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Shi F, Jiang J, Wang B, Hong L, Zhang Y, Meng Y, Zhang X, Gong L, Lin J, Diao H. Hepatitis B virus X protein promotes tumor glycolysis by downregulating lncRNA OIP5-AS1/HKDC1 in HCC. Cell Signal 2024; 119:111183. [PMID: 38636768 DOI: 10.1016/j.cellsig.2024.111183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide, with Hepatitis B virus (HBV) infection being the leading cause. This study aims to investigate the role of HBV in HCC pathogenesis involving glucose metabolism. Long non-coding RNA (lncRNA) OIP5-AS1 was significantly downregulated in HBV-positive HCC patients, and its low expression indicated a poor prognosis. This lncRNA was primarily localized in the cytoplasm, acting as a tumor suppressor. HBV protein X (HBx) repressed OIP5-AS1 expression by inhibiting a ligand-activated transcriptional factor peroxisome proliferator-activated receptor α (PPARα). Furthermore, mechanistic studies revealed that OIP5-AS1 inhibited tumor growth by suppressing Hexokinase domain component 1 (HKDC1)-mediated glycolysis. The expression of HKDC1 could be enhanced by transcriptional factor sterol regulatory element-binding protein 1 (SREBP1). OIP5-AS1 facilitated the ubiquitination and degradation of SREBP1 to suppress HKDC1 transcription, which inhibited glycolysis. The results suggest that lncRNA OIP5-AS1 plays an anti-oncogenic role in HBV-positive HCC via the HBx/OIP5-AS1/HKDC1 axis, providing a promising diagnostic marker and therapeutic target for HBV-positive HCC patients.
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MESH Headings
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Humans
- Carcinoma, Hepatocellular/virology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/virology
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Glycolysis/genetics
- Viral Regulatory and Accessory Proteins
- Trans-Activators/metabolism
- Trans-Activators/genetics
- Hexokinase/metabolism
- Hexokinase/genetics
- Gene Expression Regulation, Neoplastic
- Animals
- Hepatitis B virus
- Male
- Cell Line, Tumor
- Down-Regulation
- Mice
- Mice, Nude
- Female
- Sterol Regulatory Element Binding Protein 1/metabolism
- Sterol Regulatory Element Binding Protein 1/genetics
- Mice, Inbred BALB C
- PPAR alpha/metabolism
- PPAR alpha/genetics
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Affiliation(s)
- Fan Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Jingjing Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Baohua Wang
- Department of Ultrasound, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Liang Hong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Yongting Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Yuting Meng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China
| | - Lan Gong
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jianjun Lin
- Clinical Laboratory Department, The Affiliated Xiangshan Hospital of Wenzhou Medical University, Ningbo, Zhejiang 315700, PR China.
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, PR China.
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2
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Zhang C, Xu A, Liu R, Liu M, Zhao W, Yao A, Sun G, Ji S, Zhao K. LINC01138 expresses two novel isoforms and functions as a repressive factor in glioma cells. Heliyon 2024; 10:e32245. [PMID: 38975094 PMCID: PMC11226785 DOI: 10.1016/j.heliyon.2024.e32245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
Objective The objective of this study is to investigate the aggressive infiltration of glioblastoma into adjacent brain tissue, considering its challenging prognosis. Initially classified as an intergenic non-coding RNA, we aim to elucidate the functional implications of LINC01138 in glioblastoma. Method Glioma grading was performed utilizing H&E staining, which unveiled distinct nuclear morphology in high-grade gliomas. The downregulation of LINC01138 in glioma tissues was corroborated through qRT-PCR and gel electrophoresis, concurrently identifying two previously unrecognized LINC01138 isoforms. Expression profiling of all four LINC01138 isoforms was executed in glioma cell lines (A172, SHG-44, U251, U87-MG). The impact of LINC01138 overexpression in U87-MG and U251 cells was evaluated for cell proliferation, migration, and invasion through cell counting, CCK-8 analysis, and Transwell assays. Furthermore, the suppression of LINC01138 in SHG-44 cells substantiated its involvement in fostering tumor malignancy. Transcriptome sequencing revealed the inhibitory influence of LINC01138 on IGF1 expression. These findings contribute to an enriched comprehension of glioma biology by exploring the engagement of LINC01138 through diverse methodologies, thereby elucidating its potential therapeutic significance. Results Our investigation elucidates the intricate involvement of LINC01138 in gliomas. High-grade gliomas are characterized by elevated cell density and distinctive nuclear features. LINC01138 demonstrates a substantial downregulation in glioma tissues, with the identification of two novel isoforms. The expression of all four LINC01138 isoforms is notably diminished in both glioma tissues and cell lines. Elevated expression of LINC01138 demonstrates inhibitory effects on tumor cell proliferation, migration, and invasion, while its downregulation exacerbates malignancy. The regulatory function of LINC01138 as a repressor of IGF1 expression was elucidated through transcriptome sequencing. Conclusion The LINC01138 isoforms display notable tumor-suppressive effects, suggesting a promising potential for impeding glioma progression.
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Affiliation(s)
- Chao Zhang
- Department of Neurosrugery, Tianjin Union Medical Center, Tianjin, 300000, China
| | - Ao Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, 475000, China
| | - Ruoyu Liu
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100000, China
| | - Minghang Liu
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100000, China
| | - Wei Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, 475000, China
| | - Anhui Yao
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100000, China
- Department of Neurosurgery, The 988th hospital of PLA, Zhengzhou, Henan, 450000, China
| | - Guochen Sun
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100000, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, 475000, China
| | - Kai Zhao
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100000, China
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Sheikhnia F, Fazilat A, Rashidi V, Azizzadeh B, Mohammadi M, Maghsoudi H, Majidinia M. Exploring the therapeutic potential of quercetin in cancer treatment: Targeting long non-coding RNAs. Pathol Res Pract 2024; 260:155374. [PMID: 38889494 DOI: 10.1016/j.prp.2024.155374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/11/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
The escalating global incidence of cancer, which results in millions of fatalities annually, underscores the pressing need for effective pharmacological interventions across diverse cancer types. Long noncoding RNAs (lncRNAs), a class of RNA molecules that lack protein-coding capacity but profoundly impact gene expression regulation, have emerged as pivotal players in key cellular processes, including proliferation, apoptosis, metastasis, cellular metabolism, and drug resistance. Among natural compounds, quercetin, a phenolic compound abundantly present in fruits and vegetables has garnered attention due to its significant anticancer properties. Quercetin demonstrates the ability to inhibit cancer cell growth and induce apoptosis-a process often impaired in malignant cells. In this comprehensive review, we delve into the therapeutic potential of quercetin in cancer treatment, with a specific focus on its intricate interactions with lncRNAs. We explore how quercetin modulates lncRNA expression and function to exert its anticancer effects. Notably, quercetin suppresses oncogenic lncRNAs that drive cancer development and progression while enhancing tumor-suppressive lncRNAs that impede cancer growth and dissemination. Additionally, we discuss quercetin's role as a chemopreventive agent, which plays a crucial role in mitigating cancer risk. We address research challenges and future directions, emphasizing the necessity for in-depth mechanistic studies and strategies to enhance quercetin's bioavailability and target specificity. By synthesizing existing knowledge, this review underscores quercetin's promising potential as a novel therapeutic strategy in the ongoing battle against cancer, offering fresh insights and avenues for further investigation in this critical field.
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Affiliation(s)
- Farhad Sheikhnia
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran; Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ahmad Fazilat
- Motamed Cancer Institute, Breast Cancer Research Center, ACECR, Tehran, Iran
| | - Vahid Rashidi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Bita Azizzadeh
- Department of Biochemistry, School of Medicine, Ilam University of Medical sciences, Ilam, Iran
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Maghsoudi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran; Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran.
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Alharbi KS. The ncRNA-TGF-β axis: Unveiling new frontiers in colorectal cancer research. Pathol Res Pract 2024; 254:155138. [PMID: 38266458 DOI: 10.1016/j.prp.2024.155138] [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: 11/05/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
Colorectal cancer (CRC) poses a substantial global challenge, necessitating a deeper understanding of the molecular underpinnings governing its onset and progression. The transforming growth factor beta (TGF-β) network has been a well-recognized cornerstone in advancing CRC. Nevertheless, a recent study has highlighted the growing importance of non-coding RNAs (ncRNAs) in this context. This comprehensive review aims to present an extensive examination of the interaction between ncRNAs and TGF-signaling. Noncoding RNAs (ncRNAs), encompassing circular RNAs (circRNAs), long-ncRNAs (lncRNAs), and microRNAs (miRNAs), have surfaced as pivotal modulators governing various aspects of TGF-β signaling. MiRNAs have been discovered to target elements within the TGF-β signaling, either enhancing or inhibiting signaling, depending on the context. LncRNAs have been associated with CRC progression, functioning as miRNA sponges or directly influencing TGF-β pathway elements. Even circRNAs, a relatively recent addition to the ncRNA family, have impacted CRC, affecting TGF-β signaling through diverse mechanisms. This review encompasses recent progress in comprehending specific ncRNAs involved in TGF-β signaling, their functional roles, and their clinical relevance in CRC. We investigate the possibility of ncRNAs as targets for detection, prognosis, and therapy. Additionally, we explore the interaction of TGF-β and other pathways in CRC and the role of ncRNAs within this intricate network. As we unveil the intricate regulatory function of ncRNAs in the TGF-β signaling in CRC, we gain valuable insights into the disease's pathogenesis. Incorporating these discoveries into clinical settings holds promise for more precise diagnosis, prognosis, and targeted therapeutic approaches, ultimately enhancing the care of CRC patients. This comprehensive review underscores the ever-evolving landscape of ncRNA research in CRC and the potential for novel interventions in the battle against this formidable disease.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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5
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Arunkumar G. LncRNAs: the good, the bad, and the unknown. Biochem Cell Biol 2024; 102:9-27. [PMID: 37579511 DOI: 10.1139/bcb-2023-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are significant contributors in maintaining genomic integrity through epigenetic regulation. LncRNAs can interact with chromatin-modifying complexes in both cis and trans pathways, drawing them to specific genomic loci and influencing gene expression via DNA methylation, histone modifications, and chromatin remodeling. They can also operate as building blocks to assemble different chromatin-modifying components, facilitating their interactions and gene regulatory functions. Deregulation of these molecules has been associated with various human diseases, including cancer, cardiovascular disease, and neurological disorders. Thus, lncRNAs are implicated as potential diagnostic indicators and therapeutic targets. This review discusses the current understanding of how lncRNAs mediate epigenetic control, genomic integrity, and their putative functions in disease pathogenesis.
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Affiliation(s)
- Ganesan Arunkumar
- The LncRNA, Epigenetics, and Genome Organization Laboratory, Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
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Pan A, Xue Y, Ruan X, Dong W, Wang D, Liu Y, Liu L, Lin Y, E T, Lin H, Xu H, Liu X, Wang P. m5C modification of LINC00324 promotes angiogenesis in glioma through CBX3/VEGFR2 pathway. Int J Biol Macromol 2024; 257:128409. [PMID: 38016610 DOI: 10.1016/j.ijbiomac.2023.128409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Angiogenesis plays a major role in tumor initiation, progression, and metastasis. This is why finding antiangiogenic targets is essential in the treatment of gliomas. In this study, NSUN2 and LINC00324 were significantly upregulated in conditionally cultured glioblastoma endothelial cells (GECs). Knockdown of NSUN2 or LINC00324 inhibits GECs angiogenesis. NSUN2 increased the stability of LINC00324 by m5C modification and upregulated LINC00324 expression. LINC00324 competes with the 3'UTR of CBX3 mRNA to bind to AUH protein, reducing the degradation of CBX3 mRNA. In addition, CBX3 directly binds to the promoter region of VEGFR2, enhances VEGFR2 transcription, and promotes GECs angiogenesis. These findings demonstrated NSUN2/LINC00324/CBX3 axis plays a crucial role in regulating glioma angiogenesis, which provides new strategies for glioma therapy.
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Affiliation(s)
- Aini Pan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Weiwei Dong
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Di Wang
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yunhui Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Libo Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Tiange E
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Hongda Lin
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Hailing Xu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xiaobai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.; Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China..
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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Müller T, Mautner S, Videm P, Eggenhofer F, Raden M, Backofen R. CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites. Gigascience 2024; 13:giae022. [PMID: 38837942 DOI: 10.1093/gigascience/giae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throughput methods can lack precision because of a high false-positive rate. RESULTS We present CheRRI, the first tool to evaluate the biological relevance of putative RNA-RNA interaction sites. CheRRI filters candidates via a machine learning-based model trained on experimental RNA-RNA interactome data. Its unique setup combines interactome data and an established thermodynamic prediction tool to integrate experimental data with state-of-the-art computational models. Applying these data to an automated machine learning approach provides the opportunity to not only filter data for potential false positives but also tailor the underlying interaction site model to specific needs. CONCLUSIONS CheRRI is a stand-alone postprocessing tool to filter either predicted or experimentally identified potential RNA-RNA interactions on a genomic level to enhance the quality of interaction candidates. It is easy to install (via conda, pip packages), use (via Galaxy), and integrate into existing RNA-RNA interaction pipelines.
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Affiliation(s)
- Teresa Müller
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Stefan Mautner
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centre CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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9
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Yue Y, Wang Y, Wen C, Meng Y, Peng Y, Li X. Lnc-Malat1 promotes slow myofiber-type transformation through sponging miR-129-5p in C2C12 myotubes. Exp Cell Res 2023; 431:113761. [PMID: 37634561 DOI: 10.1016/j.yexcr.2023.113761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Long non-coding metastasis-associated lung adenocarcinoma transcript (lnc-Malat1) emerges as a novel regulator in skeletal muscle development, while its function and the related mechanism is not fully revealed yet. In this study, knockdown of lnc-Malat1 by siRNA significantly inhibited the expression of myoblast marker genes (MyHC, MyoD, and MyoG) and slow muscle fiber marker genes (MyHC I), together with repressed expression of mitochondria-related genes COX5A, ACADM, CPTA1, FABP3, and NDUFA1. Overexpression of lnc-Malat1 exerted an opposite effect, promoting myoblast differentiation and slow muscle fiber formation. Dual luciferase reporter assay revealed a direct interaction between lnc-Malat1 and miR-129-5p, and overexpression of lnc-Malat1 significantly inhibited miR-129-5p expression, thereby elevating the expression of Mef2a, miR-129-5p target protein. In addition, enforced expression of lnc-Malat1 restored the inhibitory effect of miR-129-5p on myoblast differentiation and MyHC I expression. Taken together, our results suggest that lnc-Malat1 promotes myoblast differentiation, and maintains the slow muscle fiber phenotype via adsorbing miR-129-5p.
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Affiliation(s)
- Yongqi Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
| | - Yuhe Wang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
| | - Chenglong Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
| | - Yingying Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
| | - Ying Peng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
| | - Xiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.
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10
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Wang C, Zhao F, He Y, E Y, Li S. Long non-coding RNA RMST serves as a diagnostic biomarker in patients with carotid artery stenosis and predicts the occurrence of cerebral ischemic event: A retrospective study. Vascular 2023; 31:908-913. [PMID: 35531613 DOI: 10.1177/17085381221100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES The purpose of this retrospective study is to explore the diagnostic and prognostic roles of serum RMST in carotid artery stenosis (CAS). METHODS Serum levels of RMST were detected in CAS patients, and the relationship between degree of carotid stenosis and RMST levels was analyzed. The ROC curve was drawn to evaluate RMST value in predicting the risk of CAS. Then, all CAS patients received a 5-year follow-up. K-M curve was used to analyze the significance of RMST on prognosis of CAS patients. Multi-factor cox logistic regression analysis was conducted to evaluate independent factors for outcome of CAS patients. RESULTS An increased RMST expression was certified in CAS patients when compared with healthy controls. The increase of serum RMST expression was related to high degree of carotid stenosis. In addition, serum RMST was a possible diagnosis and an independent influencing factor of prognosis in patients with CAS. CONCLUSIONS Raised serum RMST level was found in patients with CAS. Detecting RMST expression levels was of high value for predicting the occurrence and outcomes in CAS.
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Affiliation(s)
- Cui Wang
- Pre-hospital Emergency Center, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Feng Zhao
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yunliang He
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yajun E
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Shanfeng Li
- Department of Interventional Vascular Surgery, Affiliated Hospital of Hebei University, Baoding, China
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Eldash S, Sanad EF, Nada D, Hamdy NM. The Intergenic Type LncRNA (LINC RNA) Faces in Cancer with In Silico Scope and a Directed Lens to LINC00511: A Step toward ncRNA Precision. Noncoding RNA 2023; 9:58. [PMID: 37888204 PMCID: PMC10610215 DOI: 10.3390/ncrna9050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/09/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long intergenic non-coding RNA, is one type of lncRNA, exerting various cellular activities, as does ncRNA, including the regulation of gene expression and chromatin remodeling. The abnormal expression of lincRNAs can induce or suppress carcinogenesis. MAIN BODY LincRNAs can regulate cancer progression through different mechanisms and are considered as potential drug targets. Genetic variations such as single nucleotide polymorphisms (SNPs) in lincRNAs may affect gene expression and messenger ribonucleic acid (mRNA) stability. SNPs in lincRNAs have been found to be associated with different types of cancer, as well. Specifically, LINC00511 has been known to promote the progression of multiple malignancies such as breast cancer, colorectal cancer, lung cancer, hepatocellular carcinoma, and others, making it a promising cancer prognostic molecular marker. CONCLUSION LincRNAs have been proved to be associated with different cancer types through various pathways. Herein, we performed a comprehensive literature and in silico databases search listing lncRNAs, lincRNAs including LINC00511, lncRNAs' SNPs, as well as LINC00511 SNPs in different cancer types, focusing on their role in various cancer types and mechanism(s) of action.
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Affiliation(s)
- Shorouk Eldash
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), El Sherouk, Cairo 11837, Egypt; (S.E.)
| | - Eman F. Sanad
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Dina Nada
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), El Sherouk, Cairo 11837, Egypt; (S.E.)
| | - Nadia M. Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
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12
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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13
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Sharma A, Singh NK. Long Non-Coding RNAs and Proliferative Retinal Diseases. Pharmaceutics 2023; 15:pharmaceutics15051454. [PMID: 37242701 DOI: 10.3390/pharmaceutics15051454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Retinopathy refers to disorders that affect the retina of the eye, which are frequently caused by damage to the retina's vascular system. This causes leakage, proliferation, or overgrowth of blood vessels through the retina, which can lead to retinal detachment or breakdown, resulting in vision loss and, in rare cases, blindness. In recent years, high-throughput sequencing has significantly hastened the discovery of new long non-coding RNAs (lncRNAs) and their biological functions. LncRNAs are rapidly becoming recognized as critical regulators of several key biological processes. Current breakthroughs in bioinformatics have resulted in the identification of several lncRNAs that may have a role in retinal disorders. Nevertheless, mechanistic investigations have yet to reveal the relevance of these lncRNAs in retinal disorders. Using lncRNA transcripts for diagnostic and/or therapeutic purposes may aid in the development of appropriate treatment regimens and long-term benefits for patients, as traditional medicines and antibody therapy only provide temporary benefits that must be repeated. In contrast, gene-based therapies can provide tailored, long-term treatment solutions. Here, we will discuss how different lncRNAs affect different retinopathies, including age-related macular degeneration (AMD), diabetic retinopathy (DR), central retinal vein occlusion (CRVO), proliferative vitreoretinopathy (PVR), and retinopathy of prematurity (ROP), which can cause visual impairment and blindness, and how these retinopathies can be identified and treated using lncRNAs.
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Affiliation(s)
- Anamika Sharma
- Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Nikhlesh K Singh
- Integrative Biosciences Center, Wayne State University, Detroit, MI 48202, USA
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48202, USA
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14
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Tang H, Huang H, Guo Z, Huang H, Niu Z, Ji Y, Zhang Y, Bian H, Hu W. Heavy Ion-Responsive lncRNA EBLN3P Functions in the Radiosensitization of Non-Small Cell Lung Cancer Cells Mediated by TNPO1. Cancers (Basel) 2023; 15:cancers15020511. [PMID: 36672460 PMCID: PMC9856274 DOI: 10.3390/cancers15020511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
In recent decades, the rapid development of radiotherapy has dramatically increased the cure rate of malignant tumors. Heavy-ion radiotherapy, which is characterized by the "Bragg Peak" because of its excellent physical properties, induces extensive unrepairable DNA damage in tumor tissues, while normal tissues in the path of ion beams suffer less damage. However, there are few prognostic molecular biomarkers that can be used to assess the efficacy of heavy ion radiotherapy. In this study, we focus on non-small cell lung cancer (NSCLC) radiotherapy and use RNA sequencing and bioinformatic analysis to investigate the gene expression profiles of A549 cells exposed to X-ray or carbon ion irradiation to screen the key genes involved in the stronger tumor-killing effect induced by carbon ions. The potential ceRNA network was predicted and verified by polymerase chain amplification, western blotting analysis, colony formation assay, and apoptosis assay. The results of the experiments indicated that lncRNA EBLN3P plays a critical role in inhibiting carbon ion-induced cell proliferation and inducing apoptosis of NSCLC cells. These functions were achieved by the EBLN3P/miR-144-3p/TNPO1 (transportin-1) ceRNA network. In summary, the lncRNA EBLN3P functions as a ceRNA to mediate lung cancer inhibition induced by carbon ion irradiation by sponging miR-144-3p to regulate TNPO1 expression, indicating that EBLN3P may be a promising target for increasing the treatment efficacy of conventional radiotherapy for NSCLC.
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Affiliation(s)
- Haoyi Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Hao Huang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zi Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Haitong Huang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zihe Niu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yi Ji
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yuyang Zhang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Huahui Bian
- Nuclear and Radiation Incident Medical Emergency Office, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Correspondence: (H.B.); (W.H.)
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
- Correspondence: (H.B.); (W.H.)
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15
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Yang W, Lyu Y, Xiang R, Yang J. Long Noncoding RNAs in the Pathogenesis of Insulin Resistance. Int J Mol Sci 2022; 23:ijms232416054. [PMID: 36555704 PMCID: PMC9785789 DOI: 10.3390/ijms232416054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.
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Affiliation(s)
- Weili Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yixiang Lyu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
- Correspondence:
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16
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El-Sheikh NM, Abulsoud AI, Wasfey EF, Hamdy NM. Insights on the potential oncogenic impact of long non-coding RNA nicotinamide nucleotide transhydrogenase antisense RNA 1 in different cancer types; integrating pathway(s) and clinical outcome(s) association. Pathol Res Pract 2022; 240:154183. [PMID: 36327824 DOI: 10.1016/j.prp.2022.154183] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
Long non-coding RNAs (lncRNAs) are becoming more prevalent in the cancer field arena, with functional roles in both oncogenic and onco-suppressive pathways. Despite their widespread aberrant expression in a range of human malignancies, the biological activities of the ncRNAs majority are unknown. All showed the involvement of the lncRNA nicotinamide nucleotide transhydrogenase antisense RNA 1 (NNT-AS1). Since NNT-AS1 influences cellular proliferation, invasion, migration, apoptosis, and metastasis, this lncRNA appears to be linked to deregulating the normal cellular processes driving malignancy. This was observed in breast cancer (BC), gastric cancer (GC), colorectal cancer (CRC), epithelial ovarian cancer (EOC), and hepatocellular carcinoma (HCC). The current narrative non-systematic review will discuss "the significance of lncRNAs in cancer", as well as "lncRNAs future potential application(s) as diagnostic or predictive biomarkers", therefore, comprising an opportunity as treatment target(s). The review will have a special emphasis on lncRNA NNT-AS1.
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Affiliation(s)
- Nada M El-Sheikh
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, Cairo 11785, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, Cairo 11785, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's branch), Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Eman F Wasfey
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt.
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17
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Liu X, Tian W, Wang L, Zhang L, Liang J, Wang L. Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig. Foods 2022; 11:foods11223654. [PMID: 36429246 PMCID: PMC9689697 DOI: 10.3390/foods11223654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.
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Affiliation(s)
- Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weilong Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62818771
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18
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Resveratrol Inhibits Proliferation and Differentiation of Porcine Preadipocytes by a Novel LincRNA-ROFM/miR-133b/AdipoQ Pathway. Foods 2022; 11:foods11172690. [PMID: 36076875 PMCID: PMC9455634 DOI: 10.3390/foods11172690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Resveratrol (RES) has a wide range of biological and pharmacological activities with various health benefits for humans as a food additive. In animal production, RES has been considered a potential functional feed additive for producing high-quality pork. Long noncoding RNAs (lncRNAs) have emerged as essential regulators of fat metabolism, and phytochemicals can regulate fat metabolism through lncRNA. However, it is unclear whether RES can improve back-fat thickness by regulating lncRNA. In this study, we identified a novel lncRNA, which was named a long intergenic non-protein coding RNA, a regulator of fat metabolism (LincRNA-ROFM), from our previous lncRNA sequencing data. LincRNA-ROFM can inhibit adipocyte proliferation and differentiation. In-depth analyses showed that LincRNA-ROFM acts as a molecular sponge for miR-133b, and adiponectin (AdipoQ) is a direct target of miR-133b in porcine preadipocytes. In addition, the expression of LincRNA-ROFM was positively correlated with AdipoQ. RES can promote the expression of LincRNA-ROFM by PPARα and C/EBPα. Altogether, our research showed that LincRNA-ROFM acts as a ceRNA to sequester miR-133b and is upregulated by RES, leading to heightened AdipoQ expression, and thus decreased adipocyte proliferation and differentiation, which reduces back-fat thickness of pigs. Taken together, the RES/LincRNA-ROFM/miR-133b/AdipoQ regulatory network preliminarily explains the mechanism of action of RES in inhibiting fat deposition, which provides new insight into the downstream mechanism of RES inhibition of fat deposits by regulating the lncRNA.
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19
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Huang Z, Gao H, Qing L, Wang B, He C, Luo N, Lu C, Fan S, Gu P, Zhao H. A long noncoding RNA GTF2IRD2P1 suppresses cell proliferation in bladder cancer by inhibiting the Wnt/β‑catenin signaling pathway. PeerJ 2022; 10:e13220. [PMID: 35433119 PMCID: PMC9009331 DOI: 10.7717/peerj.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/14/2022] [Indexed: 01/12/2023] Open
Abstract
Background There is growing evidence that long non-coding RNAs (LncRNAs) are key in the development of a variety of human tumors. However, the role of lncRNA GTF2IRD2P1 has not been well studied in cancer. The impact of GTF2IRD2P1 on the biological function and clinical relevance in bladder cancer is largely unknown. This study aimed to investigate the biological role of GTF2IRD2P1 in bladder evolution and carcinogenesis. Methods We used bioinformatics to obtain the lncRNA GTF2IRD2P1 from bladder urothelial carcinoma (BLCA) in The Cancer Genome Atlas (TCGA) database. The expression of lncRNA GTF2IRD2P1 was detected by qRT-PCR. The CCK8 assay and flow cytometry were used to detect the lncRNA GTF2IRD2P1 function on the proliferation of bladder cancer cells. A western blot was used to calculate the protein level of cell cycle proteins and Wnt signaling pathway proteins. The effect of lncRNA GTF2IRD2P1 on tumorigenesis of bladder cancer was confirmed by a xenograft nude mouse model. Results GTF2IRD2P1 expression was found to be lower in both human bladder cancer tissues and cell lines (UM-UC-3, RT4, and 5637), and elevated in T24 compared to the corresponding normal controls. GTF2IRD2P1 expression was also enhanced after transfection of UM-UC-3 cells with the overexpression vector. Meanwhile, overexpression of GTF2IRD2P1 inhibited the proliferation of UM-UC-3 and prolonged the cell cycle. The silencing of GTF2IRD2P1 significantly increased the proliferation and shortened the cell cycle of T24 cells and induced Wnt signaling activity to promote the progression of bladder cancer. Similarly, the transplanted tumor nude mouse model demonstrated that silencing GTF2IRD2P1 strengthens the progression of bladder cancer by targeting the Wnt signaling pathway.
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Affiliation(s)
- Zhuo Huang
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Hongbin Gao
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China,Clinical Research Center for Chronic Kidney Disease, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Liangliang Qing
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Biao Wang
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Chaoyong He
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Ning Luo
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Chuncheng Lu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Shipeng Fan
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Peng Gu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China,Clinical Research Center for Chronic Kidney Disease, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
| | - Hui Zhao
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China,Clinical Research Center for Chronic Kidney Disease, First Affiliated Hospital of Kunming Medical University, Kunming Medical College, Kunming, Yunnan, People’s Republic of China
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20
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Zooming in on Long Non-Coding RNAs in Ewing Sarcoma Pathogenesis. Cells 2022; 11:cells11081267. [PMID: 35455947 PMCID: PMC9032025 DOI: 10.3390/cells11081267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Ewing sarcoma (ES) is a rare aggressive cancer of bone and soft tissue that is mainly characterized by a reciprocal chromosomal translocation. As a result, about 90% of cases express the EWS-FLI1 fusion protein that has been shown to function as an aberrant transcription factor driving sarcomagenesis. ES is the second most common malignant bone tumor in children and young adults. Current treatment modalities include dose-intensified chemo- and radiotherapy, as well as surgery. Despite these strategies, patients who present with metastasis or relapse still have dismal prognosis, warranting a better understanding of treatment resistant-disease biology in order to generate better prognostic and therapeutic tools. Since the genomes of ES tumors are relatively quiet and stable, exploring the contributions of epigenetic mechanisms in the initiation and progression of the disease becomes inevitable. The search for novel biomarkers and potential therapeutic targets of cancer metastasis and chemotherapeutic drug resistance is increasingly focusing on long non-coding RNAs (lncRNAs). Recent advances in genome analysis by high throughput sequencing have immensely expanded and advanced our knowledge of lncRNAs. They are non-protein coding RNA species with multiple biological functions that have been shown to be dysregulated in many diseases and are emerging as crucial players in cancer development. Understanding the various roles of lncRNAs in tumorigenesis and metastasis would determine eclectic avenues to establish therapeutic and diagnostic targets. In ES, some lncRNAs have been implicated in cell proliferation, migration and invasion, features that make them suitable as relevant biomarkers and therapeutic targets. In this review, we comprehensively discuss known lncRNAs implicated in ES that could serve as potential biomarkers and therapeutic targets of the disease. Though some current reviews have discussed non-coding RNAs in ES, to our knowledge, this is the first review focusing exclusively on ES-associated lncRNAs.
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21
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Wan H, Wang Y, Pan Q, Chen X, Chen S, Li X, Yao W. Quercetin attenuates the proliferation, inflammation, and oxidative stress of high glucose-induced human mesangial cells by regulating the miR-485-5p/YAP1 pathway. Int J Immunopathol Pharmacol 2022; 36:20587384211066440. [PMID: 35129398 PMCID: PMC8832592 DOI: 10.1177/20587384211066440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Diabetic nephropathy (DN) is a kidney damage caused by diabetes and the main cause of end-stage renal disease. However, the current treatment of DN has many limitations. Quercetin is a bioflavonoid compound with therapeutic benefits in metabolic diseases. This study aims to determine the therapeutic potentials and underlying mechanism of quercetin on DN. Methods We collected blood samples from DN patients and healthy controls and treated human mesangial cells (HMCs) with high glucose (HG) to establish an in vitro model of DN. Then we assessed the expression difference of miR-485-5p as well as YAP1 in serum of DN patients and healthy controls and between HG-induced HMCs and control cells. qRT-PCR and western blot were performed to assess miR-485-5p and YAP1 expression levels; CCK-8 and ELISAs were used to examine cell proliferation, inflammation, and oxidative stress. Dual luciferase reporter assay was implemented to detect the binding of miR-485-5p and YAP1 mRNA sequence. Results Quercetin suppressed proliferation, inflammation, and oxidative stress of HMCs induced by HG. As for mechanism, miR-485-5p directly bound to YAP1 and inhibited YAP1 expression. The downregulation of miR-485-5p and upregulation of YAP1 were also observed in the serum of DN patients. Quercetin modulated miR-485-5p/YAP1 axis to regulate HG-induced inflammation and oxidative stress. Conclusion: Quercetin inhibits the proliferation, inflammation, and oxidative stress of HMCs induced by HG through miR-485-5p/YAP1 axis, which might provide a novel treatment strategy for DN.
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Affiliation(s)
- Huan Wan
- Department of Radiotherapy Center, the Fifth Hospital of Wuhan, Wuhan, Hubei
| | - Yaping Wang
- Department of Endocrinology, the Fifth Hospital of Wuhan, Wuhan, Hubei
| | - Qingyun Pan
- Department of Endocrinology, the Fifth Hospital of Wuhan, Wuhan, Hubei
| | - Xia Chen
- Department ofTraditional Chinese Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai
| | - Sijun Chen
- Department of Nephrology, Yangpu Hospital, Tongji University School of Medicine, Shanghai
| | - Xiaohui Li
- Department of Paediatrics, the Fifth Hospital of Wuhan, Wuhan, Hubei
| | - Weiguo Yao
- Department of Nephrology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai
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22
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Wang F, Tao R, Zhao L, Hao XH, Zou Y, Lin Q, Liu MM, Goldman G, Luo D, Chen S. Differential lncRNA/mRNA Expression Profiling and Functional Network Analyses in Bmp2 Deletion of Mouse Dental Papilla Cells. Front Genet 2022; 12:702540. [PMID: 35003201 PMCID: PMC8727545 DOI: 10.3389/fgene.2021.702540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022] Open
Abstract
Bmp2 is essential for dentin development and formation. Bmp2 conditional knock-out (KO) mice display a similar tooth phenotype of dentinogenesis imperfecta (DGI). To elucidate a foundation for subsequent functional studies of cross talk between mRNAs and lncRNAs in Bmp2-mediated dentinogenesis, we investigated the profiling of lncRNAs and mRNAs using immortalized mouse dental Bmp2 flox/flox (iBmp2fx/fx) and Bmp2 knock-out (iBmp2ko/ko) papilla cells. RNA sequencing was implemented to study the expression of the lncRNAs and mRNAs. Quantitative real-time PCR (RT-qPCR) was used to validate expressions of lncRNAs and mRNAs. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict functions of differentially expressed genes (DEGs). Protein-protein interaction (PPI) and lncRNA-mRNA co-expression network were analyzed by using bioinformatics methods. As a result, a total of 22 differentially expressed lncRNAs (16 downregulated vs 6 upregulated) and 227 differentially expressed mRNAs (133 downregulated vs. 94 upregulated) were identified in the iBmp2ko/ko cells compared with those of the iBmp2fx/fx cells. RT-qPCR results showed significantly differential expressions of several lncRNAs and mRNAs which were consistent with the RNA-seq data. GO and KEGG analyses showed differentially expressed genes were closely related to cell differentiation, transcriptional regulation, and developmentally relevant signaling pathways. Moreover, network-based bioinformatics analysis depicted the co-expression network between lncRNAs and mRNAs regulated by Bmp2 in mouse dental papilla cells and symmetrically analyzed the effect of Bmp2 during dentinogenesis via coding and non-coding RNA signaling.
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Affiliation(s)
- Feng Wang
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Developmental Dentistry, School of Dentistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ran Tao
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Li Zhao
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xin-Hui Hao
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Zou
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Qing Lin
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meng Meng Liu
- Department of Developmental Dentistry, School of Dentistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Graham Goldman
- Department of Developmental Dentistry, School of Dentistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Daoshu Luo
- Laboratory of Clinical Applied Anatomy, Department of Human Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shuo Chen
- Department of Developmental Dentistry, School of Dentistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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23
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Zhang Y, Zheng M, Zhang L, Yuan P, Zhou J, Wang Y, Wang H. LncRNA LOXL1-AS1 Facilitates the Oncogenic Character in Cervical Cancer by the miR-526b-5p /LYPLA1 Axis. Biochem Genet 2022; 60:1298-1312. [PMID: 34984578 DOI: 10.1007/s10528-021-10182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/20/2021] [Indexed: 11/02/2022]
Abstract
Increasing reports demonstrate that long noncoding RNAs participate in the regulation of numerous malignancies, cervical cancer included. Although lncRNA LOXL1 antisense RNA 1 has been commonly accepted to be an oncogene in many cancers. Here, the role of LOXL1-AS1 in CC still need to be explored. In this study, LOXL1-AS1 was found elevated in CC tissues and cells. LOXL1-AS1 depletion restrained CC cell proliferation, migration, invasion, and angiogenesis in vivo. Furthermore, we found that LOXL1-AS1 upregulated Lysophospholipase 1 expression via sequestering miR-526b-5p. Rescue assays revealed that overexpression of LYPLA1 reversed the LOXL1-AS1 silencing-induced inhibitory effects on the malignant phenotypes of CC cells. To conclude, this study showed that LOXL1-AS1 facilitates cellular process in CC via functioning as a miR-526b-5p sponge.
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Affiliation(s)
- Yanhua Zhang
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Meng Zheng
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Lingyan Zhang
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Ping Yuan
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Jianbo Zhou
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Yongfang Wang
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China
| | - Haihong Wang
- Department of Obstetrics and Gynecology, Binhai County People's Hospital, No. 248, Fudong Middle Road, Yancheng, 224599, Jiangsu, China.
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24
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Lai L, Wang Z, Ge Y, Qiu W, Wu B, Fang F, Xu H, Chen Z. Comprehensive analysis of the long noncoding RNA-associated competitive endogenous RNA network in the osteogenic differentiation of periodontal ligament stem cells. BMC Genomics 2022; 23:1. [PMID: 34979896 PMCID: PMC8725252 DOI: 10.1186/s12864-021-08243-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUD The mechanism implicated in the osteogenesis of human periodontal ligament stem cells (PDLSCs) has been investigated for years. Previous genomics data analyses showed that long noncoding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) have significant expression differences between induced and control human PDLSCs. Competing for endogenous RNAs (ceRNA), as a widely studied mechanism in regenerative medicine, while rarely reported in periodontal regeneration. The key lncRNAs and their ceRNA network might provide new insights into molecular therapies of periodontal regeneration based on PDLSCs. RESULTS Two networks reflecting the relationships among differentially expressed RNAs were constructed. One ceRNA network was composed of 6 upregulated lncRNAs, 280 upregulated mRNAs, and 18 downregulated miRNAs. The other network contained 33 downregulated lncRNAs, 73 downregulated mRNAs, and 5 upregulated miRNAs. Functional analysis revealed that 38 GO terms and 8 pathways related with osteogenesis were enriched. Twenty-four osteogenesis-related gene-centred lncRNA-associated ceRNA networks were successfully constructed. Among these pathways, we highlighted MAPK and TGF-beta pathways that are closely related to osteogenesis. Subsequently, subnetworks potentially linking the GO:0001649 (osteoblast differentiation), MAPK and TGF-beta pathways were constructed. The qRT-PCR validation results were consistent with the microarray analysis. CONCLUSION We construct a comprehensively identified lncRNA-associated ceRNA network might be involved in the osteogenesis of PDLSCs, which could provide insights into the regulatory mechanisms and treatment targets of periodontal regeneration.
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Affiliation(s)
- Lingzhi Lai
- Department of Stomatology of Maoming People's Hospital, Maoming, 525000, China
| | - Zhaodan Wang
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Yihong Ge
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Wei Qiu
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Buling Wu
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China.,Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, 143 Dongzong Road, Pingshan District, Shenzhen, 518118, China
| | - Fuchun Fang
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Huiyong Xu
- Department of Stomatology of Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China.
| | - Zhao Chen
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, 143 Dongzong Road, Pingshan District, Shenzhen, 518118, China.
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25
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Fujii Y, Amatya VJ, Kushitani K, Suzuki R, Kai Y, Kambara T, Takeshima Y. Downregulation of lncRNA PVT1 inhibits proliferation and migration of mesothelioma cells by targeting FOXM1. Oncol Rep 2021; 47:27. [PMID: 34859258 PMCID: PMC8674703 DOI: 10.3892/or.2021.8238] [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: 08/13/2021] [Accepted: 10/12/2021] [Indexed: 11/08/2022] Open
Abstract
Malignant mesothelioma is a highly aggressive tumor, and an effective strategy for its treatment is not yet available. Long non-coding RNAs (lncRNAs) have been reported to be associated with various biological processes, including the regulation of gene expression of cancer-related pathways. Among various lncRNAs, plasmacytoma variant translocation 1 (PVT1) acts as a tumor promoter in several human cancers, but its mechanism of action has not yet been elucidated. Increased PVT1 expression was identified in ACC-MESO-1, ACC-MESO-4, CRL-5915, and CRL-5946 mesothelioma cell lines. PVT1 expression was investigated in mesothelioma cell lines by reverse transcription-quantitative polymerase chain reaction and its functional analysis by cell proliferation, cell cycle, cell migration, and cell invasion assays, as well as western blot analysis of downstream target genes. Knockdown of PVT1 expression in these cell lines by small interfering RNA transfection resulted in decreased cell proliferation and migration and increased the proportion of cells in the G2/M phase. The results of reverse transcription-quantitative polymerase chain reaction analysis revealed that PVT1 knockdown in mesothelioma cell lines caused the downregulation of Forkhead box M1 (FOXM1) expression, while the results of western blot analysis revealed that this knockdown reduced FOXM1 expression at the protein level. In addition, combined knockdown of PVT1 and FOXM1 decreased the proliferation of mesothelioma cell lines. In conclusion, PVT1 and FOXM1 were involved in the proliferation of cancer cells. Therefore, PVT1-FOXM1 pathways may be considered as candidate targets for the treatment of malignant mesothelioma.
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Affiliation(s)
- Yutaro Fujii
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Vishwa Jeet Amatya
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Kei Kushitani
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Rui Suzuki
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Yuichiro Kai
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Takahiro Kambara
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
| | - Yukio Takeshima
- Department of Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734‑8551, Japan
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26
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Zhang Y, Yang Y, Zhang Y, Liu Z. lncRNA ST8SIA6-AS1 facilitates proliferation and invasion in liver cancer by regulating miR-142-3p. Exp Ther Med 2021; 22:1348. [PMID: 34659494 PMCID: PMC8515546 DOI: 10.3892/etm.2021.10783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/09/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNA ST8 α-N-acetyl-neuraminide α-2,8-sialyltransferase 6 antisense 1 (ST8SIA6-AS1) has been identified as a novel oncogene in breast cancer. However, its involvement in liver cancer has remained elusive. In the present study, the expression of ST8SIA6-AS1 and microRNA (miR)-142-3p in liver cancer tissues and cell lines was detected by reverse transcription-quantitative PCR. Tumor cell proliferation, migration and invasion assays were performed to determine the biological functions of ST8SIA6-AS1. The targeting interaction between ST8SIA6-AS1 and miR-142-3p predicted by bioinformatics was verified by a luciferase reporter assay and a biotin pulldown assay. The results indicated that ST8SIA6-AS1 was highly expressed in liver cancer tissues and cell lines, and the high expression of ST8SIA6-AS1 in liver cancer tissues was associated with poor prognosis. Knockdown of ST8SIA6-AS1 inhibited the proliferation, metastasis and invasion of liver cancer cells. Mechanistic investigation revealed that ST8SIA6-AS1 sequesters miR-142-3p and negatively regulates miR-142-3p expression in liver cancer cells. Further investigation indicated that the tumor-inhibitory effect of ST8SIA6-AS1 silencing was reversed by miR-142-3p depletion. In conclusion, ST8SIA6-AS1 was indicated to exert an oncogenic function in liver cancer by competitively sponging miR-142-3p.
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Affiliation(s)
- Yang Zhang
- Department of General Surgery, The General Hospital of The Central Military Theater of The People's Liberation Army, Wuhan, Hubei 430030, P.R. China
| | - Yan Yang
- Department of Pediatric Hematology, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430031, P.R. China
| | - Yi Zhang
- Department of General Surgery, The General Hospital of The Central Military Theater of The People's Liberation Army, Wuhan, Hubei 430030, P.R. China
| | - Zhisu Liu
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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27
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Rincón-Riveros A, Morales D, Rodríguez JA, Villegas VE, López-Kleine L. Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions. Int J Mol Sci 2021; 22:11397. [PMID: 34768830 PMCID: PMC8583695 DOI: 10.3390/ijms222111397] [Citation(s) in RCA: 6] [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: 09/11/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.
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Affiliation(s)
- Andrés Rincón-Riveros
- Bioinformatics and Systems Biology Group, Universidad Nacional de Colombia, Bogotá 111221, Colombia;
| | - Duvan Morales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Josefa Antonia Rodríguez
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá 111221, Colombia;
| | - Victoria E. Villegas
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia;
| | - Liliana López-Kleine
- Department of Statistics, Faculty of Science, Universidad Nacional de Colombia, Bogotá 111221, Colombia
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28
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Choi S, Sathe A, Mathé E, Xing C, Pan Z. Identification of a Putative Enhancer RNA for EGFR in Hyper-Accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes. Front Oncol 2021; 11:724687. [PMID: 34722266 PMCID: PMC8554337 DOI: 10.3389/fonc.2021.724687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/20/2021] [Indexed: 01/22/2023] Open
Abstract
Abnormal genetic and epigenetic modifications play a key role in esophageal cancer. By Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq), this study compared chromatin accessibility landscapes among two esophageal squamous cell carcinoma (ESCC) cell lines, KYSE-30 and KYSE-150, and a non-cancerous esophageal epithelial cell line, HET-1A. Data showed that hyper-accessible regions in ESCC cells contained genes related with cancer hallmarks, such as epidermal growth factor receptor (EGFR). Multi-omics analysis and digital-droplet PCR results demonstrated that several non-coding RNAs in EGFR upstream were upregulated in ESCC cells. Among them, one appeared to act as an enhancer RNA responsible for EGFR overexpression. Further motif analysis and pharmacological data suggested that AP-1 family transcription factors were able to bind the hyper-accessible regions and thus to regulate cancer cell proliferation and migration. This study discovered a putative enhancer RNA for EGFR gene and the reliance of ESCC on AP-1 transcription factor.
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Affiliation(s)
- Sangyong Choi
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States
- Department of Nutritional Sciences, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, United States
| | - Adwait Sathe
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD, United States
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Zui Pan
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States
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29
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Correia CCM, Rodrigues LF, de Avila Pelozin BR, Oliveira EM, Fernandes T. Long Non-Coding RNAs in Cardiovascular Diseases: Potential Function as Biomarkers and Therapeutic Targets of Exercise Training. Noncoding RNA 2021; 7:ncrna7040065. [PMID: 34698215 PMCID: PMC8544698 DOI: 10.3390/ncrna7040065] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Despite advances in treatments and therapies, cardiovascular diseases (CVDs) remain one of the leading causes of death worldwide. The discovery that most of the human genome, although transcribed, does not encode proteins was crucial for focusing on the potential of long non-coding RNAs (lncRNAs) as essential regulators of cell function at the epigenetic, transcriptional, and post-transcriptional levels. This class of non-coding RNAs is related to the pathophysiology of the cardiovascular system. The different expression profiles of lncRNAs, in different contexts of CVDs, change a great potential in their use as a biomarker and targets of therapeutic intervention. Furthermore, regular physical exercise plays a protective role against CVDs; on the other hand, little is known about its underlying molecular mechanisms. In this review, we look at the accumulated knowledge on lncRNAs and their functions in the cardiovascular system, focusing on the cardiovascular pathology of arterial hypertension, coronary heart disease, acute myocardial infarction, and heart failure. We discuss the potential of these molecules as biomarkers for clinical use, their limitations, and how the manipulation of the expression profile of these transcripts through physical exercise can begin to be suggested as a strategy for the treatment of CVDs.
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Affiliation(s)
- Camila Caldas Martins Correia
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-030, Brazil;
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Luis Felipe Rodrigues
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Bruno Rocha de Avila Pelozin
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Edilamar Menezes Oliveira
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
| | - Tiago Fernandes
- Laboratory of Biochemistry and Molecular Biology of Exercise, School of Physical Education and Sport, University of Sao Paulo, Sao Paulo 05508-030, Brazil; (L.F.R.); (B.R.d.A.P.); (E.M.O.)
- Correspondence: ; Tel.: + 55-11-2648-1566 (ext. 05508-030)
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30
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Qiu B, Zhong H, Ming S, Zhu C. Effects of LncRNA HOX Transcript Antisense RNA Targeting miRNA-761 on Cervical Cancer Cell Proliferation and Apoptosis. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abnormal LncRNA HOTAIR level is correlated with various cancers and miR-761 can inhibit cancers. LncRNA HOTAIR targets miR-761 by StarBase 2.0 analysis. Our study investigated whether LncRNA HOTAIR can affect cervical cancer cells by regulating miR-761. The control group (NC group),
LncRNA HOTAIR group and LncRNA HOTAIR + miR-761 Mimics group were set up to measure LncRNA HOTAIR and miR-761 level by qRT-PCR. Dual fluorescein reporter assay assessed whether miR-761 binds LncRNA HOTAIR. Western blot was used to measure Cyclin D1, Bcl-2 and Tubulin expression and clone formation
assay was to assess cell proliferation and Annexin VFITC/PI staining was to detect cell apoptosis. Compared with normal tissues, LncRNA HOTAIR level was significantly higher in cervical cancer tissues, while miR-761 was lower (P < 0.01). LncRNA HOTAIR targets miR-761. Compared with
NC group, CyclinD1 and Bcl-2 in LncRNA HOTAIR group were significantly increased (P < 0.01), which were significantly lower in LncRNA HOTAIR + miR-761 Mimics group (P < 0.05). Compared to NC group, miR-761 in LncRNA HOTAIR group was significantly reduced (P <
0.01) and elevated by miR-761 Mimics. In addition, compared to NC group, the number of cell clones in LncRNA HOTAIR group was increased, cell proliferation was increased, and number of apoptotic cells was decreased, which were all reversed in the LncRNA HOTAIR + miR-761 Mimics group. LncRNA
HOTAIR targets miR-761, promotes cell proliferation and reduces cell apoptosis. miR-761 mimics can partially prevent the effects of LncRNA HOTAIR.
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Affiliation(s)
- Bin Qiu
- Department of Gynecology, Xianning Central Hospital (The First Affiliated Hospital of Hubei University of Science and Technology), Xianning, Hubei, 437100, China
| | - Hui Zhong
- Department of Gynecology, Xianning Central Hospital (The First Affiliated Hospital of Hubei University of Science and Technology), Xianning, Hubei, 437100, China
| | - Shenqiu Ming
- Department of Gynecology, Xianning Central Hospital (The First Affiliated Hospital of Hubei University of Science and Technology), Xianning, Hubei, 437100, China
| | - Chunxia Zhu
- Department of Gynecology, Xianning Central Hospital (The First Affiliated Hospital of Hubei University of Science and Technology), Xianning, Hubei, 437100, China
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31
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Potential of Long Non-Coding RNAs in Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms22179178. [PMID: 34502084 PMCID: PMC8431062 DOI: 10.3390/ijms22179178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of visual impairment in the aging population with poorly known pathogenesis and lack of effective treatment. Age and family history are the strongest AMD risk factors, and several loci were identified to contribute to AMD. Recently, also the epigenetic profile was associated with AMD, and some long non-coding RNAs (lncRNAs) were shown to involve in AMD pathogenesis. The Vax2os1/2 (ventral anterior homeobox 2 opposite strand isoform 1) lncRNAs may modulate the balance between pro- and anti-angiogenic factors in the eye contributing to wet AMD. The stress-induced dedifferentiation of retinal pigment epithelium cells can be inhibited by the ZNF503-AS1 (zinc finger protein 503 antisense RNA 2) and LINC00167 lncRNAs. Overexpression of the PWRN2 (Prader-Willi region non-protein-coding RNA 2) lncRNA aggravated RPE cells apoptosis and mitochondrial impairment induced by oxidative stress. Several other lncRNAs were reported to exert protective or detrimental effects in AMD. However, many studies are limited to an association between lncRNA and AMD in patients or model systems with bioinformatics. Therefore, further works on lncRNAs in AMD are rational, and they should be enriched with mechanistic and clinical studies to validate conclusions obtained in high-throughput in vitro research.
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32
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Liu T, Sun Y, Yang S, Liang X. Inhibitory Effect of Selenium on Esophagus Cancer Cells and the Related Mechanism. J Nutr Sci Vitaminol (Tokyo) 2021; 66:456-461. [PMID: 33132349 DOI: 10.3177/jnsv.66.456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Selenium has been associated with many malignant tumors including esophagus cancer (EC). In current study, we examined the effects of three types of selenium, sodium selenite (SSE), methylseleninic acid (MSA) and methylselenocysteine (MSC) on EC cell line Eca109. Here, selenium attenuated cell viability and increased cell apoptosis, especially in MSC, when compared with control group (p<0.05). Meanwhile, MSC and MSA, but no SSE, arrested cell cycle in G0/G1 phase (p<0.05). Mechanistically, FAL1 and PTEN were found to participate in regulating cell cycle and cell apoptosis process by decreasing cyclinD1, CDK2, and promoting caspase-3, caspase-8. In addition, we found that cyclinD1, CDK2 were significantly downregulated by MSA and MSC, while caspase-3, caspase-8 were dramatically upregulated by SSE (p<0.05). Based on these results, we concluded that MSC and MSA inhibit the viability of Eca109 mainly through reducing cell proliferation, while SSE by promoting apoptosis.
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Affiliation(s)
- Tao Liu
- Department of Cardio-Thoracic Surgery, Guangxi International Zhuang Hospital.,Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University
| | - Yu Sun
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University
| | - Shengzhuang Yang
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University
| | - Xiangsen Liang
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Guangxi Medical University
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Wang Y, Wang Y, Zhu B, Zhu Y, Jiang Y, Xiong W, Lin L, Gong Y. MALAT1: A Pivotal lncRNA in the Phenotypic Switch of Gastric Smooth Muscle Cells via the Targeting of the miR-449a/DLL1 Axis in Diabetic Gastroparesis. Front Pharmacol 2021; 12:719581. [PMID: 34385927 PMCID: PMC8353150 DOI: 10.3389/fphar.2021.719581] [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: 06/02/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Diabetic gastroparesis (DGP) is a common complication of diabetes mellitus (DM). Our previous study suggested that the expression of the long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is closely related to DGP. However, the role of MALAT1 in DGP pathogenesis remains unclear. Here, we aim to characterize the role of MALAT1 in DGP. First, we analyzed the lncRNA expression profiles through lncRNA sequencing. Next, we detected MALAT1 expression in the stomach tissues of DGP model mice and diabetic patients. Then, we investigated the role and mechanisms of MALAT1 in the proliferation, migration, phenotypic switch, and carbachol-induced intracellular Ca2+ changes in human gastric smooth muscle cells (HGSMCs) under high glucose (HG) conditions, using short hairpin RNA technology, RNA immunoprecipitation, and dual-luciferase reporter assays. We show that MALAT1 expression was upregulated in the gastric tissues of DGP model mice, the adjacent healthy tissues collected from diabetic gastric cancer patients with DGP symptoms, and in HGSMCs cultured under HG conditions. Functionally, MALAT1 knockdown in vitro impacted the viability, proliferation, migration and promoted the phenotypic switch of HGSMCs under HG conditions. Additionally, we show that MALAT1 sponged miR-449a, regulating Delta-like ligand 1 (DLL1) expression in HGSMCs; any disturbance of the MALAT1/miR-449a/DLL1 pathway affects the proliferation, migration, phenotypic switch, and carbachol-induced Ca2+ transient signals in HGSMCs under HG conditions. Collectively, our data highlight a novel regulatory signaling pathway, the MALAT1/miR-449a/DLL1 axis, in the context of DGP.
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Affiliation(s)
- Yanjuan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Boqian Zhu
- Department of Cardiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Ying Zhu
- Department of Gastroenterology, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Ya Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjie Xiong
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lin Lin
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaoyao Gong
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Xu J, Yin Y, Lin Y, Tian M, Liu T, Li X, Chen S. Long non-coding RNAs: Emerging roles in periodontitis. J Periodontal Res 2021; 56:848-862. [PMID: 34296758 DOI: 10.1111/jre.12910] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023]
Abstract
Periodontitis is a major burden of public health, affecting 20%-50% of the global population. It is a complex inflammatory disease characterized by the destruction of supporting structures of the teeth, leading to tooth loss and the emergence or worsening of systematic diseases. Understanding the molecular mechanisms underlying the physiopathology of periodontitis is beneficial for targeted therapeutics. Long non-coding RNAs (lncRNAs), transcripts made up of more than 200 nucleotides, have emerged as novel regulators of many biological and pathological processes. Recently, an increasing number of dysregulated lncRNAs have been found to be implicated in periodontitis. In this review, an overview of lncRNAs, including their biogenesis, characteristics, function mechanisms and research approaches, is provided. And we summarize recent research reports on the emerging roles of lncRNAs in regulating proliferation, apoptosis, inflammatory responses, and osteogenesis of periodontal cells to elucidate lncRNAs related physiopathology of periodontitis. Furthermore, we have highlighted the underlying mechanisms of lncRNAs in periodontitis pathology by interacting with microRNAs. Finally, the potential clinical applications, current challenges, and prospects of lncRNAs as diagnostic and prognostic biomarkers and therapeutic targets for periodontitis disease are discussed.
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Affiliation(s)
- Jingchen Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yao Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mi Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyi Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Song Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Tang Y, Xie Z, Ma M, Duan K, Li Y, Ye J. LncRNA and mRNA Expression Profiles in Methylprednisolone Stimulated Neural Stem Cells. Front Neurosci 2021; 15:669224. [PMID: 34248482 PMCID: PMC8262496 DOI: 10.3389/fnins.2021.669224] [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: 02/18/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Spinal cord injury (SCI) is a devastating neurological disorder that affects thousands of individuals each year. Previously, our study in non-human primates with SCI demonstrated that methylprednisolone (MP) resulted in the dysfunction of neural stem cells (NSCs), which may help to explain the controversial roles of MP in SCI. However, the detailed mechanism is still unclear. In this manuscript, we investigated the LncRNA and mRNA expression profiles of NSCs treated with MP. A total of 63 differentially expressed LncRNAs and 174 differentially expressed mRNAs were identified. Gene ontology (GO) analysis showed that differentially expressed mRNAs were highly associated with terms related to regulation of external stimulation, secretion, and migration. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results indicated that the PI3K-Akt signaling pathway contributed to the functions of MP treated NSCs. Besides, 3899 co-expression pairs were constructed among the differentially expressed LncRNA and mRNA, among which five predicted target mRNAs with the differentially expressed LncRNAs were identified. These results provide greater insight into the precise mechanisms of MP mediating NSC dysfunction in SCI.
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Affiliation(s)
- Yong Tang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongyu Xie
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mengjun Ma
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Kaidi Duan
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Li
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jichao Ye
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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Zhou L, Xu XL. Long Non-Coding RNA ARAP1-AS1 Facilitates the Progression of Cervical Cancer by Regulating miR-149-3p and POU2F2. Pathobiology 2021; 88:301-312. [PMID: 33965958 DOI: 10.1159/000507830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/12/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Emerging research has demonstrated that long non-coding RNAs (lncRNAs) attach great importance to the progression of cervical cancer (CC). LncRNA ARAP1-AS1 was involved in the development of several cancers; however, its role in CC is far from being elucidated. METHODS Real-time PCR (RT-PCR) was employed to detect ARAP1-AS1 and miR-149-3p expression in CC samples. CC cell lines (HeLa and C33A cells) were regarded as the cell models. The biological effect of ARAP1-AS1 on cancer cells was measured using CCK-8 assay, colony formation assay, flow cytometry, Transwell assay and wound healing assay in vitro, and subcutaneous xenotransplanted tumor model and tail vein injection model in vivo. Furthermore, interactions between ARAP1-AS1 and miR-149-3p, miR-149-3p and POU class 2 homeobox 2 (POU2F2) were determined by bioinformatics analysis, qRT-PCR, Western blot, luciferase reporter and RNA immunoprecipitation assay, respectively. RESULTS The expression of ARAP1-AS1 was enhanced in CC samples, while miR-149-3p was markedly suppressed. Additionally, ARAP1-AS1 overexpression enhanced the viability, migration, and invasion of CC cells. ARAP1-AS1 downregulated miR-149-3p via sponging it. ARAP1-AS1 and miR-149-3p exhibited a negative correlation in CC samples. On the other hand, ARAP1-AS1 enhanced the expression of POU2F2, which was validated as a target gene of miR-149-3p. CONCLUSION ARAP1-AS1 was abnormally upregulated in CC tissues and indirectly modulated the POU2F2 expression via reducing miR-149-3p expression. Our study identified a novel axis, ARAP1-AS1/miR-149-3p/POU2F2, in CC tumorigenesis.
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Affiliation(s)
- Ling Zhou
- Department of Obstetrics and Gynecology, Liyang People's Hospital, Liyang, China
| | - Xiao-Li Xu
- Department of Obstetrics and Gynecology, The First People's Hospital of Changzhou (The Third Affiliated Hospital of Suzhou University), Changzhou, China
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Wang JF, Xi ZN, Su HJ, Bao Z, Qiao YH. SP1-induced overexpression of LINC00520 facilitates non-small cell lung cancer progression through miR-577/CCNE2 pathway and predicts poor prognosis. Hum Cell 2021; 34:952-964. [PMID: 33728585 DOI: 10.1007/s13577-021-00518-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023]
Abstract
Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. Long intergenic non-protein coding RNA 520 (LINC00520) was one of the newly discovered lncRNA which has been demonstrated to be dysregulated in several cancers. So far, the function and mechanism of LINC00520 in non-small cell lung cancer (NSCLC) are unclear. In this paper, our group first showed that LINC00520 level was elevated in non-small cell lung cancer (NSCLC) tissue and cells. In addition, SP1 could bind directly to the promoter region of LINC00520 and thus promote its transcription. Increased LINC00520 was distinctly correlated with advanced tumor stage and shorter survival time in NSCLC patients. Further functional investigations provided evidences that forced down regulation of LINC00520 inhibited NSCLC cell proliferation, invasion, metastasis and EMT, while contributing to cells apoptosis. Mechanistically, we found that LINC00520 serving as a competing endogenous RNA to be involved in the modulation of miR-577 expressions, and thus affected the expression of CCNE2 which was a target gene of miR-577. Moreover, in NSCLC cells with si-LINC00520, up regulation of CCNE2 led to an increase of cell growth and invasion. Taken together, LINC00520 displayed its tumor-promotive roles through modulating the miR-577/CCNE2 axis, highlighting a potential therapeutic strategy for NSCLC patients.
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Affiliation(s)
- Ji-Fang Wang
- Department of Respiration Ward II, Henan Provincial Chest Hospital, Weiwu Road No. 1, Zhengzhou, Henan, China
| | - Zhuo-Na Xi
- Department of Respiration Ward II, Henan Provincial Chest Hospital, Weiwu Road No. 1, Zhengzhou, Henan, China
| | - Hong-Jian Su
- Department of Respiration Ward II, Henan Provincial Chest Hospital, Weiwu Road No. 1, Zhengzhou, Henan, China
| | - Zhen Bao
- Department of Respiration Ward II, Henan Provincial Chest Hospital, Weiwu Road No. 1, Zhengzhou, Henan, China
| | - Ya-Hong Qiao
- Department of Respiration Ward II, Henan Provincial Chest Hospital, Weiwu Road No. 1, Zhengzhou, Henan, China.
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Gu S, Qian L, Liu Y, Miao J, Shen H, Zhang S, Mao G. Upregulation of long non-coding RNA MYU promotes proliferation, migration and invasion of esophageal squamous cell carcinoma cells. Exp Ther Med 2021; 21:644. [PMID: 33968175 PMCID: PMC8097213 DOI: 10.3892/etm.2021.10076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignant tumour type of the digestive system. Long non-coding RNA (lncRNA) c-Myc upregulated (MYU), also known as VPS9 domain-containing 1 antisense 1, was recently discovered. However, the expression of lncRNA MYU in ESCC and its role in tumour progression have remained elusive. In the present study, the expression of lncRNA MYU, Ki-67 and the epithelial-mesenchymal transition-related proteins E-cadherin and Vimentin in ESCC tissues was detected by reverse transcription-quantitative PCR. The expression of Ki-67, E-cadherin and Vimentin in ESCC tissues was also detected by immunohistochemistry. A small interfering RNA plasmid was employed to establish a TE-2 cell line with knockdown on lncRNA MYU. The results indicated that the expression of lncRNA MYU was higher in ESCC tissues than in normal adjacent tissues and that upregulation of lncRNA MYU was a potential biomarker for poor prognosis. The results also suggested that the expression levels of lncRNA MYU were correlated with the histological grade, lymph node metastasis and TNM stage (P<0.05). Silencing of lncRNA MYU expression inhibited the proliferation, migration and invasion, while the expression of lncRNA MYU increased as cell proliferation increased. In addition, the mRNA expression of Vimentin and Ki-67 was decreased in TE-2 cells after lncRNA MYU was knocked down, while E-cadherin mRNA expression was elevated. In conclusion, the present results indicated that lncRNA MYU may regulate the proliferation, migration and invasion of ESCC cells, and may serve as a prognostic biomarker for ESCC.
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Affiliation(s)
- Shudong Gu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Li Qian
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yan Liu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jiefei Miao
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Hong Shen
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Shu Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Guoxin Mao
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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Relationship between lncRNA-Ang362 and prognosis of patients with coronary heart disease after percutaneous coronary intervention. Biosci Rep 2021; 40:225832. [PMID: 32686826 PMCID: PMC7383831 DOI: 10.1042/bsr20201524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023] Open
Abstract
The severity and complexity evaluation of coronary artery disease in patients with coronary heart disease (CHD) require objective and accurate prognosis indexes. We assessed the relationship between lncRNA-Ang362 and prognosis of CHD patients after percutaneous coronary intervention (PCI). Clinical follow-up data of CHD patients were prospectively collected. LncRNA-Ang362 levels were detected by real-time quantitative polymerase chain reaction. Survival rate was calculated by the Kaplan–Meier method, and risk ratios and 95% confidence intervals were computed using univariate and multivariate COX proportional hazard models. Finally, 434 patients were included in the follow-up cohort. The median follow-up time was 24.8 months (6.7–40). The incidence of adverse cardiovascular events was 13.6%. The high expression group significantly tended to be smoker and higher body mass index, low-density lipoprotein cholesterol, high-sensitivity C-reactive protein, creatinine, and uric acid levels compared with the low expression group. According to the SYNTAX grade, the high-risk and medium-risk groups had significantly higher lncRNA expression levels than the low-risk group. The univariate COX regression analysis indicated that high lncRAN-Ang362 expression significantly increased the risk of adverse cardiovascular events in CHD patients after PCI (hazard risk (HR) = 3.19, 95% confidence interval (CI): 1.29–7.92). Multivariate analysis found high lncRNA-Ang362 expression was independently related to worse prognosis in CHD patients after PCI (HR = 2.83, 95%CI: 1.34–6.02). Plasma lncRNA-Ang362 may be a prognosis factor in CHD patients after PCI. The patients with higher lncRNA-Ang362 expression usually have poor prognosis.
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Tetraarsenic oxide affects non-coding RNA transcriptome through deregulating polycomb complexes in MCF7 cells. Adv Biol Regul 2021; 80:100809. [PMID: 33932728 DOI: 10.1016/j.jbior.2021.100809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 11/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play important and diverse roles in mammalian cell biology and pathology. Although the functions of an increasing number of ncRNAs have been identified, the mechanisms underlying ncRNA gene expression remain elusive and are incompletely understood. Here, we investigated ncRNA gene expression in Michigan cancer foundation 7 (MCF7), a malignant breast cancer cell line, on treatment of tetraarsenic oxide (TAO), a potential anti-cancer drug. Our genomic analyses found that TAO up- or down-regulated ncRNA genes genome-wide. A subset of identified ncRNAs with critical biological and clinical functions were validated by real-time quantitative polymerase chain reaction. Intriguingly, these TAO-regulated genes included CDKN2B-AS, HOXA11-AS, SHH, and DUSP5 that are known to interact with or be targeted by polycomb repressive complexes (PRCs). In addition, the PRC subunits were enriched in these TAO-regulated ncRNA genes and TAO treatment deregulated the expression of PRC subunits. Strikingly, TAO decreased the cellular and gene-specific levels of EZH2 expression and H3K27me3. In particular, TAO reduced EZH2 and H3K27me3 and increased transcription at MALAT1 gene. Inhibiting the catalytic activity of EZH2 using GSK343 increased representative TAO-inducible ncRNA genes. Together, our findings suggest that the expression of a subset of ncRNA genes is regulated by PRC2 and that TAO could be a potent epigenetic regulator through PRCs to modulate the ncRNA gene expression in MCF7 cells.
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Gong Y, Zhang Y, Li B, Xiao Y, Zeng Q, Xu K, Duan Y, He J, Ma H. Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig. BIOLOGY 2021; 10:310. [PMID: 33917834 PMCID: PMC8068270 DOI: 10.3390/biology10040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022]
Abstract
Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only CAV1, PACSIN2, and CDC42 in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA-mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.
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Affiliation(s)
- Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
- Ningxiang Pig Farm of Dalong Livestock Technology Co. Ltd., Ningxiang 410600, China
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Yehui Duan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Science, Changsha 410125, China; (K.X.); (Y.D.)
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Y.G.); (Y.Z.); (B.L.); (Y.X.); (Q.Z.); (J.H.)
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Li A, Feng L, Niu X, Zeng Q, Li B, You Z. Downregulation of OIP5-AS1 affects proNGF-induced pancreatic cancer metastasis by inhibiting p75NTR levels. Aging (Albany NY) 2021; 13:10688-10702. [PMID: 33820868 PMCID: PMC8064169 DOI: 10.18632/aging.202847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
We aimed to explore the mechanism by which long non-coding RNA (lncRNA) OIP5-AS1 affects proNGF (precursor nerve growth factor)-induced pancreatic cancer metastasis by targeting the miR-186-5p/NGFR axis. Bioinformatics was used to analyse whether OIP5-AS1 targets miR-186-5p/NGFR and their expression characteristics in pancreatic cancer. OIP5-AS1 and NGFR were overexpressed in pancreatic cancer, and their levels showed a significant positive correlation. Clinical trials also demonstrated that high expression of OIP5-AS1 and NGFR and low expression of miR-186-5p played a pro-cancer role in pancreatic cancer. MiR-186-5p inhibited the migration and invasion of colon cancer cells by targeting NGFR-regulated p75NTR. OIP5-AS1 regulated the action of miR-186-5p on NGFR mRNA and p75NTR by targeting miR-186-5p. Downregulation of NGFR inhibited the expression of p75NTR protein and blocked the role of proNGF in promoting the migration and invasion of pancreatic cancer cells. Animal experiments also showed that the knockdown of miR-186-5p promoted cancer via the expression of NGFR mRNA and p75NTR protein, while the downregulation of proNGF blocked the effects. OIP5-AS1, as a ceRNA, promotes the progression of pancreatic cancer by targeting miR-186-5p/NGFR and affecting the prognosis of patients, which may be related to the action of proNGF.
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Affiliation(s)
- Ang Li
- Department of Pancreatic Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lei Feng
- Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaoya Niu
- Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qihui Zeng
- Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Bei Li
- Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Zhen You
- Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
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Mathias C, Pedroso GA, Pabst FR, de Lima RS, Kuroda F, Cavalli IJ, de Oliveira JC, Ribeiro EMDSF, Gradia DF. So alike yet so different. Differential expression of the long non-coding RNAs NORAD and HCG11 in breast cancer subtypes. Genet Mol Biol 2021; 44:e20200153. [PMID: 33739352 PMCID: PMC7976429 DOI: 10.1590/1678-4685-gmb-2020-0153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/07/2021] [Indexed: 01/04/2023] Open
Abstract
Breast cancer (BC) is a heterogeneous disease, and it is the leading cause of death among women. NORAD and HCG11 are highly similar lncRNAs that present binding sites for PUMILIO proteins. PUMILIO acts on hundreds of mRNA targets, contributing to the modulation of gene expression. We analyzed the expression levels of NORAD and HCG11 in the BC subtypes luminal A (LA) and basal-like (BL), and the regulatory networks associated with these lncRNAs. In the analysis of TCGA cohort (n=329) and Brazilian BC samples (n=44), NORAD was up-regulated in LA while HCG11 was up-regulated in BL subtype. An increased expression of NORAD is associated with reduced disease-free survival in basal-like patients (p = 0.002), which suggests that its prognostic value could be different in specific subtypes. The biological pathways observed for the HCG11 network are linked to the epithelial-to-mesenchymal transition; while NORAD associated pathways appear to be related to luminal epithelial cell transformation. NORAD and HCG11 regulons respectively present 36% and 21.5% of PUMILIO targets, which suggests that these lncRNAs act as a decoy for PUMILIO. These lncRNAs seem to work as players in the differentiation process that drives breast cells to acquire distinct phenotypes related to a specific BC subtype.
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Affiliation(s)
- Carolina Mathias
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós Graduação em Genética, Curitiba, PR, Brazil
| | - Gabrielle Araújo Pedroso
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós Graduação em Genética, Curitiba, PR, Brazil
| | - Fernanda Rezende Pabst
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós Graduação em Genética, Curitiba, PR, Brazil
| | | | - Flavia Kuroda
- Hospital Nossa Senhora das Graças, Centro de Doenças da Mama, Curitiba, PR, Brazil
| | - Iglenir João Cavalli
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós Graduação em Genética, Curitiba, PR, Brazil
| | | | | | - Daniela Fiori Gradia
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós Graduação em Genética, Curitiba, PR, Brazil
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Zhou X, He J, Chen J, Cui Y, Ou Z, Zu X, Liu N. Silencing of MEG3 attenuated the role of lipopolysaccharides by modulating the miR-93-5p/PTEN pathway in Leydig cells. Reprod Biol Endocrinol 2021; 19:33. [PMID: 33639974 PMCID: PMC7913434 DOI: 10.1186/s12958-021-00712-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Leydig cells reflect the activation of inflammation, decrease of androgen production, inhibition of cell growth and promotion of cell apoptosis under orchitis. Maternally expressed gene 3 (MEG3) exerts a crucial role in various human diseases, but under orchitis, the role and underlying molecular mechanism of MEG3 in Leydig cells remain unclear. METHODS Lipofectamine 2000 was used for the cell transfections. qPCR and western blots assay were applied to assess the gene expression. ELISA assay was used to measure the TNFα, IL6 and testosterone secretion. CCK8 and EdU assay was employ to test the cell viability and proliferation respectively. Luciferase reporter and RIP assay were introduced to detect the binding of miR-93-5p with MEG3 and PTEN. RESULTS Lipopolysaccharides (LPS) induced TNFα and IL6 secretion, lowered testosterone production, inhibited cell viability and proliferation, and induced cell apoptosis in Leydig cells. MEG3 was upregulated in Leydig cells treated with LPS and that knockdown of MEG3 inhibited the role of LPS in Leydig cells. MEG3 absorbed miR-93-5p and that suppression of miR-93-5p restored the role of silenced MEG3 in Leydig cells under LPS treatment. miR-93-5p inhibited PTEN expression and that over-expressed PTEN alleviated the effect of miR-93-5p in Leydig cells treated with LPS. LPS activated the MEG3/miR-93-5p/PTEN signalling pathway in Leydig cells. CONCLUSIONS This study revealed that MEG3 serves as a molecular sponge to absorb miR-93-5p, thus leading to elevation of PTEN expression in Leydig cells under LPS treatment, offering a theoretical basis on which to establish potential new treatment strategies for orchitis.
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Affiliation(s)
- Xu Zhou
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Jingliang He
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Zhenyu Ou
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
| | - Nenghui Liu
- Reproductive Medicine Center, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
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Ebrahimpour A, Sarfi M, Rezatabar S, Tehrani SS. Novel insights into the interaction between long non-coding RNAs and microRNAs in glioma. Mol Cell Biochem 2021; 476:2317-2335. [PMID: 33582947 DOI: 10.1007/s11010-021-04080-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
Glioma is the most common brain tumor of the central nervous system. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been identified to play a vital role in the initiation and progression of glioma, including tumor cell proliferation, survival, apoptosis, invasion, and therapy resistance. New documents emerged, which indicated that the interaction between long non-coding RNAs and miRNAs contributes to the tumorigenesis and pathogenesis of glioma. LncRNAs can act as competing for endogenous RNA (ceRNA), and molecular sponge/deregulator in regulating miRNAs. These interactions stimulate different molecular signaling pathways in glioma, including the lncRNAs/miRNAs/Wnt/β-catenin molecular signaling pathway, the lncRNAs/miRNAs/PI3K/AKT/mTOR molecular signaling pathway, the lncRNAs-miRNAs/MAPK kinase molecular signaling pathway, and the lncRNAs/miRNAs/NF-κB molecular signaling pathway. In this paper, the basic roles and molecular interactions of the lncRNAs and miRNAs pathway glioma were summarized to better understand the pathogenesis and tumorigenesis of glioma.
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Affiliation(s)
- Anahita Ebrahimpour
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Sarfi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Rezatabar
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Yin L, Zhu X, Novák P, Zhou L, Gao L, Yang M, Zhao G, Yin K. The epitranscriptome of long noncoding RNAs in metabolic diseases. Clin Chim Acta 2021; 515:80-89. [PMID: 33422492 DOI: 10.1016/j.cca.2021.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have abundant content and extensive functions that regulate the expression of genes at multiple levels. Recently, transcriptome-wide analysis confirmed that RNA can undergo various chemical modifications in response to stimulation by the environment that further determine the action mechanisms of RNAs and expand the diversity of the transcriptome. Modifications that occur in lncRNAs can affect their expression and the regulation of downstream molecules by changing the secondary structure, splicing, degradation or molecular stability of lncRNAs. During the development of metabolic diseases, reversible RNA modifications show a complex transcriptional landscape. Although a wide quantity and variety of lncRNA modifications have been identified, the knowledge regarding their underlying actions in alcohol use disorders (AUDs), osteoporosis, obesity, and cardiovascular disease (CVD) is still in its infancy. Herein, we will focus on the epitranscriptomic modifications that occur on lncRNAs and the crosstalk between them that affect metabolic diseases.
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Affiliation(s)
- Linjie Yin
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Xiao Zhu
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Petr Novák
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Le Zhou
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Ling Gao
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China
| | - Min Yang
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - GuoJun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People's Hospital, Qingyuan 511518, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China.
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Long non-coding RNA levels can be modulated by 5-azacytidine in Schistosoma mansoni. Sci Rep 2020; 10:21565. [PMID: 33299037 PMCID: PMC7725772 DOI: 10.1038/s41598-020-78669-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects more than 200 million people worldwide. There is only one drug indicated for treatment, praziquantel, which may lead to parasite resistance emergence. The ribonucleoside analogue 5-azacytidine (5-AzaC) is an epigenetic drug that inhibits S. mansoni oviposition and ovarian development through interference with parasite transcription, translation and stem cell activities. Therefore, studying the downstream pathways affected by 5-AzaC in S. mansoni may contribute to the discovery of new drug targets. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein coding potential that have been involved in reproduction, stem cell maintenance and drug resistance. We have recently published a catalog of lncRNAs expressed in S. mansoni life-cycle stages, tissues and single cells. However, it remains largely unknown if lncRNAs are responsive to epigenetic drugs in parasites. Here, we show by RNA-Seq re-analyses that hundreds of lncRNAs are differentially expressed after in vitro 5-AzaC treatment of S. mansoni females, including intergenic, antisense and sense lncRNAs. Many of these lncRNAs belong to co-expression network modules related to male metabolism and are also differentially expressed in unpaired compared with paired females and ovaries. Half of these lncRNAs possess histone marks at their genomic loci, indicating regulation by histone modification. Among a selected set of 8 lncRNAs, half of them were validated by RT-qPCR as differentially expressed in females, and some of them also in males. Interestingly, these lncRNAs are also expressed in other life-cycle stages. This study demonstrates that many lncRNAs potentially involved with S. mansoni reproductive biology are modulated by 5-AzaC and sheds light on the relevance of exploring lncRNAs in response to drug treatments in parasites.
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Chen GY, Zhang ZS, Chen Y, Li Y. Long non-coding RNA SNHG9 inhibits ovarian cancer progression by sponging microRNA-214-5p. Oncol Lett 2020; 21:80. [PMID: 33363617 PMCID: PMC7723070 DOI: 10.3892/ol.2020.12341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Ovarian cancer ranks 7th among the most common cancer types affecting women worldwide. A number of studies have confirmed that multiple long non-coding RNAs participate in the occurrence and progression of ovarian cancer. Small nucleolar RNA host gene 9 (SNHG9) serves a role in the progression of glioblastoma and pancreatic cancer. However, the specific biological function of SNHG9 in ovarian cancer has not yet been fully investigated. The present study aimed to determine the biological role and potential molecular mechanism underlying the influence of SNHG9 in ovarian cancer. SNHG9 expression in ovarian cancer cell lines and tissues were measured via reverse transcription-quantitative PCR analysis, and cell proliferation was detected via Cell Counting Kit-8 and colony formation assays. Flow cytometry was performed to assess cell cycle progression, and Transwell and wound healing assays were performed to assess cell invasion and migration abilities. Bioinformatics software was utilized to determine the target genes of SNHG9, which were subsequently verified via dual-luciferase reporter and RNA immunoprecipitation assays. The results demonstrated that SNHG9 expression was remarkably lower in ovarian cancer cell lines and tissues compared with the negative controls. Cell function assays demonstrated that decreased SNHG9 expression notably induced the migration, colony formation, proliferation and invasiveness of ovarian cancer cells. Furthermore, the inhibitory effect of SNHG9 on the migration, colony formation, proliferation and invasion of ovarian cancer cells was partially reversed by miR-214-5p upregulation. Thus, taken together, the current results suggest that SNHG9 may serve as a tumor suppressor gene in ovarian cancer by regulating the miR-214-5p/cryptochrome circadian regulator 2 axis.
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Affiliation(s)
- Gao-Yang Chen
- Department of Oncology, The Second People's Hospital of Taizhou City, Taizhou, Jiangsu 225300, P.R. China
| | - Zhi-Sheng Zhang
- Department of Oncology, The Second People's Hospital of Taizhou City, Taizhou, Jiangsu 225300, P.R. China
| | - Yu Chen
- Department of Oncology, Second Hospital of Shandong University, Jinan, Shandong 250000, P.R. China
| | - Yan Li
- Department of Obstetrics and Gynecology, The Second People's Hospital of Taizhou City, Taizhou, Jiangsu 225300, P.R. China
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The Role of Extracellular Vesicles (EVs) in the Epigenetic Regulation of Bone Metabolism and Osteoporosis. Int J Mol Sci 2020; 21:ijms21228682. [PMID: 33213099 PMCID: PMC7698531 DOI: 10.3390/ijms21228682] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are complex phospholipidic structures actively released by cells. EVs are recognized as powerful means of intercellular communication since they contain many signaling molecules (including lipids, proteins, and nucleic acids). In parallel, changes in epigenetic processes can lead to changes in gene function and finally lead to disease onset and progression. Recent breakthroughs have revealed the complex roles of non-coding RNAs (microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)) in epigenetic regulation. Moreover, a substantial body of evidence demonstrates that non-coding RNAs can be shuttled among the cells and tissues via EVs, allowing non-coding RNAs to reach distant cells and exert systemic effects. Resident bone cells, including osteoclasts, osteoblasts, osteocytes, and endothelial cells, are tightly regulated by non-coding RNAs, and many of them can be exported from the cells to neighboring ones through EVs, triggering pathological conditions. For these reasons, researchers have also started to exploit EVs as a theranostic tool to address osteoporosis. In this review, we summarize some recent findings regarding the EVs’ involvement in the fine regulation of non-coding RNAs in the context of bone metabolism and osteoporosis.
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50
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LINC00473 as an Immediate Early Gene under the Control of the EGR1 Transcription Factor. Noncoding RNA 2020; 6:ncrna6040046. [PMID: 33198374 PMCID: PMC7712511 DOI: 10.3390/ncrna6040046] [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: 10/28/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
Immediate early genes play an essential role in cellular responses to different stimuli. Many of them are transcription factors that regulate the secondary response gene expression. Non-coding RNAs may also be involved in this regulatory cascade. In fact, they are emerging as key actors of gene expression regulation, and evidence suggests that their dysregulation may underly pathological states. We previously took a snapshot of both coding and long non-coding RNAs differentially expressed in neuronal cells after brain-derived neurotrophic factor stimulation. Among these, the transcription factor EGR1 (a well-known immediate early gene) and LINC00473 (a primate-specific long non-coding RNA) that has emerged as an interesting RNA candidate involved in neuronal function and in cancer. In this work, we demonstrated that LINC00473 gene expression kinetics resembled that of immediate early genes in SH-SY5Y and HEK293T cells under different cell stimulation conditions. Moreover, we showed that the expression of LINC00473 is under the control of the transcription factor EGR1, providing evidence for an interesting functional relationship in neuron function.
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