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Meng X, Long M, Yue N, Li Q, Chen J, Zhao H, Deng W. LncRNA MEG3 Restrains Hepatic Lipogenesis via the FOXO1 Signaling Pathway in HepG2 Cells. Cell Biochem Biophys 2024; 82:1253-1259. [PMID: 38713402 PMCID: PMC11344712 DOI: 10.1007/s12013-024-01278-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/08/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) become a main public health concern, and is characterized by lipid accumulation in the hepatocytes. We found that overexpression of lncRNA MEG3 significantly reduced the expression of FOXO1, ACC1, and FAS, and subsequently decreased the lipid accumulation in HepG2 cells. Moreover, inhibition of lncRNA MEG3 could increase the lipid accumulation and the mRNA and protein levels of FOXO1, ACC1, and FAS. Further study showed that lncRNA MEG3 regulates the lipogenesis process by inhibiting the entry of FOXO1 into the nucleus translocation. Our study demonstrated that lncRNA MEG3 regulates de novo lipogenesis by decreasing the expression and nucleus translocation of FOXO1 in HepG2 cells, suggesting that lncRNA MEG3 could be a promising therapeutic target in lipid metabolic disorders.
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Affiliation(s)
- Xiangyu Meng
- The Central Laboratory, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Mei Long
- Department of Cardiology, ZiBo Central Hospital, Zibo, Shandong, 255000, China
| | - Nanxi Yue
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Neural and Vascular Biology, Ministry of Education of China, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Quan Li
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Jia Chen
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Hongye Zhao
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Neural and Vascular Biology, Ministry of Education of China, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China.
| | - Wei Deng
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China.
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Jasim SA, Majeed AA, Uinarni H, Alshuhri M, Alzahrani AA, Ibrahim AA, Alawadi A, Abed Al-Abadi NK, Mustafa YF, Ahmed BA. Long non-coding RNA (lncRNA) PVT1 in drug resistance of cancers: Focus on pathological mechanisms. Pathol Res Pract 2024; 254:155119. [PMID: 38309019 DOI: 10.1016/j.prp.2024.155119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
According to estimates, cancer will be the leading cause of death globally in 2022, accounting for 9.6 million deaths. At present, the three main therapeutic modalities utilized to treat cancer are radiation therapy, chemotherapy, and surgery. However, during treatment, tumor cells resistant to chemotherapy may arise. Drug resistance remains a major oppose since it often leads to therapeutic failure. Furthermore, the term "acquired drug resistance" describes the situation where tumor cells already display drug resistance before undergoing chemotherapy. However, little is still known about the basic mechanisms underlying chemotherapy-induced drug resistance. The development of new technologies and bioinformatics has led to the discovery of additional genes associated with drug resistance. Long noncoding RNA plasmacytoma variant translocation 1 (PVT1) has been linked to an increased risk of cancer, according to a growing body of research. Apart from biological functions associated with cell division, development, pluripotency, and cell cycle, lncRNA PVT1 contributes significantly to the regulation of various aspects of genome function, such as transcription, splicing, and epigenetics. The article will address the mechanism by which lncRNA PVT1 influences drug resistance in cancer cells.
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Affiliation(s)
- Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, Al-maarif University College, Anbar, Iraq; Biotechnology department, College of Applied Science, Fallujah University, Anbar, Iraq
| | - Ali A Majeed
- Department of Pathological Analyses, Faculty of Science, University of Kufa, Najaf, Iraq.
| | - Herlina Uinarni
- Department of Anatomy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Indonesia; Radiology Department of Pantai Indah Kapuk Hospital, Jakarta, Indonesia.
| | - Mohammed Alshuhri
- Radiology and Medical Imaging Department, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Kharj, Sauadi Arabia
| | | | - Abeer A Ibrahim
- Inorganic Chemistry Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Babylon, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
| | - Batool Ali Ahmed
- Department of Medical Engineering, Al-Nisour University College, Baghdad, Iraq
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3
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Mukhopadhyay A, Deshpande SN, Bhatia T, Thelma BK. Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case-control association study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1677-1691. [PMID: 37009928 DOI: 10.1007/s00406-023-01596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes-tardive dyskinesia (n = 176) and cognition (n = 565) using a case-control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Affiliation(s)
- Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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Saadh MJ, Arellano MTC, Saini RS, Amin AH, Sharma N, Arias-Gonzáles JL, Alsandook T, Cotrina-Aliaga JC, Akhavan-Sigari R. Molecular mechanisms of long non-coding RNAs in differentiation of T Helper17 cells. Int Immunopharmacol 2023; 123:110728. [PMID: 37572506 DOI: 10.1016/j.intimp.2023.110728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
T helper (Th) 17 cells are one of the most important T cell subsets in a number of autoimmune and chronic inflammatory diseases. During infections, Th17 cells appear to play an important role in the clearance of extracellular pathogens. Th17 cells, on the other hand, are engaged in inflammation and have been linked to the pathophysiology of a number of autoimmune illnesses and human inflammatory disorders. A diverse group of RNA molecules known as lncRNAs serve critical functions in gene expression regulation. They may interact with a wide range of molecules, including DNA, RNA, and proteins, and have a complex structure. LncRNAs, which have restricted or no protein-coding activity, are implicated in a number of illnesses due to their regulatory impact on a variety of biological processes such as cell proliferation, apoptosis, and differentiation. Several lncRNAs have been associated with Th7 cell development in the context of immune cell differentiation. In this article, we cover new studies on the involvement of lncRNAs in Th17 cell differentiation in a variety of disorders, including auto-immune diseases, malignancies, asthma, heart disease, and infections.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman 11831, Jordan; Applied Science Research Center. Applied Science Private University, Amman, Jordan.
| | | | | | - Ali H Amin
- Deanship of Scientific Research, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Nidhi Sharma
- Department of Computer Engineering & Application, GLA University, Mathura, India.
| | | | - Tahani Alsandook
- Dentistry Department, Al-Turath University College, Baghdad, Iraq.
| | | | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Germany; Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Poland.
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Hazra S, Moulick D, Mukherjee A, Sahib S, Chowardhara B, Majumdar A, Upadhyay MK, Yadav P, Roy P, Santra SC, Mandal S, Nandy S, Dey A. Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107940. [PMID: 37738864 DOI: 10.1016/j.plaphy.2023.107940] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.
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Affiliation(s)
- Swati Hazra
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | | | - Synudeen Sahib
- S. S. Cottage, Njarackal, P.O.: Perinad, Kollam, 691601, Kerala, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh 792103, India.
| | - Arnab Majumdar
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, West Bengal 741246, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
| | - Priyabrata Roy
- Department of Molecular Biology and Biotechnology, University of Kalyani, West Bengal 741235, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal 741235, India.
| | - Sayanti Mandal
- Department of Biotechnology, Dr. D. Y. Patil Arts, Commerce & Science College (affiliated to Savitribai Phule Pune University), Sant Tukaram Nagar, Pimpri, Pune, Maharashtra-411018, India.
| | - Samapika Nandy
- School of Pharmacy, Graphic Era Hill University, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India; Department of Botany, Vedanta College, 33A Shiv Krishna Daw Lane, Kolkata-700054, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal 700073, India.
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Al-Hawary SIS, Kashikova K, Ioffe EM, Izbasarova A, Hjazi A, Tayyib NA, Alsalamy A, Hussien BM, Hameed M, Abdalkareem MJ. Pathological role of LncRNAs in immune-related disease via regulation of T regulatory cells. Pathol Res Pract 2023; 249:154709. [PMID: 37586216 DOI: 10.1016/j.prp.2023.154709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023]
Abstract
Human regulatory T cells (Tregs) are essential in pathogenesis of several diseases such as autoimmune diseases and cancers, and their imbalances may be promoting factor in these disorders. The development of the proinflammatory T cell subset TH17 and its balance with the generation of regulatory T cells (Treg) is linked to autoimmune disease and cancers. Long non-coding RNAs (lncRNAs) have recently emerged as powerful regulatory molecules in a variety of diseases and can regulate the expression of significant genes at multiple levels through epigenetic regulation and by modulating transcription, post-transcriptional processes, translation, and protein modification. They may interact with a wide range of molecules, including DNA, RNA, and proteins, and have a complex structural makeup. LncRNAs are implicated in a range of illnesses due to their regulatory impact on a variety of biological processes such as cell proliferation, apoptosis, and differentiation. In this regard, a prominent example is lncRNA NEAT1 which several studies have performed to determine its role in the differentiation of immune cells. Many other lncRNAs have been linked to Treg cell differentiation in the context of immune cell differentiation. In this study, we review recent research on the various roles of lncRNAs in differentiation of Treg cell and regulation of the Th17/Treg balance in autoimmune diseases and tumors in which T regs play an important role.
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Affiliation(s)
| | - Khadisha Kashikova
- Caspian University, International School of Medicine, Almaty, Kazakhstan
| | - Elena M Ioffe
- Department of Military Clinical Hospital, Ministry of Defence, Almaty, Kazakhstan.
| | | | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Nahla A Tayyib
- Faculty of Nursing, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ali Alsalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Beneen M Hussien
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Mohamood Hameed
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
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Sarshar M, Scribano D, Palamara AT, Ambrosi C, Masotti A. The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions. Front Mol Biosci 2022; 9:1088783. [PMID: 36619166 PMCID: PMC9810633 DOI: 10.3389/fmolb.2022.1088783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein-RNA and RNA-RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,Department of Infectious Diseases, National Institute of Health, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,IRCCS San Raffaele Roma, Rome, Italy
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,*Correspondence: Meysam Sarshar, ; Andrea Masotti,
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Li H, Liu H, Hao Q, Liu X, Yao Y, Cao M. Oncogenic signaling pathway-related long non-coding RNAs for predicting prognosis and immunotherapy response in breast cancer. Front Immunol 2022; 13:891175. [PMID: 35990668 PMCID: PMC9386474 DOI: 10.3389/fimmu.2022.891175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe clinical outcomes of breast cancer (BC) are unpredictable due to the high level of heterogeneity and complex immune status of the tumor microenvironment (TME). When set up, multiple long non-coding RNA (lncRNA) signatures tended to be employed to appraise the prognosis of BC. Nevertheless, predicting immunotherapy responses in BC is still essential. LncRNAs play pivotal roles in cancer development through diverse oncogenic signal pathways. Hence, we attempted to construct an oncogenic signal pathway–based lncRNA signature for forecasting prognosis and immunotherapy response by providing reliable signatures.MethodsWe preliminarily retrieved RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) database and extracted lncRNA profiles by matching them with GENCODE. Following this, Gene Set Variation Analysis (GSVA) was used to identify the lncRNAs closely associated with 10 oncogenic signaling pathways from the TCGA-BRCA (breast-invasive carcinoma) cohort and was further screened by the least absolute shrinkage and selection operator Cox regression model. Next, an lncRNA signature (OncoSig) was established through the expression level of the final 29 selected lncRNAs. To examine survival differences in the stratification described by the OncoSig, the Kaplan–Meier (KM) survival curve with the log-rank test was operated on four independent cohorts (n = 936). Subsequently, multiple Cox regression was used to investigate the independence of the OncoSig as a prognostic factor. With the concordance index (C-index), the time-dependent receiver operating characteristic was employed to assess the performance of the OncoSig compared to other publicly available lncRNA signatures for BC. In addition, biological differences between the high- and low-risk groups, as portrayed by the OncoSig, were analyzed on the basis of statistical tests. Immune cell infiltration was investigated using gene set enrichment analysis (GSEA) and deconvolution tools (including CIBERSORT and ESTIMATE). The combined effect of the Oncosig and immune checkpoint genes on prognosis and immunotherapy was elucidated through the KM survival curve. Ultimately, a pan-cancer analysis was conducted to attest to the prevalence of the OncoSig.ResultsThe OncoSig score stratified BC patients into high- and low-risk groups, where the latter manifested a significantly higher survival rate and immune cell infiltration when compared to the former. A multivariate analysis suggested that OncoSig is an independent prognosis predictor for BC patients. In addition, compared to the other four publicly available lncRNA signatures, OncoSig exhibited superior predictive performance (AUC = 0.787, mean C-index = 0.714). The analyses of the OncoSig and immune checkpoint genes clarified that a lower OncoSig score meant significantly longer survival and improved response to immunotherapy. In addition to BC, a high OncoSig score in several other cancers was negatively correlated with survival and immune cell infiltration.ConclusionsOur study established a trustworthy and discriminable prognostic signature for BC patients with similar clinical profiles, thus providing a new perspective in the evaluation of immunotherapy responses. More importantly, this finding can be generalized to be applicable to the vast majority of human cancers.
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Affiliation(s)
- Huamei Li
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hongjia Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | - Qiongyu Hao
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| | - Xianglin Liu
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yongzhong Yao
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Yongzhong Yao, ; Meng Cao,
| | - Meng Cao
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Yongzhong Yao, ; Meng Cao,
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Long non-coding RNA signatures and related signaling pathway in T-cell acute lymphoblastic leukemia. Clin Transl Oncol 2022; 24:2081-2089. [DOI: 10.1007/s12094-022-02886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022]
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10
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Ji H, Qu J, Peng W, Yang L. Downregulation of lncRNA MALAT1 Inhibits Angiotensin II-induced Hypertrophic Effects of Cardiomyocytes by Regulating SIRT4 via miR-93-5p. Int Heart J 2022; 63:602-611. [PMID: 35650160 DOI: 10.1536/ihj.21-332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cardiac hypertrophy is a leading risk for heart failure and sudden death. Long non-coding RNAs (lncRNAs) have been implicated in a variety of human diseases, including cardiac hypertrophy. We aimed to investigate the potential role and functional mechanism of lncRNA metastasis-associated in lung adenocarcinoma transcript 1 (MALAT1) in cardiac hypertrophy. C57BL/6 mice underwent transverse aortic constriction (TAC) to induce cardiac hypertrophy in vivo. The expression of MALAT1, miR-93-5p, and sirtuin 4 (SIRT4) mRNA was detected using a quantitative real-time polymerase chain reaction. The protein levels of cardiac hypertrophy-related markers, including atrial natriuretic peptide (ANP), B-type natriuretic peptide (BNP) and β-myosin heavy chain (β-MHC), and SIRT4 were measured via western blotting. The putative interaction between miR-93-5p and MALAT1 or SIRT4 was verified using a dual-luciferase reporter assay, RNA immunoprecipitation assay, or pull-down assay. Consequently, the expression of MALAT1 and SIRT4 was increased in TAC-treated mouse heart and angiotensin II (Ang-II)-induced cardiomyocytes, whereas the expression of miR-93-5p was decreased. Ang-II promoted the expression of ANP, BNP, and β-MHC and the surface area of cardiomyocytes, whereas MALAT1 downregulation impaired their expression and cell area. MiR-93-5p was a target of MALAT1, and its inhibition reversed the effects of MALAT1 downregulation. More importantly, MALAT1 modulated SIRT4 expression by degrading miR-93-5p. The expression of ANP, BNP, and β-MHC suppressed by miR-93-5p restoration was recovered by SIRT4 promotion. Overall, MALAT1 knockdown ameliorated cardiac hypertrophy partly by regulating the miR-93-5p/SIRT4 network, indicating that MALAT1 was a substantial indicator of cardiac hypertrophy.
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Affiliation(s)
- Huanchun Ji
- Department of Cardiology, Dalian Second People's Hospital
| | - Jingxian Qu
- Department of Cardiology, Dalian Second People's Hospital
| | - Wei Peng
- Department of Cardiology, Dalian Second People's Hospital
| | - Long Yang
- Department of Cardiology, Dalian Second People's Hospital
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Sargazi S, Mukhtar M, Rahdar A, Bilal M, Barani M, Díez-Pascual AM, Behzadmehr R, Pandey S. Opportunities and challenges of using high-sensitivity nanobiosensors to detect long noncoding RNAs: A preliminary review. Int J Biol Macromol 2022; 205:304-315. [PMID: 35182562 DOI: 10.1016/j.ijbiomac.2022.02.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022]
Abstract
The two types ofncRNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are responsible for several biological processes within cells, such as the immune responses, cell growth and invasion, and regulation of the cell cycle. Rapidly expanding class of ncRNAs, lncRNAsinteract with other molecules to form chromatin-remodeling complexes. These potential hallmarks of diseases contribute to transcriptional and post-transcriptional regulation of several genes, possibly via cross-talk with other RNAs. Aberrant expression of lncRNAshas drawn increasing attention to the pathophysiology of different diseases, includingcancer and cardiovasculardiseases. Unfortunately, circulating lncRNAs are presented in the bloodstream at very low levels, making sensitive detection difficult. Currently, there are few methods for detecting these ncRNAs from which quantitative real-time-polymerase chain reaction (qRT-PCR) is the most routinely used technique. These techniqueslack sensitivity for intracellular detection of lncRNAs. Moreover, they are tedious and require a large sample size. Currently, nanotechnology has taken over the diagnostic field because of the tunable properties and modification opportunities. Furthermore, these conventional techniques can be merged with nanotechnology to improve detection sensitivity.This review highlights some of the most recent findings on nanotechnology-based methods and possible obstacles intheir application for moreaccurate sensing of lncRNAs.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran
| | - Mahwash Mukhtar
- Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, University of Szeged, Eötvösutca 6, Szeged 6720, Hungary
| | - Abbas Rahdar
- Department of Physics, Faculty of Science, University of Zabol, 538-98615 Zabol, Iran.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mahmood Barani
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Ana M Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain
| | - Razieh Behzadmehr
- Department of Radiology, Zabol university of medical sciences, Zabol, Iran
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
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12
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Xin XH, Zhang YY, Gao CQ, Min H, Wang L, Du PF. SGII: Systematic Identification of Essential lncRNAs in Mouse and Human Genome With lncRNA-Protein-Protein Heterogeneous Interaction Network. Front Genet 2022; 13:864564. [PMID: 35386279 PMCID: PMC8978670 DOI: 10.3389/fgene.2022.864564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/02/2022] [Indexed: 12/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play important roles in a variety of biological processes. Knocking out or knocking down some lncRNA genes can lead to death or infertility. These lncRNAs are called essential lncRNAs. Identifying the essential lncRNA is of importance for complex disease diagnosis and treatments. However, experimental methods for identifying essential lncRNAs are always costly and time consuming. Therefore, computational methods can be considered as an alternative approach. We propose a method to identify essential lncRNAs by combining network centrality measures and lncRNA sequence information. By constructing a lncRNA-protein-protein interaction network, we measure the essentiality of lncRNAs from their role in the network and their sequence together. We name our method as the systematic gene importance index (SGII). As far as we can tell, this is the first attempt to identify essential lncRNAs by combining sequence and network information together. The results of our method indicated that essential lncRNAs have similar roles in the LPPI network as the essential coding genes in the PPI network. Another encouraging observation is that the network information can significantly boost the predictive performance of sequence-based method. All source code and dataset of SGII have been deposited in a GitHub repository (https://github.com/ninglolo/SGII).
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Affiliation(s)
- Xiao-Hong Xin
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Ying-Ying Zhang
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Chu-Qiao Gao
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Hui Min
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Likun Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing, China
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, China
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13
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Sasa GBK, Xuan C, Chen M, Jiang Z, Ding X. Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review. Transl Cancer Res 2022; 10:5406-5429. [PMID: 35116387 PMCID: PMC8799054 DOI: 10.21037/tcr-21-1607] [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: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
Objective To explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action. Background LUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods. Methods In this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university's online library, among other sources. Conclusions LncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.
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Affiliation(s)
- Gabriel B K Sasa
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Xuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meiyue Chen
- The fourth affiliated hospital, Zhejiang University of Medicine, Hangzhou, China
| | - Zhenggang Jiang
- Department of Science Research and Information Management, Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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14
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Huang X, Zhu S, Zhang K, Tan W, Chen Y, Shang C. High Expression of Long Non-Coding RNA TMCO1-AS1 is Associated With Poor Prognosis of Hepatocellular Carcinoma. Front Mol Biosci 2022; 9:814058. [PMID: 35141283 PMCID: PMC8819098 DOI: 10.3389/fmolb.2022.814058] [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: 11/12/2021] [Accepted: 01/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The molecular pathways along with the clinical significance of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) remain uncertain. Our study sought to identify and characterize lncRNAs associated with HCC. Methods: LncRNA TMCO1-AS1 was identified by differential expression analysis, receiver operating characteristic (ROC) analysis, and univariate analysis using RNA sequencing and clinical information of HCC from the public database. Then clinical correlations and survival analysis were conducted to further appraise the prognostic significance of lncRNA TMCO1-AS1 in HCC. Hepatoma and adjoining normal tissues from 66 patients who received surgical operation at our center were used to verify the results of the bioinformatics analysis. A survival prognostic model was established combining TMCO1-AS1 expression and other clinical characteristics. Results: Bioinformatics analysis showed the aberrant high expression of TMCO1-AS1 in HCC tissue. TMCO1-AS1 expression was positively correlated with alpha-fetoprotein (AFP) level, vascular invasion, tumor stage, as well as tumor differentiation. Moreover, survival analysis found a significant inverse association between the expression of TMCO1-AS1 and the survival of patients with HCC. Cox analysis indicated that TMCO1-AS1 was an independent factor for HCC prognosis. Analysis of the HCC tissues from patients at our center provided results similar to those of the bioinformatics analysis. Risk models for overall survival (OS) and recurrence-free survival (RFS) incorporating TMCO1-AS1 exhibited better sensitivity and specificity than using clinical characteristics alone. Conclusion: High TMCO1-AS1 expression is significantly correlated with the unfavorable poor prognosis of HCC, indicating its potential of being a novel prognostic marker for HCC.
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Affiliation(s)
- Xuelian Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sicong Zhu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kelin Zhang
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenliang Tan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yajin Chen
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yajin Chen, ; Changzhen Shang,
| | - Changzhen Shang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yajin Chen, ; Changzhen Shang,
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15
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Abstract
Cardiac hypertrophy, characterized by the enlargement of cardiomyocytes, is initially an adaptive response to physiological and pathological stimuli. Decompensated cardiac hypertrophy is related to fibrosis, inflammatory cytokine, maladaptive remodeling, and heart failure. Although pathological myocardial hypertrophy is the main cause of hypertrophy-related morbidity and mortality, our understanding of its mechanism is still poor. Long noncoding RNAs (lncRNAs) are noncoding RNAs that regulate various physiological and pathological processes through multiple molecular mechanisms. Recently, accumulating evidence has indicated that lncRNA-H19 is a potent regulator of the progression of cardiac hypertrophy. For the first time, this review summarizes the current studies about the role of lncRNA-H19 in cardiac hypertrophy, including its pathophysiological processes and underlying pathological mechanism, including calcium regulation, fibrosis, apoptosis, angiogenesis, inflammation, and methylation. The context within which lncRNA-H19 might be developed as a target for cardiac hypertrophy treatment is then discussed to gain better insight into the possible biological functions of lncRNA-H19 in cardiac hypertrophy.
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16
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Ji G, Ren R, Fang X. Identification and Characterization of Non-Coding RNAs in Thymoma. Med Sci Monit 2021; 27:e929727. [PMID: 34219124 PMCID: PMC8268976 DOI: 10.12659/msm.929727] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Thymoma is the most common tumor of the anterior mediastinum, and can be caused by infrequent malignancies arising from the epithelial cells of the thymus. Unfortunately, blood-based diagnostic markers are not currently available. High-throughput sequencing technologies, such as RNA-seq with next-generation sequencing, have facilitated the detection and characterization of both coding and non-coding RNAs (ncRNAs), which play significant roles in genomic regulation, transcriptional and post-transcriptional regulation, and imprinting and epigenetic modification. The knowledge about fusion genes and ncRNAs in thymomas is scarce. MATERIAL AND METHODS For this study, we gathered large-scale RNA-seq data belonging to samples from 25 thymomas and 25 healthy thymus specimens and analyzed them to identify fusion genes, lncRNAs, and miRNAs. RESULTS We found 21 fusion genes, including KMT2A-MAML2, HADHB-REEP1, COQ3-CGA, MCM4-SNTB1, and IFT140-ACTN4, as the most frequent and significant in thymomas. We also detected 65 differentially-expressed lncRNAs in thymomas, including AFAP1-AS1, LINC00324, ADAMTS9-AS1, VLDLR-AS1, LINC00968, and NEAT1, that have been validated with the TCGA database. Moreover, we identified 1695 miRNAs from small RNA-seq data that were overexpressed in thymomas. Our network analysis of the lncRNA-mRNA-miRNA regulation axes identified a cluster of miRNAs upregulated in thymomas, that can trigger the expression of target protein-coding genes, and lead to the disruption of several biological pathways, including the PI3K-Akt signaling pathway, FoxO signaling pathway, and HIF-1 signaling pathway. CONCLUSIONS Our results show that overexpression of this miRNA cluster activates PI3K-Akt, FoxO, HIF-1, and Rap-1 signaling pathways, suggesting pathway inhibitors may be therapeutic candidates against thymoma.
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Affiliation(s)
- Guanglei Ji
- First Department of Thoracic Surgery, Linyi Cancer Hospital, Linyi, Shandong, PR China
| | - Rongrong Ren
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Xichao Fang
- Second Department of Thoracic Surgery, Linyi Cancer Hospital, Linyi, Shandong, PR China
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17
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Abstract
Long noncoding RNAs (lncRNAs) are involved in many regulatory mechanisms in practically every step of the RNA cycle, from transcription to RNA stability and translation. They are a highly heterogeneous class of molecules in terms of site of production, interaction networks, and functions. More and more databases are available on the web with the aim to make public information about lncRNA accessible to the scientific community. Here we review the most interesting resources with the purpose to organize a compendium of useful tools to interrogate before studying a lncRNA of interest.
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18
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Suravajhala R, Gupta S, Kumar N, Suravajhala P. Deciphering LncRNA-protein interactions using docking complexes. J Biomol Struct Dyn 2020; 40:3769-3776. [PMID: 33280525 DOI: 10.1080/07391102.2020.1850354] [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: 02/07/2023]
Abstract
Deciphering RNA-protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, viz. including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein-RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Renuka Suravajhala
- Department of Chemistry, School of Basic Science, Manipal University, Manipal, India
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Department of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Narayan Kumar
- Department of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India.,Bioclues.org, India
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19
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Karimzadeh MR, Seyedtaghia MR, Soudyab M, Nezamnia M, Kidde J, Sahebkar A. Exosomal Long Noncoding RNAs: Insights into Emerging Diagnostic and Therapeutic Applications in Lung Cancer. JOURNAL OF ONCOLOGY 2020; 2020:7630197. [PMID: 33224198 PMCID: PMC7671817 DOI: 10.1155/2020/7630197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022]
Abstract
Lung cancer is the most common cause of cancer-related deaths worldwide. Annually, millions of people die from lung cancer because of late detection and ineffective therapies. Recently, exosomes have been introduced as new therapeutic players with the potential to improve upon current diagnostic and treatment options. Exosomes are small membranous vesicles produced during endosomal merging. This allows for cell packaging of nucleic acids, proteins, and lipids and transfer to adjacent or distant cells. While exosomes are a part of normal intercellular signaling, they also allow malignant cells to transfer oncogenic material leading to tumor spread and metastasis. Exosomes are an interesting field of discovery for biomarkers and therapeutic targets. Among exosomal materials, lncRNAs have priority; lncRNAs are a class of noncoding RNAs longer than 200 base pairs. In the case of cancer, primary interest regards their oncogene and tumor suppressor functions. In this review, the advantages of exosomal lncRNAs as biomarkers and therapeutic targets will be discussed in addition to reviewing studies of their application in lung cancer.
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Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of Medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Mohammad Reza Seyedtaghia
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Soudyab
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maria Nezamnia
- Department of Obstetrics and Gynecology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Jason Kidde
- Department of Emergency Medicine, University of Utah, Salt Lake City, UT, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Halal Research Center of IRI, FDA, Tehran, Iran
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20
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Ryu J, Ahn Y, Kook H, Kim YK. The roles of non-coding RNAs in vascular calcification and opportunities as therapeutic targets. Pharmacol Ther 2020; 218:107675. [PMID: 32910935 DOI: 10.1016/j.pharmthera.2020.107675] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Vascular calcification (VC) is characterized by an accumulation of calcium phosphate crystals inside the vessel wall. VC is often associated with diabetes, chronic kidney disease (CKD), atherosclerosis, and cardiovascular disease (CVD). Even though the number of patients with VC remains prevalent, there are still no approved therapies for the treatment of VC. Since the pathogenesis of VC is diverse and involves multiple factors and mechanisms, it is critical to reveal the novel mechanisms involved in VC. Although protein-coding RNAs involved in VC have been extensively studied, the roles of non-coding RNAs (ncRNAs) are not yet fully understood. The field of ncRNAs has recently received attention, and accumulating evidence from studies in VC suggests that ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play an important role in the regulation of VC. NcRNAs can modulate VC by acting as promoters or inhibitors and may be useful in the clinical diagnosis and treatment of VC. In this article, we review and discuss ncRNAs that regulate VC and present the therapeutic implications of these ncRNAs.
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Affiliation(s)
- Juhee Ryu
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea
| | - Youngkeun Ahn
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Cardiology, Cardiovascular Center, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Hyun Kook
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Pharmacology, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.
| | - Young-Kook Kim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Jeollanam-do, Republic of Korea; Department of Biomedical Sciences, Center for Creative Biomedical Scientists at Chonnam National University, Jeollanam-do, Republic of Korea; Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Republic of Korea.
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21
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Shi Y, Yang R, Tu L, Liu D. Long non‑coding RNA HOTAIR promotes burn wound healing by regulating epidermal stem cells. Mol Med Rep 2020; 22:1811-1820. [PMID: 32582996 PMCID: PMC7411415 DOI: 10.3892/mmr.2020.11268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Local transplantation of epidermal stem cells (ESCs) exerts a therapeutic effect on burn wounds. However, cell viability can impede their clinical application. HOX antisense intergenic RNA (HOTAIR) is involved in regulating adult tissue stem cells, as well as in developmental patterning and pluripotency. However, little is known about its role in regulating ESCs. The present study was performed to investigate the effects of HOTAIR in the modulation of ESCs and wound repair. Firstly, reverse transcription-quantitative PCR was used to detect the relative expression of HOTAIR during burn wound healing in mice to determine whether HOTAIR is associated with wound healing. Subsequently, ESCs derived from mouse skin were transfected with a lentiviral vector to overexpress or knockdown HOTAIR. The effects of HOTAIR on cell proliferation and differentiation were measured by 5-bromodeoxyuridine and MTT assays, and by assessing NANOG mRNA expression. Lastly, mice with burns were administered a subcutaneous injection of HOTAIR-overexpressing ESCs. Images were captured and histological analyses were performed to evaluate wound healing. The results revealed that the expression of HOTAIR gradually increased and peaked at day 7 post-burn and maintained at relatively high levels until day 14 post-burn during wound healing. Furthermore, overexpression of HOTAIR promoted ESC proliferation and maintained the stem cell state in vitro. By contrast, suppression of HOTAIR inhibited cell proliferation and cell stemness. It was also identified that HOTIR-overexpressing ESCs accelerated re-epithelialization and facilitated burn wound repair. In conclusion, the present findings confirmed an essential role of HOTAIR in the regulation of ESC proliferation and stemness. Therefore, targeting HOTAIR in ESCs may be a potentially promising therapy for burn wound healing.
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Affiliation(s)
- Yan Shi
- Burns Institute, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Ronghua Yang
- Burns Department, The First People's Hospital of Foshan, Foshan, Guangdong 528000, P.R. China
| | - Longxiang Tu
- Burns Institute, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Dewu Liu
- Burns Institute, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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22
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Salah SMM, Matboli M, Nasser HET, Abdelnaiem IA, Shafei AES, El-Asmer MF. Dysregulation in the expression of (lncRNA-TSIX, TP53INP2 mRNA, miRNA-1283) in spinal cord injury. Genomics 2020; 112:3315-3321. [PMID: 32535070 DOI: 10.1016/j.ygeno.2020.06.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/22/2022]
Abstract
AIM The objective of this study is to examine the alterations in the levels of expression of serum lncRNA-TSIX, TP53INP2 mRNA, miRNA-1283 in spinal cord injured (SCI) patients versus healthy control. METHOD The expression of the selected RNAs in the sera was determined in 23 patients suffering from acute spinal cord injury, 41 individuals with chronic spinal cord injury, and 36 healthy control using real-time reverse-transcription polymerase chain reaction method. RESULTS The results showed that lncRNA-TSIX and the TP53INP2 mRNA expression levels in SCI patients was overexpressed in comparison to the control group alongside with a significant downregulation of miR-1283. Statistically,there was a highly significant positive correlation between lnc-RNA-TRIX and TP53INP2 mRNA with inverse correlation between miRNA-1283 and lnc-RNA-TRIX based on fold changes. CONCLUSION Up-regulation of lncRNA-TSIX, TP53INP2 mRNA with downregulation of miRNA-1283 might be closely associated with progression of SCI.
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Affiliation(s)
| | - Marwa Matboli
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Hanaa El-Tayeb Nasser
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | | | - Mohamed Farid El-Asmer
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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23
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Cai P, Otten ABC, Cheng B, Ishii MA, Zhang W, Huang B, Qu K, Sun BK. A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis. Genome Res 2019; 30:22-34. [PMID: 31804951 PMCID: PMC6961571 DOI: 10.1101/gr.251561.119] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies indicate that many disease susceptibility regions reside in non-protein-coding regions of the genome. Long noncoding RNAs (lncRNAs) are a major component of the noncoding genome, but their biological impacts are not fully understood. Here, we performed a CRISPR interference (CRISPRi) screen on 2263 epidermis-expressed lncRNAs and identified nine novel candidate lncRNAs regulating keratinocyte proliferation. We further characterized a top hit from the screen, progenitor renewal associated non-coding RNA (PRANCR), using RNA interference–mediated knockdown and phenotypic analysis in organotypic human tissue. PRANCR regulates keratinocyte proliferation, cell cycle progression, and clonogenicity. PRANCR-deficient epidermis displayed impaired stratification with reduced expression of differentiation genes that are altered in human skin diseases, including keratins 1 and 10, filaggrin, and loricrin. Transcriptome analysis showed that PRANCR controls the expression of 1136 genes, with strong enrichment for late cell cycle genes containing a CHR promoter element. In addition, PRANCR depletion led to increased levels of both total and nuclear CDKN1A (also known as p21), which is known to govern both keratinocyte proliferation and differentiation. Collectively, these data show that PRANCR is a novel lncRNA regulating epidermal homeostasis and identify other lncRNA candidates that may have roles in this process as well.
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Affiliation(s)
- Pengfei Cai
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Auke B C Otten
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Binbin Cheng
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Mitsuhiro A Ishii
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
| | - Wen Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Beibei Huang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Kun Qu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.,CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Bryan K Sun
- Department of Dermatology, University of California-San Diego, La Jolla, California 92109, USA
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24
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Matboli M, Shafei AE, Agwa SHA, Elzahy SS, Anwar AK, Mansour AR, Gaber AI, Said AEA, Lwis P, Hamdy M. Identification of Novel Molecular Network Expression in Acute Myocardial Infarction. Curr Genomics 2019; 20:340-348. [PMID: 32476991 PMCID: PMC7235391 DOI: 10.2174/1389202920666190820142043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
Background: In the current study, we aimed to analyze the hypothesis that human myocardial-specific extracellular RNAs expression could be used for acute myocardial injury(AMI) diagnosis. Methodology: We used bioinformatics’ analysis to identify RNAs linked to ubiquitin system and specific to AMI, named, (lncRNA-RP11-175K6.1), (LOC101927740), microRNA-106b-5p (miR-106b-5p) and Anaphase, promoting complex 11 (ANapc11mRNA). We measured the serum expression of the chosen RNAs in 69 individuals with acute coronary syndromes, 31 individuals with angina pectoris without MI and non-cardiac chest pain and 31 healthy control individuals by real-time reverse-transcription PCR. Results: Our study revealed a significant decrease in both lncRNA-RP11-175K6.1 and ANapc11mRNA expression of in the sera samples of AMI patients compared to that of the two control groups alongside with significant upregulation of miR-106b-5p. Conclusion: Of note, the investigated serum RNAs decrease the false discovery rate of AMI to 3.2%.
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Affiliation(s)
- Marwa Matboli
- Medicinal Biochemistry and Molecular Biology Department, Ain Shams University, Faculty of Medicine, Cairo, Egypt
| | - Ayman E Shafei
- Biomedical Research Department, Military Medical Academy, Cairo, Egypt.,Biomedical Research Department, Faculty of Medicine, Modern University for Technology and Information, Cairo, Egypt
| | - Sara H A Agwa
- Clinical Pathology, Medical Ain Shams Research Institute (MASRI), Cairo, Egypt
| | - Sherif Sammir Elzahy
- Cardiovascular Medicine Department, Ain Shams University, Faculty of Medicine, Cairo, Egypt
| | | | | | | | | | - Paula Lwis
- Armed Forces College of Medicine, Cairo, Egypt
| | - Marwa Hamdy
- Medicinal Biochemistry and Molecular Biology Department, Ain Shams University, Faculty of Medicine, Cairo, Egypt
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25
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Smolander J, Stupnikov A, Glazko G, Dehmer M, Emmert-Streib F. Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients. BMC Cancer 2019; 19:1176. [PMID: 31796020 PMCID: PMC6892207 DOI: 10.1186/s12885-019-6338-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to be functional in part. Yet the importance of these RNAs especially for higher biological functions remains under investigation. METHODS In this paper, we analyze RNA-seq data, including non-coding and protein coding RNAs, from lung adenocarcinoma patients, a histologic subtype of non-small-cell lung cancer, with deep learning neural networks and other state-of-the-art classification methods. The purpose of our paper is three-fold. First, we compare the classification performance of different versions of deep belief networks with SVMs, decision trees and random forests. Second, we compare the classification capabilities of protein coding and non-coding RNAs. Third, we study the influence of feature selection on the classification performance. RESULTS As a result, we find that deep belief networks perform at least competitively to other state-of-the-art classifiers. Second, data from non-coding RNAs perform better than coding RNAs across a number of different classification methods. This demonstrates the equivalence of predictive information as captured by non-coding RNAs compared to protein coding RNAs, conventionally used in computational diagnostics tasks. Third, we find that feature selection has in general a negative effect on the classification performance which means that unfiltered data with all features give the best classification results. CONCLUSIONS Our study is the first to use ncRNAs beyond miRNAs for the computational classification of cancer and for performing a direct comparison of the classification capabilities of protein coding RNAs and non-coding RNAs.
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Affiliation(s)
- Johannes Smolander
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Alexey Stupnikov
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, USA
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Matthias Dehmer
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Steyr, Austria
- Department of Mechatronics and Biomedical Computer Science, UMIT, Hall in Tyrol, Austria
- College of Artificial Intelligence, Nankai University, China, Tianjin, China
| | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
- Institute of Biosciences and Medical Technology, Tampere, Finland
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26
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Chatterjee M, Dass J. FP, Sengupta S. Nuclear stress bodies: Interaction of its components in oncogenic regulation. J Cell Biochem 2019; 120:14700-14710. [DOI: 10.1002/jcb.28731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
| | - Febin Prabhu Dass J.
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
| | - Sonali Sengupta
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
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27
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Song W, Gu Y, Lu S, Wu H, Cheng Z, Hu J, Qian Y, Zheng Y, Fan H. LncRNA TRERNA1 facilitates hepatocellular carcinoma metastasis by dimethylating H3K9 in the CDH1 promoter region via the recruitment of the EHMT2/SNAI1 complex. Cell Prolif 2019; 52:e12621. [PMID: 31012192 PMCID: PMC6668973 DOI: 10.1111/cpr.12621] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Objectives Long non‐coding RNAs (LncRNAs) play an important role in hepatocellular carcinoma development, however, as a crucial driver of hepatocellular carcinoma (HCC) metastasis, their functions in tumour metastasis remain largely unknown. Materials and methods The lncRNA TRERNA1 expression levels were detected in HCC by quantitative real‐time PCR (qPCR). The function of TRERNA1 was examined by wound‐healing assays, transwell assays and tail vein injection experiments. The potential regulatory mechanisms of TRERNA1 on its target genes were explored by ChIP, RIP, IP and WB assays. Results Elevated TRERNA1 levels promoted HCC cell migration and invasion in vitro and in vivo. TRERNA1 recruited EHMT2 to dimethylate H3K9 in the CDH1 promoter region. Furthermore, EHMT2 bound to SNAI1 to suppress CDH1 expression in HCC cells. After inhibiting TRERNA1, the expression level of CDH1 was restored and was involved in the regulation of the EHMT2/SNAI1 complex. The level of TRERNA1 was positively correlated with tumour metastasis and was negatively correlated with the expression of CDH1 in HCC tissues. Conclusions For the first time, the current study reveals that TRERNA1 promotes cell metastasis and the invasion of HCC via the recruitment of EHMT2 and/or the EHMT2/SNAI1 complex to suppress CDH1. These data identify a novel mechanism that regulates TRERNA1 in metastatic HCC and provides a potential targeted therapy for HCC patients.
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Affiliation(s)
- Wei Song
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.,School of Life Science, Southeast University, Nanjing, China
| | - Yuejun Gu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.,School of Life Science, Southeast University, Nanjing, China
| | - Sen Lu
- The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huazhang Wu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.,School of Life Science, Southeast University, Nanjing, China
| | - Zhenxing Cheng
- Department of Pathophysiology, Medical School of Southeast University, Nanjing, China
| | - Jiaojiao Hu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.,School of Life Science, Southeast University, Nanjing, China
| | - Yanyan Qian
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Ying Zheng
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.,School of Life Science, Southeast University, Nanjing, China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
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RNA-Sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Prefrontal Cortex of Mice Following Repeated Social Defeat Stress. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7505260. [PMID: 31032362 PMCID: PMC6457290 DOI: 10.1155/2019/7505260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/01/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Background Repeated or continuous chronic psychological stress may induce diverse neuropsychiatric disorders; however, the underlying mechanisms remain unclear. In this study, we explored the expression profiles of long noncoding RNAs (lncRNAs) and mRNAs, along with their biological function and regulatory network, in mice after repeated social defeat (RSD) stress to explore their potential involvement in the development of anxiety-like behaviors. Main Methods RNA-sequencing was used to screen all differentially expressed (DE) lncRNAs and mRNAs between the RSD and control groups. Quantitative real-time polymerase chain reaction (qRT-PCR) was used for confirmation of the RNA-sequencing results. The function of DE lncRNAs was predicted by Gene Ontology (GO) enrichment and pathway analyses of target mRNAs. In addition, the functional regulatory network of the target mRNAs was constructed to reveal potential relationships between lncRNAs and their target genes with bioinformatics approaches. Key Findings In mice experiencing RSD, 373 and 454 lncRNAs, along with 1142 and 654, mRNAs were significantly upregulated and downregulated, respectively. The detailed regulatory network included 126 eligible lncRNA-mRNA pairs. Among them, 14 genes such as Arhgef1, Chchd2, Fam107a, Dlg1, Nova2, Dpf1, and Shank3 involved in neurite growth, neural development, and synaptic plasticity were direct targets of the DE lncRNAs. qRT-PCR of four of the DE lncRNAs and mRNAs confirmed the reliability of RNA-sequencing. GO clustering analyses showed that the top enriched biological process, cellular component, and molecular function terms were synaptic transmission, neuron spine, and glutamate receptor binding, respectively. Further, the top three significant enriched pathways were synaptic adhesion-like molecule (SALM) protein interactions at the synapses, trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, as well as glutamate binding, activation of AMPA receptors, and synaptic plasticity. Significance Hundreds of lncRNAs and mRNAs are dysregulated after RSD, and many of these lncRNAs might participate in the development of anxiety-like behaviors via multiple complex mechanisms such as target regulation. Available informatics evidence highlighted the likely role of synapse dysfunction and abnormal synaptic neurotransmission in these behaviors. Thus, our findings provide potential candidate biomarkers or intervention targets for chronic psychological stress-induced neuropsychiatric disorders.
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29
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Long non-coding RNA MALAT1 regulates cardiomyocytes apoptosis after hypoxia/reperfusion injury via modulating miR-200a-3p/PDCD4 axis. Biomed Pharmacother 2019; 111:1036-1045. [DOI: 10.1016/j.biopha.2018.12.122] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/29/2018] [Accepted: 12/30/2018] [Indexed: 12/12/2022] Open
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30
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Cardoso C, Serafim RB, Kawakami A, Gonçalves Pereira C, Vazquez VL, Valente V, Fisher DE, Espreafico EM. The lncRNA RMEL3 protects immortalized cells from serum withdrawal-induced growth arrest and promotes melanoma cell proliferation and tumor growth. Pigment Cell Melanoma Res 2019; 32:303-314. [PMID: 30457212 PMCID: PMC6613776 DOI: 10.1111/pcmr.12751] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
RMEL3 is a recently identified lncRNA associated with BRAFV600E mutation and melanoma cell survival. Here, we demonstrate strong and moderate RMEL3 upregulation in BRAF and NRAS mutant melanoma cells, respectively, compared to melanocytes. High expression is also more frequent in cutaneous than in acral/mucosal melanomas, and analysis of an ICGC melanoma dataset showed that mutations in RMEL3 locus are preponderantly C > T substitutions at dipyrimidine sites including CC > TT, typical of UV signature. RMEL3 mutation does not correlate with RMEL3 levels, but does with poor patient survival, in TCGA melanoma dataset. Accordingly, RMEL3 lncRNA levels were significantly reduced in BRAFV600E melanoma cells upon treatment with BRAF or MEK inhibitors, supporting the notion that BRAF-MEK-ERK pathway plays a role to activate RMEL3 gene transcription. RMEL3 overexpression, in immortalized fibroblasts and melanoma cells, increased proliferation and survival under serum starvation, clonogenic ability, and xenografted melanoma tumor growth. Although future studies will be needed to elucidate the mechanistic activities of RMEL3, our data demonstrate that its overexpression bypasses the need of mitogen activation to sustain proliferation/survival of non-transformed cells and suggest an oncogenic role for RMEL3.
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Affiliation(s)
- Cibele Cardoso
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rodolfo B. Serafim
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristiano Gonçalves Pereira
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Vinicius L. Vazquez
- Molecular Oncology Research Center (CPOM) and Melanoma/sarcoma Surgery Department, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Valeria Valente
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, SP, 14800-903, Brazil; Center for Cell-Based Therapy CEPID/FAPESP, Ribeirão Preto, Brazil
| | - David E. Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Enilza M. Espreafico
- Department of Cell and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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31
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Zhang J, Liang Y, Huang X, Guo X, Liu Y, Zhong J, Yuan J. STAT3-induced upregulation of lncRNA MEG3 regulates the growth of cardiac hypertrophy through miR-361-5p/HDAC9 axis. Sci Rep 2019; 9:460. [PMID: 30679521 PMCID: PMC6346020 DOI: 10.1038/s41598-018-36369-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/19/2018] [Indexed: 02/02/2023] Open
Abstract
Cardiac hypertrophy is closely correlated with diverse cardiovascular diseases, augmenting the risk of heart failure and sudden death. Long non-coding RNAs (lncRNAs) have been studied in cardiac hypertrophy for their regulatory function. LncRNA MEG3 has been reported in human cancers. Whereas, it is unknown whether MEG3 regulates the growth of cardiac hypertrophy. Therefore, this study aims to investigate the specific role of MEG3 in the progression of cardiac hypertrophy. Here, we found that MEG3 contributed to the pathogenesis of cardiac hypertrophy. MEG3 expression was remarkably strengthened in the mice heart which undergone the transverse aortic constriction (TAC). Moreover, qRT-PCR analysis revealed that MEG3 was upregulated in the cardiomyocytes which were treated with Ang-II. Silenced MEG3 inhibited the increasing size of hypertrophic cardiomyocytes and reversed other hypertrophic responses. Mechanically, MEG3 could affect cardiac hypertrophy by regulating gene expression. Mechanically, we found that MEG3 could be upregulated by the transcription factor STAT3 and could regulate miR-361-5p and HDAC9 by acting as a ceRNA. Finally, rescue assays were made to do further confirmation. All our findings revealed that STAT3-inducetd upregulation of lncRNA MEG3 controls cardiac hypertrophy by regulating miR-362-5p/HDAC9 axis.
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Affiliation(s)
- Jingchang Zhang
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
| | - Yi Liang
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China.
| | - Xuecheng Huang
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
| | - Xiaoyan Guo
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
| | - Yang Liu
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
| | - Jiming Zhong
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
| | - Jielin Yuan
- Department of Cardiology, The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530031, China
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32
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Wu Z, Liang S, Kuai W, Hu L, Qian A. MicroRNAs and long noncoding RNAs: new regulators in cell fate determination of mesenchymal stem cells. RSC Adv 2019; 9:37300-37311. [PMID: 35542270 PMCID: PMC9075730 DOI: 10.1039/c9ra06563f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells that are able to differentiate into numerous cell types, including well-known inherent osteoblasts, adipocytes, and chondrocytes, and other cell types, such as hepatocytes, cardiomyocytes and nerve cells. They have become a favorite source of cell-based therapy. Therefore, knowing the mechanism that determines the cell fate of MSCs is important not only for deep understanding of the MSC function but also for the manipulation of MSCs for clinical application. Recently, studies have demonstrated that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two best studied noncoding RNAs, show key roles in cell fate determination of MSCs by functioning as vital regulators of their target gene expression or signaling transduction. Here, we summarize the characteristics of miRNAs and lncRNAs, and review the recent advances proving their profound involvement in determining the cell fate of MSCs to inherent osteoblast, adipocyte, and chondrocyte cells, and to several key cell types including hepatocytes, cardiomyocytes and nerve cells. This will provide researchers with a deep understanding of the role of miRNAs and lncRNAs in MSCs and provide guidance for future research. The recent advances of miRNAs and lncRNAs in determining the cell fate of MSCs.![]()
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Affiliation(s)
- Zixiang Wu
- Laboratory for Bone Metabolism
- Key Laboratory for Space Biosciences and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Shujing Liang
- Laboratory for Bone Metabolism
- Key Laboratory for Space Biosciences and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Wenyu Kuai
- Laboratory for Bone Metabolism
- Key Laboratory for Space Biosciences and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Lifang Hu
- Laboratory for Bone Metabolism
- Key Laboratory for Space Biosciences and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
| | - Airong Qian
- Laboratory for Bone Metabolism
- Key Laboratory for Space Biosciences and Biotechnology
- School of Life Sciences
- Northwestern Polytechnical University
- Xi'an 710072
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33
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Huang L, Dong H, Zhou D, Li M, Liu Y, Zhang F, Feng Y, Yu D, Lin S, Cao J. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:203-222. [PMID: 29975432 DOI: 10.1111/tpj.14016] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/18/2018] [Accepted: 06/26/2018] [Indexed: 05/21/2023]
Abstract
The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs expressed during pollen development and fertilization has been elusive. We performed a time series of RNA-seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12 051 putative lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.
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Affiliation(s)
- Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Ming Li
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yanhong Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Fang Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yaoyao Feng
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
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34
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The Bipartite Network Projection-Recommended Algorithm for Predicting Long Non-coding RNA-Protein Interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:464-471. [PMID: 30388620 PMCID: PMC6205413 DOI: 10.1016/j.omtn.2018.09.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 01/23/2023]
Abstract
With the development of science and biotechnology, many evidences show that ncRNAs play an important role in the development of important biological processes, especially in chromatin modification, cell differentiation and proliferation, RNA progressing, human diseases, etc. Moreover, lncRNAs account for the majority of ncRNAs, and the functions of lncRNAs are expressed by the related RNA-binding proteins. It is well known that the experimental verification of lncRNA-protein relationships is a waste of time and expensive. So many time-saving and inexpensive computational methods are proposed to uncover potential lncRNA-protein interactions. In this work, we propose a novel computational method to predict the potential lncRNA-protein interactions with the bipartite network projection recommended algorithm (LPI-BNPRA). Our approach is a semi-supervised method based on the lncRNA similarity matrix, protein similarity matrix, and lncRNA-protein interaction matrix. Compared with three previous methods under the leave-one-out cross-validation, our model has a more high-confidence result with the AUC value of 0.8754 and the AUPR value of 0.6283. We also do case studies by the Mus musculus dataset to further reflect the reliability of our approach. This suggests that LPI-BNPRA will be a reliable computational method to uncover lncRNA-protein interactions in biomedical research.
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35
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Liu JX, Li W, Li JT, Liu F, Zhou L. Screening key long non-coding RNAs in early-stage colon adenocarcinoma by RNA-sequencing. Epigenomics 2018; 10:1215-1228. [PMID: 30182733 DOI: 10.2217/epi-2017-0155] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We aim to identify the key long noncoding RNAs (lncRNAs) in early-stage colon adenocarcinoma (COAD). PATIENTS & METHODS Compared with colonic intraepithelial neoplasia, differentially expressed lncRNAs (DElncRNAs) in early-stage COAD were obtained by RNA-sequencing. Our previous work has obtained the differentially expressed mRNAs and miRNAs (DEmRNAs and DEmiRNAs) in early-stage COAD. DEmiRNA-DElncRNA-DEmRNA interaction analysis and functional annotation were performed. Validation of expression and receiver-operating characteristic analyses were performed based on The Cancer Genome Atlas. RESULTS Seventy-nine significantly DElncRNAs in early-stage COAD were obtained. MiR-153-3p-TUG1-DAPK1/ARNT2/KLK3/PLD1/SMAD2 and miR-153-3p-SNHG17-COL11A1/IGFBP3/KLF6 interactions were associated with early-stage COAD. Five DElncRNAs (ELFN1-AS1, LINC01234, SNHG17, UCA1 and LOC101929549) involved in early-stage COAD with potential diagnostic value. CONCLUSION LncRNAs involve in early-stage COAD by interaction with COAD-regulated genes and miRNAs.
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Affiliation(s)
- Ji-Xi Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Wen Li
- Department of Surgical ICU, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Jing-Tao Li
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Fang Liu
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Lei Zhou
- Department of General Surgery, China-Japan Friendship Hospital, Beijing 100029, PR China
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36
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Pan L, Liu D, Zhao L, Wang L, Xin M, Li X. Retracted
: Long noncoding RNA MALAT1 alleviates lipopolysaccharide‐induced inflammatory injury by upregulating microRNA‐19b in murine chondrogenic ATDC5 cells. J Cell Biochem 2018; 119:10165-10175. [DOI: 10.1002/jcb.27357] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Lin Pan
- Department of Rheumatology Qilu Hospital of Shandong University Jinan China
- Department of Rheumatology and Clinical Immunology The Affiliated Hospital of Qingdao University Qingdao China
| | - Deheng Liu
- Department of Hand and Foot Surgery Qilu Hospital of Shandong University (Qingdao) Qingdao China
| | - Lei Zhao
- Department of Rheumatology and Clinical Immunology The Affiliated Hospital of Qingdao University Qingdao China
| | - Liqin Wang
- Department of Rheumatology and Clinical Immunology The Affiliated Hospital of Qingdao University Qingdao China
| | - Miaomiao Xin
- Department of Rheumatology and Clinical Immunology The Affiliated Hospital of Qingdao University Qingdao China
| | - Xingfu Li
- Department of Rheumatology Qilu Hospital of Shandong University Jinan China
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37
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Liu G, Zhang W. Long non-coding RNA HOTAIR promotes UVB-induced apoptosis and inflammatory injury by up-regulation of PKR in keratinocytes. ACTA ACUST UNITED AC 2018; 51:e6896. [PMID: 29898032 PMCID: PMC6002131 DOI: 10.1590/1414-431x20186896] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 04/09/2018] [Indexed: 12/14/2022]
Abstract
Excessive exposure to ultraviolet (UV) rays can cause damage of the skin and may
induce cancer, immunosuppression, photoaging, and inflammation. The long
non-coding RNA (lncRNA) HOX antisense intergenic RNA (HOTAIR) is involved in
multiple human biological processes. However, its role in UVB-induced
keratinocyte injury is unclear. This study was performed to investigate the
effects of HOTAIR in UVB-induced apoptosis and inflammatory injury in human
keratinocytes (HaCaT cells). Quantitative real-time polymerase chain reaction
was performed to analyze the expression levels of HOTAIR, PKR, TNF-α, and IL-6.
Cell viability was measured using trypan blue exclusion method and cell
apoptosis using flow cytometry and western blot. ELISA was used to measure the
concentrations of TNF-α and IL-6. Western blot was used to measure the
expression of PKR, apoptosis-related proteins, and PI3K/AKT and NF-κB pathway
proteins. UVB induced HaCaT cell injury by inhibiting cell viability and
promoting cell apoptosis and expressions of IL-6 and TNF-α. UVB also promoted
the expression of HOTAIR. HOTAIR suppression increased cell viability and
decreased apoptosis and expression of inflammatory factors in UVB-treated cells.
HOTAIR also promoted the expression of PKR. Overexpression of HOTAIR decreased
cell viability and increased cell apoptosis and expression of inflammatory
factors in UVB-treated cells by upregulating PKR. Overexpression of PKR
decreased cell viability and promoted cell apoptosis in UVB-treated cells.
Overexpression of PKR activated PI3K/AKT and NF-κB pathways. Our findings
identified an essential role of HOTAIR in promoting UVB-induced apoptosis and
inflammatory injury by up-regulating PKR in keratinocytes.
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Affiliation(s)
- Guo Liu
- Department of Burns and Plastic Surgery, Jining No.1 People's Hospital, Jining, Shandong, China
| | - Wenhao Zhang
- Department of Burns and Plastic Surgery, Jining No.1 People's Hospital, Jining, Shandong, China
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38
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Zhao J, Zhang C, Gao Z, Wu H, Gu R, Jiang R. Long non-coding RNA ASBEL promotes osteosarcoma cell proliferation, migration, and invasion by regulating microRNA-21. J Cell Biochem 2018; 119:6461-6469. [PMID: 29323740 DOI: 10.1002/jcb.26671] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/09/2018] [Indexed: 12/11/2022]
Abstract
Osteosarcoma is the most common malignant bone tumor in children and adolescents with high rate of incidence, high frequency of recurrence, and high degree of metastasis. This study aimed to investigate the effects of long noncoding RNA antisense ncRNA in the abundant in neuroepithelium area (ANA)/B-cell translocation gene 3 (BTG3) locus (lncRNA ASBEL) on the pathogenesis of osteosarcoma. The expression levels of ASBEL in human osteoblast cells and human osteosarcoma cells were evaluated using qRT-PCR. Effects of ASBEL knockdown on cell viability, migration, and invasion were detected using trypan blue exclusion assay, cell migration, and cell invasion assay, respectively. The regulatory effects of ASBEL on microRNA-21 (miR-21) were analyzed using qRT-PCR. The roles of miR-21 and protein phosphatase 2A (PP2A), the possible downstream factor of miR-21, in osteosarcoma cell proliferation, migration, and invasion were also explored. The results showed that ASBEL was highly expressed in osteosarcoma cells. Knockdown of ASBEL inhibited osteosarcoma cell viability, migration, and invasion, as well as the expression level of miR-21. PP2A was a direct target of miR-21, which participated in the effects of ASBEL and miR-21 on the activation of phosphatidylinositol 3-kinase/protein kinase 3/glycogen synthase kinase-3β (PI3K/AKT/GSK3β) and mitogen-activated protein kinase/extracellular regulated protein kinase (MEK/ERK) signaling pathways as well as the enhancement of osteosarcoma cell proliferation, migration, and invasion. In conclusion, we verified that ASBEL-miR-21-PP2A pathway might play critical regulatory effects on the pathogenesis of osteosarcoma and could be as the potential therapeutic target and biomarker for osteosarcoma treatment.
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Affiliation(s)
- Jianhui Zhao
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Chao Zhang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Zhongli Gao
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Han Wu
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Rui Gu
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Rui Jiang
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
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39
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Hu X, Liu J, Zhao G, Zheng J, Qin X. Retracted
: Long non‐coding RNA GAS5 aggravates hypoxia injury in PC‐12 cells via down‐regulating miR‐124. J Cell Biochem 2018; 119:6765-6774. [DOI: 10.1002/jcb.26870] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/21/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Xiaoli Hu
- Department of Rehabilitation MedicinePeople's Hospital of RizhaoRizhaoShandongChina
| | - Juan Liu
- Department of NeurologyPeople's Hospital of RizhaoRizhaoShandongChina
| | - Gang Zhao
- Department of Rehabilitation MedicinePeople's Hospital of RizhaoRizhaoShandongChina
| | - Jiaping Zheng
- Department of NeurologyPeople's Hospital of RizhaoRizhaoShandongChina
| | - Xia Qin
- Department of NeurologyPeople's Hospital of RizhaoRizhaoShandongChina
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40
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Zhou G, Li C, Feng J, Zhang J, Fang Y. lncRNA UCA1 Is a Novel Regulator in Cardiomyocyte Hypertrophy through Targeting the miR-184/HOXA9 Axis. Cardiorenal Med 2018; 8:130-139. [PMID: 29616999 DOI: 10.1159/000487204] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/24/2018] [Indexed: 01/12/2023] Open
Abstract
Cardiac hypertrophy is closely associated with a series of cardiovascular diseases, including heart failure and sudden death in particular. An in-depth comprehension of the pathogenesis of cardiac hypertrophy will improve the diagnosis and therapy of cardiac hypertrophy. It has been acknowledged that long noncoding RNAs/microRNAs (lncRNAs/miRNAs) are crucial regulators in diverse biological processes, including various cardiovascular diseases, in multiple manners. Nevertheless, the biological roles of lncRNA UCA1 and miR-184 in cardiac hypertrophy are scarcely reported. In this paper, qRT-PCR analysis exhibited that lncRNA UCA1 was highly expressed in mice heart treated with transverse aortic constriction (TAC) and the cardiomyocytes treated with phenylephrine (PE). On the contrary, miR-184 was downregulated under the same conditions. In addition, it was deduced that lncRNA UCA1 was reversely related with miR-184 in PE-triggered hypertrophic cardiomyocytes, confirmed by the Spearman correlation analysis. The knockdown of UCA1 or the overexpression of miR-184 lessened the enlarged surface area of cardiomyocytes and the elevated expressions of fetal genes (ANP and BNP) induced by PE. Later, it was determined that miR-184 was a direct target of UCA1, whereas the mRNA HOXA9 was a target of miR-184. Rescue assays indicated that UCA1 promoted the progression of cardiac hypertrophy through competitively binding with miR-184 to enhance the expression of HOXA9.
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MESH Headings
- Animals
- Blotting, Western
- Cardiomyopathy, Hypertrophic/genetics
- Cardiomyopathy, Hypertrophic/metabolism
- Cardiomyopathy, Hypertrophic/pathology
- Cells, Cultured
- Disease Models, Animal
- Gene Expression Regulation
- Homeodomain Proteins/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- MicroRNAs/metabolism
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- RNA, Long Noncoding/biosynthesis
- RNA, Long Noncoding/genetics
- Real-Time Polymerase Chain Reaction
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41
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Huanca-Mamani W, Arias-Carrasco R, Cárdenas-Ninasivincha S, Rojas-Herrera M, Sepúlveda-Hermosilla G, Caris-Maldonado JC, Bastías E, Maracaja-Coutinho V. Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert. Genes (Basel) 2018; 9:genes9030170. [PMID: 29558449 PMCID: PMC5867891 DOI: 10.3390/genes9030170] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been defined as transcripts longer than 200 nucleotides, which lack significant protein coding potential and possess critical roles in diverse cellular processes. Long non-coding RNAs have recently been functionally characterized in plant stress-response mechanisms. In the present study, we perform a comprehensive identification of lncRNAs in response to combined stress induced by salinity and excess of boron in the Lluteño maize, a tolerant maize landrace from Atacama Desert, Chile. We use deep RNA sequencing to identify a set of 48,345 different lncRNAs, of which 28,012 (58.1%) are conserved with other maize (B73, Mo17 or Palomero), with the remaining 41.9% belonging to potentially Lluteño exclusive lncRNA transcripts. According to B73 maize reference genome sequence, most Lluteño lncRNAs correspond to intergenic transcripts. Interestingly, Lluteño lncRNAs presents an unusual overall higher expression compared to protein coding genes under exposure to stressed conditions. In total, we identified 1710 putatively responsive to the combined stressed conditions of salt and boron exposure. We also identified a set of 848 stress responsive potential trans natural antisense transcripts (trans-NAT) lncRNAs, which seems to be regulating genes associated with regulation of transcription, response to stress, response to abiotic stimulus and participating of the nicotianamine metabolic process. Reverse transcription-quantitative PCR (RT-qPCR) experiments were performed in a subset of lncRNAs, validating their existence and expression patterns. Our results suggest that a diverse set of maize lncRNAs from leaves and roots is responsive to combined salt and boron stress, being the first effort to identify lncRNAs from a maize landrace adapted to extreme conditions such as the Atacama Desert. The information generated is a starting point to understand the genomic adaptabilities suffered by this maize to surpass this extremely stressed environment.
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Affiliation(s)
- Wilson Huanca-Mamani
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
| | - Raúl Arias-Carrasco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
| | | | - Marcelo Rojas-Herrera
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
| | | | - José Carlos Caris-Maldonado
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
- Departamento de Bioquímica y Biologia Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile.
| | - Elizabeth Bastías
- Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile.
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
- Departamento de Bioquímica y Biologia Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile.
- Instituto Vandique, João Pessoa 58000-000, Brazil.
- Beagle Bioinformatics, Santiago 7500554, Chile.
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42
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Abstract
Significant advancements have been made in unraveling and understanding the non-coding elements of the human genome. New insights into the structure and function of noncoding RNAs have emerged. Their relevance in the context of both physiological cellular homeostasis and human diseases is getting appreciated. As a result, exploration of noncoding RNAs, in particular microRNAs (miRs), as therapeutic agents or targets of therapeutic strategies is under way. This review summarizes and discusses in depth the current literature on the role of miRs in neurodegenerative diseases.
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Affiliation(s)
- Salil Sharma
- Department of Psychological and Brain Sciences, The Linda and Jack Gill Center for Bimolecular Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Hui-Chen Lu
- Department of Psychological and Brain Sciences, The Linda and Jack Gill Center for Bimolecular Sciences, Indiana University, Bloomington, IN 47405, USA
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43
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Li Y, Wang J, Sun L, Zhu S. RETRACTED: LncRNA myocardial infarction-associated transcript (MIAT) contributed to cardiac hypertrophy by regulating TLR4 via miR-93. Eur J Pharmacol 2018; 818:508-517. [PMID: 29157986 DOI: 10.1016/j.ejphar.2017.11.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief after concerns were raised about the article on PubPeer (https://pubpeer.com/publications/88E67BAC524E92069B2AA3474D2BB8?utm_source=Chrome&utm_medium=BrowserExtension&utm_campaign=Chrome). In addition the editor found more issues in some Western Blot figures. 1. Bands of figure 1C ANF 30min , 60min, 12h, 24h are identical to those in Fig 4C ANF control, AngII, AngII+si-NC and AngII+si-MAT 2. Beta-actin bands of Fig 1C are identical to those in Fig 4C, but blots represent different experimental conditions/samples. 3. Bands in Fig 6 D AngII and AngII+mir-NC show similarities with these of AngII+mir-93 and AngII+mir93+vector (band shapes and irregularities appear identical) After several attempts to reach out to the corresponding author, no response was provided. The manipulation of images casts doubts on all the data, and accordingly also the conclusions based on that data, in this publication. As such this article represents a severe abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.
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Affiliation(s)
- Yunwei Li
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China.
| | - Juan Wang
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
| | - Lili Sun
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
| | - Shengnan Zhu
- Department of Cardiology, Huaihe Hospital of Henan University, Kaifeng 475000, China
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44
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He Q, Liu Y, Sun W. Statistical analysis of non-coding RNA data. Cancer Lett 2018; 417:161-167. [PMID: 29306017 DOI: 10.1016/j.canlet.2017.12.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
With rapid progress in high-throughput genome technology, the study of noncoding RNA has arisen as a highly popular topic in biomedical research. Noncoding RNA plays fundamental roles in cell proliferation, cell differentiation and epigenetic regulation, and the study of noncoding RNA will yield novel insights into gene regulation and provide new clues for disease treatment. However, due to the large volume and diverse functions of noncoding RNAs, the analysis of these RNAs has proved to be a challenging task. In this review, we review the commonly used computational tools for the identification of noncoding RNAs, and discuss popular statistical tools for their analysis. Due to the large body of noncoding RNA classes, we focus on the analysis of microRNA and long noncoding RNA, two of the most widely studied classes of noncoding RNAs. Specific examples are provided to show the context of the analysis. This review aims to provide up-to-date information on existing tools and methods for identifying and analyzing noncoding RNA.
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Affiliation(s)
- Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Yang Liu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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45
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Song C, Zhang J, Liu Y, Pan H, Qi HP, Cao YG, Zhao JM, Li S, Guo J, Sun HL, Li CQ. Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy. Oncotarget 2017; 7:10827-40. [PMID: 26872060 PMCID: PMC4905442 DOI: 10.18632/oncotarget.7312] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/28/2016] [Indexed: 01/08/2023] Open
Abstract
Cardiac hypertrophy (CH) could increase cardiac after-load and lead to heart failure. Recent studies have suggested that long non-coding RNA (lncRNA) played a crucial role in the process of the cardiac hypertrophy, such as Mhrt, TERMINATOR. Some studies have further found a new interacting mechanism, competitive endogenous RNA (ceRNA), of which lncRNA could interact with micro-RNAs (miRNA) and indirectly interact with mRNAs through competing interactions. However, the mechanism of ceRNA regulated by lncRNA in the CH remained unclear. In our study, we generated a global triple network containing mRNA, miRNA and lncRNA, and extracted a CH related lncRNA-mRNA network (CHLMN) through integrating the data from starbase, miRanda database and gene expression profile. Based on the ceRNA mechanism, we analyzed the characters of CHLMN and found that 3 lncRNAs (SLC26A4-AS1, RP11-344E13.3 and MAGI1-IT1) were high related to CH. We further performed cluster module analysis and random walk with restart for the CHLMN, finally 14 lncRNAs had been discovered as the potential CH related disease genes. Our results showed that lncRNA played an important role in the CH and could shed new light to the understanding underlying mechanisms of the CH.
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Affiliation(s)
- Chao Song
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Yan Liu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hao Pan
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Han-Ping Qi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yong-Gang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian-Mei Zhao
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Shang Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Jing Guo
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hong-Li Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Chun-Quan Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
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46
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Zhou J, Fan Y, Chen H. Analyses of long non-coding RNA and mRNA profiles in the spinal cord of rats using RNA sequencing during the progression of neuropathic pain in an SNI model. RNA Biol 2017; 14:1810-1826. [PMID: 28854101 DOI: 10.1080/15476286.2017.1371400] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The pathogenesis of neuropathic pain (NP) is characterized by an increased responsiveness of nociceptive neurons in the nervous system. However, the molecular mechanisms underpinning the NP still remain elusive. Recent data suggest that long non-coding RNAs (lncRNAs) regulate expression of NP-associated genes. Herein, we analyzed lncRNAs and mRNA profiles in the spinal cord of rats by RNA sequencing during the progression of NP in a spared nerve injury (SNI) model. Sprague-Dawley (SD) rats were employed for the establishment of the SNI models, and nociceptive responses to mechanical and thermal stimuli were measured 3 hours prior to surgery and on postoperative days 1, 3, 7 and 14, with L4-5 spinal cords extracted from three SD rats under deep anesthesia at each time point after behavioral test. SNI rats exhibited higher sensitivity to mechanical stimuli from days 1 to 14. Mechanical hyperalgesia reached a steady peak at day14 after surgery, whereas thermal allodynia did not develop. The results of second-generation sequencing suggested that the expression profiles of lncRNAs and mRNAs were significantly altered in spinal cords of SNI rats versus the control rats at different stages during NP. Differentially expressed (DE) lncRNAs and mRNAs were demonstrated at each stage during the NP course using Volcano Plot, Venn and Hcluster heatmap analyses. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analyses were performed to predict the functionalities of differentially expressed lncRNAs and target genes. Protein interaction networks were constructed based on the correlation analyses of DE lncRNA target proteins at 7 and 14 days after SNI, respectively. Taken together, our results revealed the profiles of lncRNAs and mRNAs in the rat spinal cord under an NP condition. These lncRNAs and mRNAs may represent new therapeutic targets for the treatment of NP.
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Affiliation(s)
- Jun Zhou
- a Department of Anesthesiology, The First People's Hospital of Foshan , Foshan , Guangdong Province , China
| | - Youling Fan
- b Department of Anesthesiology, Guangzhou Panyu Central Hospital of Panyu District , Guangzhou , Guangdong Province , China
| | - Hongtao Chen
- c Department of Anesthesiology, The Eighth People's Hospital of Guangzhou , Guangzhou , Guangdong Province , China
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47
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Yang Y, Junjie P, Sanjun C, Ma Y. Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions. J Cancer 2017; 8:3212-3225. [PMID: 29158793 PMCID: PMC5665037 DOI: 10.7150/jca.19794] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of the colorectal adenoma-carcinoma sequence with its corresponding genetic and epigenetic alterations has significantly increased our knowledge of the etiopathogenesis of colorectal cancer (CRC). However, the molecular mechanisms of colorectal carcinogenesis and metastasis haven't been clearly elucidated. Long non-coding ribonucleic acids (lncRNAs) are key participants of gene regulations rather than “noises”. Accumulative studies have implicated that the aberrant expressions of lncRNAs are tightly corelated to CRC screening, diagnosis, prognosis and therapeutic outcomes. Our review focuses on recent findings on the involvement of lncRNAs in CRC oncogenesis and the lncRNA-based clinical implications in patients with CRC.
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Affiliation(s)
- Yongzhi Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Peng Junjie
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cai Sanjun
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
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48
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Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig. Sci Rep 2017; 7:8704. [PMID: 28821716 PMCID: PMC5562803 DOI: 10.1038/s41598-017-07998-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/06/2017] [Indexed: 02/06/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes. Gene ontology and pathway analyses indicated that many potential target genes (PTGs) of lincRNAs were involved in skeletal-muscle-related processes, such as muscle contraction and muscle system process. Combined our previous studies, we found a potential regulatory mechanism in which the promoter methylation of lincRNAs can negatively regulate lincRNA expression and then positively regulate PTG expression, which can finally result in abnormal phenotypes of cloned piglets through a certain unknown pathway. This work detailed a number of lincRNAs and their target genes involved in skeletal muscle growth and development and can facilitate future studies on their roles in skeletal muscle growth and development.
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49
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Abstract
The emerging complexity of the transcriptional landscape poses great challenges to our conventional preconceptions of how the genome regulates brain function and dysfunction. Non-protein-coding RNAs (ncRNAs) confer a high level of intricate and dynamic regulation of various molecular processes in the CNS and they have been implicated in neurodevelopment and brain ageing, as well as in synapse function and cognitive performance, in both health and disease. ncRNA-mediated processes may be involved in various aspects of the pathogenesis of neurodegenerative disorders. Understanding these events may help to develop novel diagnostic and therapeutic tools. Here, we provide an overview of the complex mechanisms that are affected by the diverse ncRNA classes that have been implicated in neurodegeneration.
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Li J, Xue W, Lv J, Han P, Liu Y, Cui B. Identification of potential long non-coding RNA biomarkers associated with the progression of colon cancer. Oncotarget 2017; 8:75834-75843. [PMID: 29100272 PMCID: PMC5652666 DOI: 10.18632/oncotarget.17924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/03/2017] [Indexed: 12/18/2022] Open
Abstract
Increasing evidence has suggested that dysregulated lncRNA expression played important roles in the development and progression of human cancers. Although prognostic roles of lncRNAs have been recognized for colon cancer (CC) patients, the search for novel lncRNA biomarkers potentially involved in CC progression is an urgent and still largely unmet medical need. In this study, we evaluated the lncRNA expression changes during the progression of CC by analyzing two cohorts of previously published expression profiles of CC patients and identified hundreds of differentially expressed lncRNAs. Then we identified eight lncRNAs that closely associated with the progression of CC patients from a large number of significantly altered lncRNAs using random forest supervised classification algorithm. Finally, an SVM-based lncRNA risk classifier was developed to discriminate high-risk CC patients from persons with early-stage and validated in both the training dataset and testing dataset by survival analysis and five-fold cross-validation strategy. Our pathway enrichment analysis based on protein-coding genes that are co-expressed with lncRNAs, suggested that variation in expression of eight lncRNAs biomarkers might affect critical pathways involved in CC progression. With further validation, these eight lncRNAs might have significant implications for the clinical management of CC patients with early stage and improve our understanding of cancer progression.
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Affiliation(s)
- Jingwen Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Weinan Xue
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Junli Lv
- Department of Science, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Peng Han
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
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