targeted by Narenmandula in a rat model of nephropathy. Methods Fifteen rats exhibiting normal renal function were randomized to three study arms. Nephropathy was induced in n = 10 rats using doxorubicin hydrochloride, followed by either Narenmandula treatment (treatment group) or no treatment (control group). In n = 5 rats, no doxorubicin was given and renal function remained unchanged (healthy group). Microarray analysis identified miRNAs which were differentially expressed (DE-miRNAs) between groups. Target genes of DE-miRNAs were predicted using miRWalk version 2.0, followed by enrichment analysis using DAVID, and construction of the miRNA coregulatory network using Cytoscape. Results Nephropathy was successfully induced, with doxorubicin resulting in differential expression of 3645 miRNAs (1324 upregulated and 2321 downregulated). Narenmandula treatment induced differential expression of a total of 159 miRNAs (102 upregulated and 57 downregulated). Upregulated DE-miRNAs (e.g., miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, and miR-30e-5p) and downregulated DE-miRNAs (e.g., miR-330-3p and miR-214-3p) regulated a high number of target genes. Moreover, the miRNA pairs (e.g., miR-195-5p—miR-497-5p, miR-181a-5p—miR-181c-5p, and miR-30e-5p—miR-30a-5p) coregulated a high number of genes. Enrichment analysis indicated functional synergy between miR-30e-5p—miR-30a-3p, miR-34a-5p—miR-30e-5p, miR-30e-5p—miR-195-3p, and miR-30a-3p—miR-195-3p pairs. Conclusion Narenmandula may modulate doxorubicin-induced nephropathy via targeting miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, miR-30e-5p, miR-330-3p, miR-214-3p, miR-34a-5p, miR-30a-3p, and miR-30a-5p.
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Identification of miRNAs as the Crosstalk in the Interaction between Neural Stem/Progenitor Cells and Endothelial Cells. DISEASE MARKERS 2020; 2020:6630659. [PMID: 33381243 PMCID: PMC7758130 DOI: 10.1155/2020/6630659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
Aim This study is aimed at identifying genetic and epigenetic crosstalk molecules and their target drugs involved in the interaction between neural stem/progenitor cells (NSPCs) and endothelial cells (ECs). Materials and Methods Datasets pertaining to reciprocal mRNA and noncoding RNA changes induced by the interaction between NSPCs and ECs were obtained from the GEO database. Differential expression analysis (DEA) was applied to identify NSPC-induced EC alterations by comparing the expression profiles between monoculture of ECs and ECs grown in EC/NSPC cocultures. DEA was also utilized to identify EC-induced NSPC alterations by comparing the expression profiles between monoculture of NSPCs and NSPCs grown in EC/NSPC cocultures. The DEGs and DEmiRNAs shared by NSPC-induced EC alterations and EC-induced NSPC alterations were then identified. Furthermore, miRNA crosstalk analysis and functional enrichment analysis were performed, and the relationship between DEmiRNAs and small molecular drug targets/environment chemical compounds was investigated. Results One dataset (GSE29759) was included and analyzed in this study. Six genes (i.e., MMP14, TIMP3, LOXL1, CCK, SMAD6, and HSPA2), three miRNAs (i.e., miR-210, miR-230a, and miR-23b), and three pathways (i.e., Akt, ERK1/2, and BMPs) were identified as crosstalk molecules. Six small molecular drugs (i.e., deptropine, fluphenazine, lycorine, quinostatin, resveratrol, and thiamazole) and seven environmental chemical compounds (i.e., folic acid, dexamethasone, choline, doxorubicin, thalidomide, bisphenol A, and titanium dioxide) were identified to be potential target drugs of the identified DEmiRNAs. Conclusion To conclude, three miRNAs (i.e., miR-210, miR-230a, and miR-23b) were identified to be crosstalks linking the interaction between ECs and NSPCs by implicating in both angiogenesis and neurogenesis. These crosstalk molecules might provide a basis for devising novel strategies for fabricating neurovascular models in stem cell tissue engineering.
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Narayan V, Shivapurkar N, Baraniuk JN. Informatics Inference of Exercise-Induced Modulation of Brain Pathways Based on Cerebrospinal Fluid Micro-RNAs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. NETWORK AND SYSTEMS MEDICINE 2020; 3:142-158. [PMID: 33274349 PMCID: PMC7703497 DOI: 10.1089/nsm.2019.0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 12/29/2022] Open
Abstract
Introduction: The post-exertional malaise of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) was modeled by comparing micro-RNA (miRNA) in cerebrospinal fluid from subjects who had no exercise versus submaximal exercise. Materials and Methods: Differentially expressed miRNAs were examined by informatics methods to predict potential targets and regulatory pathways affected by exercise. Results: miR-608, miR-328, miR-200a-5p, miR-93-3p, and miR-92a-3p had higher levels in subjects who rested overnight (nonexercise n=45) compared to subjects who had exercised before their lumbar punctures (n=15). The combination was examined in DIANA MiRpath v3.0, TarBase, Cytoscape, and Ingenuity software® to select the intersection of target mRNAs. DIANA found 33 targets that may be elevated after exercise, including TGFBR1, IGFR1, and CDC42. Adhesion and adherens junctions were the most frequent pathways. Ingenuity selected seven targets that had complementary mechanistic pathways involving GNAQ, ADCY3, RAP1B, and PIK3R3. Potential target cells expressing high levels of these genes included choroid plexus, neurons, and microglia. Conclusion: The reduction of this combination of miRNAs in cerebrospinal fluid after exercise suggested upregulation of phosphoinositol signaling pathways and altered adhesion during the post-exertional malaise of ME/CFS. Clinical Trial Registration Nos.: NCT01291758 and NCT00810225.
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Affiliation(s)
- Vaishnavi Narayan
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University, Washington, District of Columbia, USA
| | - Narayan Shivapurkar
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University, Washington, District of Columbia, USA
| | - James N. Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University, Washington, District of Columbia, USA
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Cao R, Wang K, Long M, Guo M, Sheng L, Zhan M, Yang R, Wang H, Yang L. miR-3613-5p enhances the metastasis of pancreatic cancer by targeting CDK6. Cell Cycle 2020; 19:3086-3095. [PMID: 33073681 DOI: 10.1080/15384101.2020.1831254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Pancreatic cancer (PC) is a leading cause of cancer mortality and is expected to continue increasing incidence. Abnormally expressed microRNAs have been demonstrated tightly correlated with the development and progression of PC. However, the molecular mechanisms remain largely unknown. In this study through combing both the TCGA database and our two verification PC cohorts, we found the consistent reduction of miR-3613-5p in PC tumors, which significantly correlated with reduced cumulative survival rate among PC patients. PC patients with higher lymph node metastasis rate show reduced miR-3613-5p expression. Through further mechanistic investigation, we demonstrate that miR-3613-5p down-regulated CDK6 in repressing the metastasis capacity of PC cells in vitro and in vivo. Elevated CDK6 were also found in PC samples, which also correlate with poor prognosis. Thus, our study found a novel tumor repressor miR-3613-5p in PC progression.
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Affiliation(s)
- Rong Cao
- Department of General Surgery, Wuxi Eighth People's Hospital , Wuxi, China.,Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China
| | - Keqi Wang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University , Fujian, China
| | - Manmei Long
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Miaomiao Guo
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Lulu Sheng
- Department of Emergency Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai, China
| | - Ming Zhan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China
| | - Ruimeng Yang
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine , Shanghai, China
| | - Hui Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China
| | - Linhua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai, China
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32
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Nie H, Zhang K, Xu J, Liao K, Zhou W, Fu Z. Combining Bioinformatics Techniques to Study Diabetes Biomarkers and Related Molecular Mechanisms. Front Genet 2020; 11:367. [PMID: 32425976 PMCID: PMC7204005 DOI: 10.3389/fgene.2020.00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/25/2020] [Indexed: 01/16/2023] Open
Abstract
Objective To explore the mechanism of plasma circulating miRNA-126 and miRNA-28-3p in diabetes mellitus (DM) patients, and to identify the related bioinformatics analysis. Methods Randomly selected 120 DM patients as the observation group and 120 non- DM patients as the control group. The plasma circulating miRNA-126 and miRNA-28-3p were analyzed by qRT-PCR, and their target genes, biological information, related lncRNA and circRNA were predicted. Results The circulating miRNA-126 (0.1162 ± 0.0236 vs. 0.0018 ± 0.0862) and miRNA-28-3p (0.1378 ± 0.0268 vs. 0.0006 ± 0.0167) levels in the observation group were significantly higher than those in the control group, and differences were statistically significant (P < 0.01). The Pearson correlation coefficient of miRNA-126 and miRNA- 28-3p was 0.4337 (P < 0.01). ROC curve analysis of miRNA-126 and miRNA-28-3p showed that the differences of the area under curve were statistically significant between the two groups (P < 0.01). Bioinformatics prediction showed that miRNA-126 and miRNA-28-3p may be involved in regulation of the insulin signaling pathway, insulin receptor signaling pathway, insulin/insulin growth factor signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway and angiogenesis. Moreover, it may be associated with a variety of lncRNA and cir-cRNA. Conclusion Circulating miRNA-126 and miRNA-28-3p can be a potential biomarker of DM and it may play an important role in the DM by regulating insulin or insulin growth factor related signaling pathways.
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Affiliation(s)
- Han Nie
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kaihua Zhang
- Department of General Surgery, Jiujiang Hospital Affiliated to Nanchang University, Nanchang, China
| | - Jiasheng Xu
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kaili Liao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Weimin Zhou
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhonghua Fu
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Bhattacharya M, Sharma AR, Sharma G, Patra BC, Lee SS, Chakraborty C. Interaction between miRNAs and signaling cascades of Wnt pathway in chronic lymphocytic leukemia. J Cell Biochem 2020; 121:4654-4666. [PMID: 32100920 DOI: 10.1002/jcb.29683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
Chronic lymphocytic leukemia (CLL), a severe problem all over the world and represents around 25% of all total leukemia cases, is generating the need for novel targets against CLL. Wnt signaling cascade regulates cell proliferation, differentiation, and cell death processes. Thus, any alteration of the Wnt signaling pathway protein cascade might develop into various types of cancers, either by upregulation or downregulation of the Wnt signaling pathway protein components. In addition, it is reported that activation of the Wnt signaling pathway is associated with the transcriptional activation of microRNAs (miRNAs) by binding to its promoter region, suggesting feedback regulation. Considering the protein regulatory functions of various miRNAs, they can be approached therapeutically as modulatory targets for protein components of the Wnt signaling pathway. In this article, we have discussed the potential role of miRNAs in the regulation of Wnt signaling pathway proteins related to the pathogenesis of CLL via crosstalk between miRNAs and Wnt signaling pathway proteins. This might provide a clear insight into the Wnt protein regulatory function of various miRNAs and provide a better understanding of developing advanced and promising therapeutic approaches against CLL.
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Affiliation(s)
- Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, Republic of Korea.,Department of Zoology, Vidyasagar University, Midnapore, West Bengal, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Garima Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, Republic of Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
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Navarro E, Mallén A, Cruzado JM, Torras J, Hueso M. Unveiling ncRNA regulatory axes in atherosclerosis progression. Clin Transl Med 2020; 9:5. [PMID: 32009226 PMCID: PMC6995802 DOI: 10.1186/s40169-020-0256-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
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Affiliation(s)
- Estanislao Navarro
- Independent Researcher, Barcelona, Spain. .,Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| | - Adrian Mallén
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Josep M Cruzado
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Joan Torras
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Miguel Hueso
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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Codolo G, Toffoletto M, Chemello F, Coletta S, Soler Teixidor G, Battaggia G, Munari G, Fassan M, Cagnin S, de Bernard M. Helicobacter pylori Dampens HLA-II Expression on Macrophages via the Up-Regulation of miRNAs Targeting CIITA. Front Immunol 2020; 10:2923. [PMID: 31969878 PMCID: PMC6960189 DOI: 10.3389/fimmu.2019.02923] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/28/2019] [Indexed: 12/17/2022] Open
Abstract
Macrophages have a major role in infectious and inflammatory diseases, and the available data suggest that Helicobacter pylori persistence can be explained in part by the failure of the bacterium to be killed by professional phagocytes. Macrophages are cells ready to kill the engulfed pathogen, through oxygen-dependent and -independent mechanisms; however, their killing potential can be further augmented by the intervention of T helper (Th) cells upon the specific recognition of human leukocyte antigen (HLA)-II–peptide complexes on the surface of the phagocytic cells. As it pertains to H. pylori, the bacterium is engulfed by macrophages, but it interferes with the phagosome maturation process leading to phagosomes with an altered degradative capacity, and to megasomes, wherein H. pylori resists killing. We recently showed that macrophages infected with H. pylori strongly reduce the expression of HLA-II molecules on the plasma membrane and this compromises the bacterial antigen presentation to Th lymphocytes. In this work, we demonstrate that H. pylori hampers HLA-II expression in macrophages, activated or non-activated by IFN-γ, by down-regulating the expression of the class II major histocompatibility complex transactivator (CIITA), the “master control factor” for the expression of HLA class II genes. We provided evidence that this effect relies on the up-regulation of let-7f-5p, let-7i-5p, miR-146b-5p, and -185-5p targeting CIITA. MiRNA expression analysis performed on biopsies from H. pylori-infected patients confirmed the up-regulation of let-7i-5p, miR-146b-5p, and -185-5p in gastritis, in pre-invasive lesions, and in gastric cancer. Taken together, our results suggest that specific miRNAs may be directly involved in the H. pylori infection persistence and may contribute to confer the risk of developing gastric neoplasia in infected patients.
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Affiliation(s)
- Gaia Codolo
- Department of Biology, University of Padua, Padua, Italy
| | | | - Francesco Chemello
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Sara Coletta
- Department of Biology, University of Padua, Padua, Italy
| | | | | | - Giada Munari
- Istituto Oncologico Veneto (IRCCS), Padua, Italy
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy.,CIR-Myo Myology Center, University of Padua, Padua, Italy
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Chen R, Shi C, Yao J, Chen W. Online Databases and Non-coding RNAs in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:65-78. [PMID: 32285405 PMCID: PMC7153034 DOI: 10.1007/978-981-15-1671-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Cardiovascular disease is characterized by its highest morbidity and mortality. One of the main pathological basis of this disease is the dysregulation of gene expression. Non-coding RNA (ncRNA) is a kind of functional RNA, which is transcript from DNA but not translated into proteins. More and more studies have established the important roles of ncRNAs, including transcription, RNA maturation, translation, protein degradation, and their involvement in the pathogenesis of diseases such as cancer and cardiovascular diseases. This chapter will focus on the biological functions of ncRNAs and their advances in cardiovascular disease. With the development of sequencing and computer technology, more and more databases can be easily obtained on the internet. In another part of this chapter, we will summarize some commonly used non-coding RNA databases, which can be easily and quickly used for relevant research.
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Affiliation(s)
- Rui Chen
- Shanghai Applied Radiation Institute, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Chao Shi
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Jianhua Yao
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Wei Chen
- Emergency Department, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
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MiRNA-disease interaction prediction based on kernel neighborhood similarity and multi-network bidirectional propagation. BMC Med Genomics 2019; 12:185. [PMID: 31865912 PMCID: PMC6927119 DOI: 10.1186/s12920-019-0622-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Studies have shown that miRNAs are functionally associated with the development of many human diseases, but the roles of miRNAs in diseases and their underlying molecular mechanisms have not been fully understood. The research on miRNA-disease interaction has received more and more attention. Compared with the complexity and high cost of biological experiments, computational methods can rapidly and efficiently predict the potential miRNA-disease interaction and can be used as a beneficial supplement to experimental methods. Results In this paper, we proposed a novel computational model of kernel neighborhood similarity and multi-network bidirectional propagation (KNMBP) for miRNA-disease interaction prediction, especially for new miRNAs and new diseases. First, we integrated multiple data sources of diseases and miRNAs, respectively, to construct a novel disease semantic similarity network and miRNA functional similarity network. Secondly, based on the modified miRNA-disease interactions, we use the kernel neighborhood similarity algorithm to calculate the disease kernel neighborhood similarity and the miRNA kernel neighborhood similarity. Finally, we utilize bidirectional propagation algorithm to predict the miRNA-disease interaction scores based on the integrated disease similarity network and miRNA similarity network. As a result, the AUC value of 5-fold cross validation for all interactions by KNMBP is 0.93126 based on the commonly used dataset, and the AUC values for all interactions, for all miRNAs, for all disease is 0.93795、0.86363、0.86937 based on another dataset extracted by ourselves, which are higher than other state-of-the-art methods. In addition, our model has good parameter robustness. The case study further demonstrated the predictive performance of the model for novel miRNA-disease interactions. Conclusions Our KNMBP algorithm efficiently integrates multiple omics data from miRNAs and diseases to stably and efficiently predict potential miRNA-disease interactions. It is anticipated that KNMBP would be a useful tool in biomedical research.
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Görücü Yılmaz Ş, Bozkurt H, Ndadza A, Thomford NE, Karaoğlan M, Keskin M, Benlier N, Dandara C. Childhood Obesity Risk in Relationship to Perilipin 1 ( PLIN1) Gene Regulation by Circulating microRNAs. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 24:43-50. [PMID: 31851864 DOI: 10.1089/omi.2019.0150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Childhood obesity is a growing public health burden in many countries. The lipid perilipin 1 (PLIN1) gene is involved in regulation of lipolysis, and thus represents a viable candidate mechanism for obesity genetics research in children. In addition, the regulation of candidate gene expression by circulating microRNAs (miRNAs) offers a new research venue for diagnostic innovation. We report new findings on associations among circulating miRNAs, regulation of the PLIN1 gene, and susceptibility to childhood obesity. In a sample of 135 unrelated subjects, 35 children with obesity (between ages 3 and 13) and 100 healthy controls (between ages 4 and 16), we examined the expression levels of four candidate miRNAs (hsa-miR-4777-3p, hsa-miR-642b-3p, hsa-miR-3671-1, and hsa-miR-551b-2) targeting the PLIN1 as measured by real-time polymerase chain reaction in whole blood samples. We found that the full genetic model, including the four candidate miRNAs and the PLIN1 gene, explained a statistically significant 12.7% of the variance in childhood obesity risk (p = 0.0034). The four miRNAs together explained 10.1% of the risk (p = 0.008). The percentage of variation in childhood obesity risk explained by hsa-miR-642b-3p and age was 19%. In accordance with biological polarity of the observed association, for example, hsa-miR-642b-3p was upregulated, while the PLIN1 expression decreased in obese participants compared to healthy controls. To the best of our knowledge, this is the first clinical association study of these candidate miRNAs targeting the PLIN1 in childhood obesity. These data offer new molecular leads for future clinical biomarker and diagnostic discovery for childhood obesity.
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Affiliation(s)
- Şenay Görücü Yılmaz
- Department of Nutrition and Dietetics, Gaziantep University, Gaziantep, Turkey
| | - Hakan Bozkurt
- Department of Neurology, Medical Park Hospital, Gaziantep, Turkey
| | - Arinao Ndadza
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicholas Ekow Thomford
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Murat Karaoğlan
- Department of Pediatric Endocrinology, Gaziantep University, Gaziantep, Turkey
| | - Mehmet Keskin
- Department of Pediatric Endocrinology, Gaziantep University, Gaziantep, Turkey
| | - Necla Benlier
- Department of Medical Pharmacology, Sanko University, Gaziantep, Turkey
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Zhang J, Li D, Zhang Y, Ding Z, Zheng Y, Chen S, Wan Y. Integrative analysis of mRNA and miRNA expression profiles reveals seven potential diagnostic biomarkers for non‑small cell lung cancer. Oncol Rep 2019; 43:99-112. [PMID: 31746439 PMCID: PMC6908938 DOI: 10.3892/or.2019.7407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to explore specific molecular targets for the diagnosis and treatment of non-small cell lung cancer (NSCLC). The expression profiles of microRNAs (miRNAs) and mRNAs were downloaded from the GEO (GSE102286 and GSE101929) and TCGA databases. After data preprocessing, differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in cancer and normal tissues were selected and used to construct a DEM-DEG regulatory network and a protein-protein interaction (PPI) network. The genes and miRNAs in these networks were subjected to functional enrichment and survival analyses. Several key DEMs and DEGs were verified using RT-qPCR, and the results were statistically interpreted using a multivariate logistic regression analysis. In this study, 25 DEMs and 789 DEGs common to all datasets were identified, which were then used for the construction of a DEM-DEG regulatory network and a PPI network module. Survival analyses of 19 DEMs in the DEM-DEG regulatory network and 36 DEGs in the PPI network module revealed that 34 DEGs (including TOP2A, CCNB1, BIRC5, and TTK) and two miRNAs (miR-21-5p and miR-31-5p) were significantly associated with NSCLC prognosis. Moreover, RT-qPCR analysis identified three DEGs and five DEMs that had changes in expression consistent with those observed in the bioinformatic analysis. Finally, a multivariate logistic regression analysis of the data showed that TOP2A, CCNB1, BIRC5, miR-21-5p, miR-193b-3p, miR-210-3p and miR-31-5p could be combined for the diagnosis of NSCLC. In conclusion, TOP2A, CCNB1, BIRC5, miR-21-5p, miR-193b-3p, miR-210-3p and miR-31-5p may therefore serve as important biomarkers and diagnostic targets for NSCLC.
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Affiliation(s)
- Jie Zhang
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Dong Li
- Department of Ear‑Nose‑Throat, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Yueming Zhang
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Zongli Ding
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Yulong Zheng
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Song Chen
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu 223300, P.R. China
| | - Yufeng Wan
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
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Hadavi R, Mohammadi-Yeganeh S, Razaviyan J, Koochaki A, Kokhaei P, Bandegi A. Expression of Bioinformatically Candidate miRNAs including, miR-576-5p, miR-501-3p and miR-3143, Targeting PI3K Pathway in Triple-Negative Breast Cancer. Galen Med J 2019; 8:e1646. [PMID: 34466540 PMCID: PMC8343935 DOI: 10.31661/gmj.v8i0.1646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/03/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is an invasive and lethal form of breast cancer. PI3K pathway, which often activated in TNBC patients, can be a target of miRNAs. The purpose of this study was bioinformatic prediction of miRNAs targeting the key genes of this pathway and evaluation of the expression of them and their targets in TNBC. Materials and Methods We predicted miRNAs targeting PIK3CA and AKT1 genes using bioinformatics tools. Extraction of total RNA, synthesis of cDNA and quantitative real-time polymerase chain reaction were performed from 18 TNBC samples and normal adjacent tissues and cell lines. Results Our results demonstrated that miR-576-5p, miR-501-3p and miR-3143 were predicted to target PIK3CA, AKT1 and both of these mRNAs, respectively and were down-regulated while their target mRNAs were up-regulated in clinical samples and cell lines. The analysis of the receiver operating characteristic curve was done for the evaluation of the diagnostic value of predicted miRNAs in TNBC patients. Conclusion The findings of our study demonstrated the reverse correlation between miRNAs and their target genes and therefore the possibility of these miRNAs to be proposed as new candidates for TNBC targeted therapies.
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Affiliation(s)
- Razie Hadavi
- Department of Biochemistry, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Razaviyan
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - Ameneh Koochaki
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Kokhaei
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Ahmadreza Bandegi
- Department of Biochemistry, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Research Center of Physiology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Correspondence to: Ahmadreza Bandegi, Damghan Road, Semnan University of Medical Sciences, Semnan, Iran Telephone Number: 33654162-023 Email Address: .
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Qin H, Wen DY, Que Q, Zhou CY, Wang XD, Peng YT, He Y, Yang H, Liao BM. Reduced expression of microRNA-139-5p in hepatocellular carcinoma results in a poor outcome: An exploration the roles of microRNA-139-5p in tumorigenesis, advancement and prognosis at the molecular biological level using an integrated meta-analysis and bioinformatic investigation. Oncol Lett 2019; 18:6704-6724. [PMID: 31807180 PMCID: PMC6876336 DOI: 10.3892/ol.2019.11031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is generally considered one of the most common gastrointestinal malignant tumors, characterized by high invasiveness and metastatic rate, as well as insidious onset. A relationship between carcinogenicity and aberrant microRNA-139-5p (miR-139-5p) expression has been identified in multiple tumors while the specific molecular mechanisms of miR-139-5p in HCC have not yet been thoroughly elucidated. A meta-analysis of available data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, ArrayExpress and Oncomine databases, as well as the published literature, was comprehensively conducted with the aim of examining the impact of miR-139-5p expression on HCC. Additionally, predicted downstream target genes were confirmed using a series of bioinformatics tools. Moreover, a correlative biological analysis was performed to ascertain the precise function of miR-139-5p in HCC. The results revealed that the expression of miR-139-5p was noticeably lower in HCC compared with non-tumor liver tissues according to the pooled standard mean difference, which was -0.84 [95% confidence interval (CI): -1.36 to -0.32; P<0.001]. Furthermore, associations were detected between miR-139-5p expression and certain clinicopathological characteristics of TCGA samples, including tumor grade, pathological stage and T stage. Moreover, the pooled hazard ratio (HR) for overall survival (HR=1.37; 95% CI: 1.07-1.76; P=0.001) indicated that decreased miR-139-5p expression was a risk factor for adverse outcomes. Additionally, 382 intersecting genes regulated by miR-139-5p were obtained and assembled in signaling pathways, including 'transcription factor activity, sequence-specific DNA binding', 'pathways in cancer' and 'Ras signaling pathway'. Notably, four targeted genes that were focused in 'pathways in cancer' were identified as hub genes and immunohistochemical staining of the proteins encoded by these four hub genes in liver tissues, explored using the Human Protein Atlas database, confirmed their expression patterns in HCC and normal liver tissues Findings of the present study suggest that reduced miR-139-5p expression is capable of accelerating tumor progression and is associated with a poor clinical outcome by modulating the expression of downstream target genes involved in tumor-associated signaling pathways.
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Affiliation(s)
- Hui Qin
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dong-Yue Wen
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qiao Que
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Chuan-Yang Zhou
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiao-Dong Wang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Ting Peng
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yun He
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong Yang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Bo-Ming Liao
- Department of Internal Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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42
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He QL, Qin SY, Tao L, Ning HJ, Jiang HX. Prognostic value and prospective molecular mechanism of miR-100-5p in hepatocellular carcinoma: A comprehensive study based on 1,258 samples. Oncol Lett 2019; 18:6126-6142. [PMID: 31788087 PMCID: PMC6865135 DOI: 10.3892/ol.2019.10962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
The prognostic value and molecular mechanism of microRNA-100-5p (miR-100-5p) in hepatocellular carcinoma (HCC) are still unclear. To explore the prognostic value and the mechanism of miR-100-5p in HCC, the present study analyzed the results of 18 previous studies and bioinformatic datasets. The clinical significance of miR-100-5p and its targets in HCC were investigated using The Cancer Genome Atlas and the Gene Expression Omnibus, as well as relevant literature. In total, 12 online tools were used to predict the target genes of miR-100-5p. Bioinformatics analysis and Spearman correlation analysis were performed, and genomic alterations of the hub genes were evaluated. A meta-analysis with 1,258 samples revealed that miR-100-5p was significantly downregulated in HCC [standard mean difference (SMD), −0.94; 95% confidence interval (CI), −1.14 to −0.74; I2, 35.2%]. Lower miR-100-5p expression was associated with poorer clinical characteristics and a poorer prognosis for patients with HCC. Additionally, bioinformatics analysis revealed that the ‘regulation of transcription’, ‘chromatin remodeling complex’, ‘transcription regulator activity’, ‘pathways in cancer’ and ‘heparan sulfate biosynthesis’ were the most enriched terms. Furthermore, expression of histone deacetylase (HDAC)2, HDAC3, SHC-transforming protein 1 (SHC1), Ras-related protein Rac1 (RAC1) and E3 ubiquitin-protein ligase CBL (CBL) was negatively correlated with miR-100-5p expression. Among these, upregulated HDAC2 [hazard ratio (HR), 1.910; 95% CI, 1.309–2.787; P=0.0007], HDAC3 (HR, 1.474; 95% CI, 1.012–2.146; P=0.0435), SHC1 (HR, 1.52; 95% CI, 1.043–2.215; P=0.0281) and RAC1 (HR, 1.817; 95% CI, 1.248–2.645; P=0.0022) were associated with shorter survival. Alterations in HDAC2, SHC1, RAC1 and IGF1R were linked with a poorer outcome for HCC, and alternative splicing of SHC and RAC1 were significantly decreased and increased in HCC, respectively. In summary, the downregulation of miR-100-5p may be involved in the progression and prognosis of HCC. The upregulation of HDAC2, HDAC3, SHC1 and RAC1 may indicate a poorer survival rate for patients with HCC. Thus, miR-100-5p and these 4 potential target genes may provide novel therapeutic targets and prognostic predictors for patients with HCC.
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Affiliation(s)
- Qing-Lin He
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Shan-Yu Qin
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Lin Tao
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Jian Ning
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hai-Xing Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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43
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Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Brief Bioinform 2019; 20:1836-1852. [PMID: 29982332 PMCID: PMC7414524 DOI: 10.1093/bib/bby054] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.
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Affiliation(s)
- Liang Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Liisa Heikkinen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Changliang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Yang Yang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
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44
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Chen X, Xie D, Zhao Q, You ZH. MicroRNAs and complex diseases: from experimental results to computational models. Brief Bioinform 2019; 20:515-539. [PMID: 29045685 DOI: 10.1093/bib/bbx130] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/13/2017] [Indexed: 12/22/2022] Open
Abstract
Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one of the most important components in the cell, miRNAs play a growing important role in various essential and important biological processes. For the recent few decades, amounts of experimental methods and computational models have been designed and implemented to identify novel miRNA-disease associations. In this review, the functions of miRNAs, miRNA-target interactions, miRNA-disease associations and some important publicly available miRNA-related databases were discussed in detail. Specially, considering the important fact that an increasing number of miRNA-disease associations have been experimentally confirmed, we selected five important miRNA-related human diseases and five crucial disease-related miRNAs and provided corresponding introductions. Identifying disease-related miRNAs has become an important goal of biomedical research, which will accelerate the understanding of disease pathogenesis at the molecular level and molecular tools design for disease diagnosis, treatment and prevention. Computational models have become an important means for novel miRNA-disease association identification, which could select the most promising miRNA-disease pairs for experimental validation and significantly reduce the time and cost of the biological experiments. Here, we reviewed 20 state-of-the-art computational models of predicting miRNA-disease associations from different perspectives. Finally, we summarized four important factors for the difficulties of predicting potential disease-related miRNAs, the framework of constructing powerful computational models to predict potential miRNA-disease associations including five feasible and important research schemas, and future directions for further development of computational models.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Di Xie
- School of Mathematics, Liaoning University
| | - Qi Zhao
- School of Mathematics, Liaoning University
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science
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45
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Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I. mirDIP 4.1-integrative database of human microRNA target predictions. Nucleic Acids Res 2019; 46:D360-D370. [PMID: 29194489 PMCID: PMC5753284 DOI: 10.1093/nar/gkx1144] [Citation(s) in RCA: 348] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are important regulators of gene expression, achieved by binding to the gene to be regulated. Even with modern high-throughput technologies, it is laborious and expensive to detect all possible microRNA targets. For this reason, several computational microRNA-target prediction tools have been developed, each with its own strengths and limitations. Integration of different tools has been a successful approach to minimize the shortcomings of individual databases. Here, we present mirDIP v4.1, providing nearly 152 million human microRNA-target predictions, which were collected across 30 different resources. We also introduce an integrative score, which was statistically inferred from the obtained predictions, and was assigned to each unique microRNA-target interaction to provide a unified measure of confidence. We demonstrate that integrating predictions across multiple resources does not cumulate prediction bias toward biological processes or pathways. mirDIP v4.1 is freely available at http://ophid.utoronto.ca/mirDIP/.
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Affiliation(s)
- Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Chiara Pastrello
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Andrea E M Rossos
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Mark Abovsky
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | | | - Mike Tsay
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Richard Lu
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, 845 10, Slovakia
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46
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Gloor Y, Schvartz D, F Samer C. Old problem, new solutions: biomarker discovery for acetaminophen liver toxicity. Expert Opin Drug Metab Toxicol 2019; 15:659-669. [PMID: 31293190 DOI: 10.1080/17425255.2019.1642323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Although the hepatotoxicity of acetaminophen is a well-known problem, the search for reliable biomarker of toxicity is still a current issue as clinical tools are missing to assess patients intoxicated following chronic use, sequential ingestion, use of modified release formulations or in case of delayed arrival to hospital. The need for new specific and robust biomarkers for acetaminophen toxicity has prompted many studies exploring the use of blood levels of acetaminophen derivatives, mitochondrial damage markers, liver cell apoptosis and/or necrosis markers and circulating microRNAs. Areas covered: In this review, we present a concise overview of the most promising biomarkers currently under evaluation including descriptions of their properties with respect to exposure type, APAP specificity, and potential clinical application. In addition, we illustrate the power of new technologies for biomarker research and describe their current application to the field of acetaminophen-induced hepatotoxicity. Expert opinion: Recently the use of extracellular vesicles isolation in combination with omics techniques has opened a new perspective to the field of biomarker research. However, the potential of those new technologies for the prediction and monitoring of hepatic diseases and acetaminophen toxicity has not yet been fully taken into consideration.
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Affiliation(s)
- Yvonne Gloor
- a Division of clinical pharmacology and toxicology, Geneva University Hospital , Geneva , Switzerland.,b Laboratory of clinical pharmacology, Faculty of Medicine, University of Geneva , Geneva , Switzerland
| | - Domitille Schvartz
- c Department of internal medicine specialties, Faculty of Medicine, University of Geneva , Geneva , Switzerland
| | - Caroline F Samer
- a Division of clinical pharmacology and toxicology, Geneva University Hospital , Geneva , Switzerland.,b Laboratory of clinical pharmacology, Faculty of Medicine, University of Geneva , Geneva , Switzerland
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47
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Maemura T, Fukuyama S, Sugita Y, Lopes TJS, Nakao T, Noda T, Kawaoka Y. Lung-Derived Exosomal miR-483-3p Regulates the Innate Immune Response to Influenza Virus Infection. J Infect Dis 2019; 217:1372-1382. [PMID: 29373693 DOI: 10.1093/infdis/jiy035] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/18/2018] [Indexed: 01/21/2023] Open
Abstract
Exosomes regulate cell-cell communication by transferring functional proteins and RNAs between cells. Here, to clarify the function of exosomes during influenza virus infection, we characterized lung-derived exosomal microRNAs (miRNAs). Among the detected miRNAs, miR-483-3p was present at high levels in bronchoalveolar lavage fluid (BALF) exosomes during infection of mice with various strains of influenza virus, and miR-483-3p transfection potentiated gene expression of type I interferon and proinflammatory cytokine upon viral infection of MLE-12 cells. RNF5, a regulator of the RIG-I signaling pathway, was identified as a target gene of miR-483-3p. Moreover, we found that CD81, another miR-483-3p target, functions as a negative regulator of RIG-I signaling in MLE-12 cells. Taken together, this study indicates that BALF exosomal miRNAs may mediate the antiviral and inflammatory response to influenza virus infection.
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Affiliation(s)
- Tadashi Maemura
- Division of Virology, Department of Microbiology and Immunology, Japan.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Japan
| | - Satoshi Fukuyama
- Division of Virology, Department of Microbiology and Immunology, Japan
| | - Yukihiko Sugita
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Japan
| | - Tiago J S Lopes
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Japan
| | - Tomomi Nakao
- Division of Virology, Department of Microbiology and Immunology, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Japan.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Japan
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48
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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49
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Zhao H, Lai X, Zhang W, Zhu H, Zhang S, Wu W, Wang S, Tang M, Deng Z, Tan J. MiR-30a-5p frequently downregulated in prostate cancer inhibits cell proliferation via targeting PCLAF. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:278-289. [PMID: 30669858 DOI: 10.1080/21691401.2018.1553783] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) have vastly expanded our view of RNA world in intracellular signal regulating networks. Here, we functionally characterized a normally highly expressed miRNA, miR-30a-5p (MIMAT0000087), which exhibits downregulated expression profiles in prostate cancer samples. MiR-30a-5p knockdown and overexpression in PC-3 cell line alters cell proliferation supporting a tumour suppressor role. We also discovered that PCLAF is the direct target of miR-30a-5p. Notably, PC-3 cell proliferation is inhibited by miR-30a-5p/PCLAF axis. miR-30a-5p represents a novel molecule of functionally important miRNAs which may shed light on the novel therapeutic targets for prostate cancer.
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Affiliation(s)
- Hu Zhao
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China.,b Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Xiaofeng Lai
- c Department of Clinical Genetics and Experimental Medicine, 900 Hospital of the Joint Logistics Team, Xiamen University School of Medicine, Fuzhou, Fujian, P. R. China
| | - Wei Zhang
- d Department of Urology, Bayi Hospital affiliated Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Hehuan Zhu
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China
| | - Shenhang Zhang
- e ChinaFujian Key Laboratory of Exercise Rehabilitation, College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, P. R. China
| | - Weizhen Wu
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China.,b Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Shuiliang Wang
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China
| | - Minying Tang
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China.,b Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Zhen Deng
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China.,b Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fujian Medical University, Fuzhou, Fujian, P. R. China
| | - Jianming Tan
- a Fujian Provincial Key Laboratory of Transplant Biology, Fuzhou Dongfang Hospital of Xiamen University (900 Hospital of the Joint Logistics Team), Fuzhou, Fujian, P.R. China.,b Fujian Provincial Key Laboratory of Transplant Biology, 900 Hospital of the Joint Logistics Team, Fujian Medical University, Fuzhou, Fujian, P. R. China
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Zhu J, Xu C, Ruan L, Wu J, Li Y, Zhang X. MicroRNA-146b Overexpression Promotes Human Bladder Cancer Invasion via Enhancing ETS2-Mediated mmp2 mRNA Transcription. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:531-542. [PMID: 31071529 PMCID: PMC6506625 DOI: 10.1016/j.omtn.2019.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/20/2019] [Accepted: 04/07/2019] [Indexed: 01/20/2023]
Abstract
Although microRNAs have been validated to play prominent roles in the occurrence and development of human bladder cancer (BC), alterations and function of many microRNAs (miRNAs) in bladder cancer invasion are not fully explored yet. miR-146b was reported to be a tumor suppressor or oncomiRNA in various types of cancer. However, its accurate expression, function, and mechanism in bladder cancer remain unclear. Here we discovered that miR-146b was frequently upregulated in bladder cancer tissues compared with adjacent non-cancerous tissues. Inhibition of miR-146b resulted in a significant inhibitory effect on the invasion of bladder cancer cells by reducing mmp2 mRNA transcription and protein expression. We further demonstrated that knockdown of miR-146b attenuated ETS2 expression, which was the transcription factor of matrix metalloproteinase (MMP)2. Moreover, mechanistic studies revealed that miR-146b inhibition stabilized ARE/poly(U)-binding/degradation factor 1 (auf1) mRNA by directly binding to its mRNA 3′ UTR, further reduced ets2 mRNA stability, and finally inhibited mmp2 transcription and attenuated bladder cancer invasion abilities. The identification of the miR-146b/AUF1/ETS2/MMP2 mechanism for promoting bladder cancer invasion provides significant insights into understanding the nature of bladder cancer metastasis. Targeting the pathway described here may be a novel approach for inhibiting invasion and metastasis of bladder cancer.
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Affiliation(s)
- Junlan Zhu
- The Precision Medicine Laboratory, Beilun People's Hospital, Ningbo, Zhejiang, China.
| | - Chunxia Xu
- The Precision Medicine Laboratory, Beilun People's Hospital, Ningbo, Zhejiang, China
| | - Liming Ruan
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianping Wu
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yang Li
- Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, Zhejiang, China.
| | - Xingguo Zhang
- The Precision Medicine Laboratory, Beilun People's Hospital, Ningbo, Zhejiang, China.
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