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Kumar J, Kowluru RA. Mitochondrial DNA transcription and mitochondrial genome-encoded long noncoding RNA in diabetic retinopathy. Mitochondrion 2024; 78:101925. [PMID: 38944370 DOI: 10.1016/j.mito.2024.101925] [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: 02/14/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
In diabetic retinopathy, mitochondrial DNA (mtDNA) is damaged and mtDNA-encoded genes and long noncoding RNA cytochrome B (LncCytB) are downregulated. LncRNAs lack an open reading frame, but they can regulate gene expression by associating with DNA/RNA/protein. Double stranded mtDNA has promoters on both heavy (HSP) and light (LSP) strands with binding sites for mitochondrial transcription factor A (TFAM) between them. The aim was to investigate the role of LncCytB in mtDNA transcription in diabetic retinopathy. Using human retinal endothelial cells incubated in high glucose, the effect of regulation of LncCytB on TFAM binding at mtDNA promoters was investigated by Chromatin immunoprecipitation, and binding of LncCytB at TFAM by RNA immunoprecipitation and RNA fluorescence in situ hybridization. High glucose decreased TFAM binding at both HSP and LSP, and binding of LncCytB at TFAM. While LncCytB overexpression ameliorated decrease in TFAM binding and transcription of genes encoded by both H- and L- strands, LncCytB-siRNA further downregulated them. Maintenance of mitochondrial homeostasis by overexpressing mitochondrial superoxide dismutase or Sirtuin-1 protected diabetes-induced decrease in TFAM binding at mtDNA and LncCytB binding at TFAM, and mtDNA transcription. Similar results were obtained from mouse retinal microvessels from streptozotocin-induced diabetic mice. Thus, LncCytB facilitates recruitment of TFAM at HSP and LSP, and its downregulation in diabetes compromises the binding, resulting in the downregulation of polypeptides encoded by mtDNA. Regulation of LncCytB, in addition to protecting mitochondrial genomic stability, should also help in maintaining the transcription of mtDNA encoded genes and electron transport chain integrity in diabetic retinopathy.
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Affiliation(s)
- Jay Kumar
- Ophthalmology, Visual and Anatomical Sciences, Wayne State University, 4717 St. Antoine, Detroit, MI 48201, USA
| | - Renu A Kowluru
- Ophthalmology, Visual and Anatomical Sciences, Wayne State University, 4717 St. Antoine, Detroit, MI 48201, USA.
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2
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Weiss M, Hettrich S, Hofmann T, Hachim S, Günther S, Braun T, Boettger T. Mitolnc controls cardiac BCAA metabolism and heart hypertrophy by allosteric activation of BCKDH. Nucleic Acids Res 2024; 52:6629-6646. [PMID: 38567728 PMCID: PMC11194096 DOI: 10.1093/nar/gkae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 06/25/2024] Open
Abstract
Enzyme activity is determined by various different mechanisms, including posttranslational modifications and allosteric regulation. Allosteric activators are often metabolites but other molecules serve similar functions. So far, examples of long non-coding RNAs (lncRNAs) acting as allosteric activators of enzyme activity are missing. Here, we describe the function of mitolnc in cardiomyocytes, a nuclear encoded long non-coding RNA, located in mitochondria and directly interacting with the branched-chain ketoacid dehydrogenase (BCKDH) complex to increase its activity. The BCKDH complex is critical for branched-chain amino acid catabolism (BCAAs). Inactivation of mitolnc in mice reduces BCKDH complex activity, resulting in accumulation of BCAAs in the heart and cardiac hypertrophy via enhanced mTOR signaling. We found that mitolnc allosterically activates the BCKDH complex, independent of phosphorylation. Mitolnc-mediated regulation of the BCKDH complex constitutes an important additional layer to regulate the BCKDH complex in a tissue-specific manner, evading direct coupling of BCAA metabolism to ACLY-dependent lipogenesis.
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Affiliation(s)
- Maria Weiss
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Sara Hettrich
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Theresa Hofmann
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Salma Hachim
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Stefan Günther
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Thomas Braun
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Thomas Boettger
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
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3
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Tan Z, Luan S, Wang X, Jiao W, Jiang P. Mechanism study of lncRNA RMRP regulating esophageal squamous cell carcinoma through miR-580-3p/ATP13A3 axis. Discov Oncol 2024; 15:150. [PMID: 38722543 PMCID: PMC11082096 DOI: 10.1007/s12672-024-00990-6] [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: 07/27/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVE It is well-known that lncRNAs regulate energy metabolism in tumors. This study focused on the action of RMRP on esophageal squamous cell carcinoma (ESCC) cell proliferation, apoptosis, and glycolysis. METHODS In the resected ESCC tissues and adjacent tissues from patients, RMRP/miR-580-3p/ATP13A3 expressions were evaluated. ESCC cell proliferation rates and apoptotic rates were measured by CCK-8 and flow cytometry, respectively. Apoptosis related markers were examined by Western blot. Moreover, glucose uptake, lactic acid, and ATP were measured by commercial kits, whereas HK2 and PKM2 were evaluated by Western blot to study ESCC cell glycolysis. Finally, the editing program of RMRP/miR-580-3p/ATP13A3 was translated by luciferase reporter assay and RIP analysis. RESULTS RMRP and ATP13A3 were induced, while miR-580-3p was reduced in their expression in ESCC tissues. Silencing RMRP reduced proliferation, glycolysis, and anti-apoptosis ability of ESCC cells. RMRP sequestered miR-580-3p to target ATP13A3. Silenced ATP13A3 or overexpressed miR-580-3p rescued overexpressed RMRP-mediated promotion of proliferation, glycolysis, and anti-apoptosis of ESCC cells. CONCLUSION RMRP accelerates ESCC progression through the miR-580-3p/ATP13A3 axis, renewing a reference for lncRNA-based therapies for tumors.
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Affiliation(s)
- ZiRui Tan
- The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Chang'an District, Shijiazhuang City, 050000, Hebei Province, China
| | - ShengJie Luan
- Department of Tumor Chemoradiotherapy, Central Hospital of Qinghe County, Xingtai City, 054800, Hebei Province, China
| | - XiaoPeng Wang
- Department of Tumor Chemoradiotherapy, Central Hospital of Qinghe County, Xingtai City, 054800, Hebei Province, China
| | - WenPeng Jiao
- The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Chang'an District, Shijiazhuang City, 050000, Hebei Province, China
| | - Pu Jiang
- The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Chang'an District, Shijiazhuang City, 050000, Hebei Province, China.
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4
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Mohammad G, Kumar J, Kowluru RA. Mitochondrial Genome-Encoded Long Noncoding RNA Cytochrome B and Mitochondrial Dysfunction in Diabetic Retinopathy. Antioxid Redox Signal 2023; 39:817-828. [PMID: 37464864 PMCID: PMC10654995 DOI: 10.1089/ars.2023.0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023]
Abstract
Aims: Mitochondrial dysfunction is closely associated with the development of diabetic complications. In diabetic retinopathy, electron transport chain is compromised and mitochondrial DNA (mtDNA) is damaged, downregulating transcription of mtDNA-encoded cytochrome B (CYTB) and its antisense long noncoding RNA, long noncoding RNA cytochrome B (LncCytB). Our goal was to investigate the role of LncCytB in the regulation of CYTB and mitochondrial function in diabetic retinopathy. Methods: Using human retinal endothelial cells, genetically manipulated for LncCytB (overexpression or silencing), the effect of high glucose (20 mM d-glucose) on LncCytB-CYTB interactions (by chromatin isolation by RNA purification), CYTB gene expression (by real-time quantitative polymerase chain reaction), complex III activity, mitochondrial free radicals, and oxygen consumption rate (OCR, by Seahorse XF analyzer) was investigated. Key results were confirmed in the retinal microvessels from streptozotocin-induced diabetic mice. Results: High glucose decreased LncCytB-CYTB interactions, and while LncCytB overexpression ameliorated glucose-induced decrease in CYTB gene transcripts, complex III activity and OCR and increase in mitochondrial reactive oxygen species, LncCytB-siRNA further attenuated CYTB gene transcription, complex III activity, and OCR. Similar decrease in LncCytB-CYTB interactions and CYTB transcription was observed in diabetic mice. Furthermore, maintenance of mitochondrial homeostasis by overexpressing superoxide dismutase or sirtuin 1 in mice ameliorated diabetes-induced decrease in LncCytB-CYTB interactions and CYTB gene transcripts, and also improved complex III activity and mitochondrial respiration. Innovation and Conclusion: LncCytB downregulation in hyperglycemic milieu downregulates CYTB transcription, which inhibits complex III activity and compromises mitochondrial stability and OCR. Thus, preventing LncCytB downregulation in diabetes has potential of inhibiting the development of diabetic retinopathy, possibly via maintaining mitochondrial respiration. Antioxid. Redox Signal. 39, 817-828.
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Affiliation(s)
- Ghulam Mohammad
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jay Kumar
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Renu A. Kowluru
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
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5
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Roso-Mares A, Andújar I, Díaz Corpas T, Sun BK. Non-coding RNAs as skin disease biomarkers, molecular signatures, and therapeutic targets. Hum Genet 2023:10.1007/s00439-023-02588-4. [PMID: 37580609 DOI: 10.1007/s00439-023-02588-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/23/2023] [Indexed: 08/16/2023]
Abstract
Non-coding RNAs (ncRNAs) are emerging as biomarkers, molecular signatures, and therapeutic tools and targets for diseases. In this review, we focus specifically on skin diseases to highlight how two classes of ncRNAs-microRNAs and long noncoding RNAs-are being used to diagnose medical conditions of unclear etiology, improve our ability to guide treatment response, and predict disease prognosis. Furthermore, we explore how ncRNAs are being used as both as drug targets and associated therapies have unique benefits, risks, and challenges to development, but offer a distinctive promise for improving patient care and outcomes.
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Affiliation(s)
- Andrea Roso-Mares
- Department of Dermatology, University of California San Diego, San Diego, CA, USA
- Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Isabel Andújar
- Department of Pharmacology, University of Valencia, Valencia, Spain
| | - Tania Díaz Corpas
- Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Department of Dermatology, Hospital Dr Peset, Valencia, Spain
| | - Bryan K Sun
- Department of Dermatology, University of California San Diego, San Diego, CA, USA.
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6
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Wang Y, Zhang W, Xu G, Shi C, Wang X, Qu J, Wang H, Liu C. The role of TRPV4 in the regulation of retinal ganglion cells apoptosis in rat and mouse. Heliyon 2023; 9:e17583. [PMID: 37456002 PMCID: PMC10338314 DOI: 10.1016/j.heliyon.2023.e17583] [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: 10/06/2022] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Retinal ganglion cell (RGC) damages are common in glaucoma, causing atrophy of the optic papilla, visual field damage, and visual loss. Transient receptor potential vanilloid 4 (TRPV4) is significantly expressed in the eyeball and is sensitive to mechanical and osmotic pressure. However, the specific role and mechanism of TRPV4 in glaucoma and RGC progression remain unclear. TRPV4 expression was detected in RGCs under different pressure culture conditions. We also explored the pressure effect on TRPV4 expression and the role and mechanism behind the functional regulation of RGCs. Immunofluorescence staining, western blotting, and TUNEL were utilized in this study. Our results established that TRPV4 was expressed in RGCs. TRPV4 expression was decreased at 40 mmHg and 60 mmHg, and the expression of BAX at 40 mmHg, 60 mmHg. Additionally, the expression of caspase 9 protein increased at 40 mmHg with the pressure increase compared with the conventional culture group. TUNEL staining revealed that the apoptosis rate of RGCs was elevated at 40 mmHg and 60 mmHg, compared with the traditional culture group. Therefore, the expression of BAX and caspase 9 increased, along with the apoptosis rate of RGCs compared with the control group. However, after TRPV4 antagonist treatment, the expression of BAX and caspase 9 decreased, and the apoptosis rate of RGCs decreased. Thus, TRPV4 may affect the mitochondrial apoptosis pathway, such as BAX and caspase 9, leading to the apoptosis of RGCs. The antagonists of TRPV4 could provide a new idea for clinically treating acute glaucoma.
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Affiliation(s)
- Yi Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, 271000, China
| | - Wei Zhang
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Guozheng Xu
- Department of Physiology and Neurobiology, Functional Laboratory, Shandong First Medical University, Jinan, Shandong, 250117, China
| | - Changwei Shi
- Department of Physiology and Neurobiology, Functional Laboratory, Shandong First Medical University, Jinan, Shandong, 250117, China
| | - Xiang Wang
- School of Clinical Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, 271016, China
| | - Jianfeng Qu
- Medical Engineering and Technology Research Center, Shandong First Medical University, Taian, Shandong, 271000, China
| | - Hongmei Wang
- School of Medicine, Southeast University, Nanjing, 210009, China
| | - Chunhua Liu
- Department of Physiology and Neurobiology, Functional Laboratory, Shandong First Medical University, Jinan, Shandong, 250117, China
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7
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Gallo Cantafio ME, Torcasio R, Viglietto G, Amodio N. Non-Coding RNA-Dependent Regulation of Mitochondrial Dynamics in Cancer Pathophysiology. Noncoding RNA 2023; 9:ncrna9010016. [PMID: 36827549 PMCID: PMC9964195 DOI: 10.3390/ncrna9010016] [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: 01/04/2023] [Revised: 02/07/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023] Open
Abstract
Mitochondria are essential organelles which dynamically change their shape and number to adapt to various environmental signals in diverse physio-pathological contexts. Mitochondrial dynamics refers to the delicate balance between mitochondrial fission (or fragmentation) and fusion, that plays a pivotal role in maintaining mitochondrial homeostasis and quality control, impinging on other mitochondrial processes such as metabolism, apoptosis, mitophagy, and autophagy. In this review, we will discuss how dysregulated mitochondrial dynamics can affect different cancer hallmarks, significantly impacting tumor growth, survival, invasion, and chemoresistance. Special emphasis will be given to emerging non-coding RNA molecules targeting the main fusion/fission effectors, acting as novel relevant upstream regulators of the mitochondrial dynamics rheostat in a wide range of tumors.
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Affiliation(s)
| | - Roberta Torcasio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Laboratory of Cellular and Molecular Cardiovascular Pathophysiology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Arcavacata di Rende, 87036 Cosenza, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
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8
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Kowluru RA, Mohammad G. Epigenetic modifications in diabetes. Metabolism 2022; 126:154920. [PMID: 34715117 DOI: 10.1016/j.metabol.2021.154920] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/25/2022]
Abstract
Diabetes is now considered as a 'silent epidemic' that claims over four million lives every year, and the disease knows no socioeconomic boundaries. Despite extensive efforts by the National and International organizations, and cutting-edge research, about 11% world's population is expected to suffer from diabetes (and its complications) by year 2045. This life-long disease damages both the microvasculature and the macrovasculature of the body, and affects many metabolic and molecular pathways, altering the expression of many genes. Recent research has shown that external factors, such as environmental factors, lifestyle and pollutants can also regulate gene expression, and contribute in the disease development and progression. Many epigenetic modifications are implicated in the development of micro- and macro- vascular complications including DNA methylation and histone modifications of several genes implicated in their development. Furthermore, several noncoding RNAs, such as micro RNAs and long noncoding RNAs, are also altered, affecting many biochemical pathways. Epigenetic modifications, however, have the advantage that they could be passed to the next generation, or can be erased. They are now being explored as therapeutical target(s) in the cancer field, which opens up the possibility to use them for treating diabetes and preventing/slowing down its complications.
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Affiliation(s)
- Renu A Kowluru
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, USA.
| | - Ghulam Mohammad
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, USA
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9
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Mohammad G, Kowluru RA. Nuclear Genome-Encoded Long Noncoding RNAs and Mitochondrial Damage in Diabetic Retinopathy. Cells 2021; 10:cells10123271. [PMID: 34943778 PMCID: PMC8699566 DOI: 10.3390/cells10123271] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022] Open
Abstract
Retinal mitochondria are damaged in diabetes-accelerating apoptosis of capillary cells, and ultimately, leading to degenerative capillaries. Diabetes also upregulates many long noncoding RNAs (LncRNAs), including LncMALAT1 and LncNEAT1. These RNAs have more than 200 nucleotides and no open reading frame for translation. LncMALAT1 and LncNEAT1 are encoded by nuclear genome, but nuclear-encoded LncRNAs can also translocate in the mitochondria. Our aim was to investigate the role of LncMALAT1 and LncNEAT1 in mitochondrial homeostasis. Using human retinal endothelial cells, the effect of high glucose on LncMALAT1 and LncNEAT1 mitochondrial localization was examined by RNA fluorescence in situ hybridization. The role of these LncRNAs in mitochondrial membrane potential (by JC-I staining), mtDNA integrity (by extended length PCR) and in protective mtDNA nucleoids (by SYBR green staining) was examined in MALAT1- or NEAT1-siRNA transfected cells. High glucose increased LncMALAT1 and LncNEAT1 mitochondrial expression, and MALAT1-siRNA or NEAT1-siRNA ameliorated glucose-induced damage to mitochondrial membrane potential and mtDNA, and prevented decrease in mtDNA nucleoids. Thus, increased mitochondrial translocation of LncMALAT1 or LncNEAT1 in a hyperglycemic milieu plays a major role in damaging the mitochondrial structural and genomic integrity. Regulation of these LncRNAs can protect mitochondrial homeostasis, and ameliorate formation of degenerative capillaries in diabetic retinopathy.
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Affiliation(s)
- Ghulam Mohammad
- Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, MI 48201, USA;
| | - Renu A. Kowluru
- Kresge Eye Institute, 4717 St. Antoine, Detroit, MI 48201, USA
- Correspondence: ; Tel.: +1-313-993-6714
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10
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Chitneedi PK, Weikard R, Arranz JJ, Martínez-Valladares M, Kuehn C, Gutiérrez-Gil B. Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep. Front Genet 2021; 12:685341. [PMID: 34194481 PMCID: PMC8236958 DOI: 10.3389/fgene.2021.685341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene co-expression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection.
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Affiliation(s)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.,Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Christa Kuehn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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11
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Zhao Y, Zhou L, Li H, Sun T, Wen X, Li X, Meng Y, Li Y, Liu M, Liu S, Kim SJ, Xiao J, Li L, Zhang S, Li W, Cohen P, Hoffman AR, Hu JF, Cui J. Nuclear-Encoded lncRNA MALAT1 Epigenetically Controls Metabolic Reprogramming in HCC Cells through the Mitophagy Pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:264-276. [PMID: 33425485 PMCID: PMC7773746 DOI: 10.1016/j.omtn.2020.09.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial dysfunction is a metabolic hallmark of cancer cells. In search of molecular factors involved in this dysregulation in hepatocellular carcinoma (HCC), we found that the nuclear-encoded long noncoding RNA (lncRNA) MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) was aberrantly enriched in the mitochondria of hepatoma cells. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we showed that MALAT1 interacted with multiple loci on mitochondrial DNA (mtDNA), including D-loop, COX2, ND3, and CYTB genes. MALAT1 knockdown induced alterations in the CpG methylation of mtDNA and in mitochondrial transcriptomes. This was associated with multiple abnormalities in mitochondrial function, including altered mitochondrial structure, low oxidative phosphorylation (OXPHOS), decreased ATP production, reduced mitophagy, decreased mtDNA copy number, and activation of mitochondrial apoptosis. These alterations in mitochondrial metabolism were associated with changes in tumor phenotype and in pathways involved in cell mitophagy, mitochondrial apoptosis, and epigenetic regulation. We further showed that the RNA-shuttling protein HuR and the mitochondria transmembrane protein MTCH2 mediated the transport of MALAT1 in this nuclear-mitochondrial crosstalk. This study provides the first evidence that the nuclear genome-encoded lncRNA MALAT1 functions as a critical epigenetic player in the regulation of mitochondrial metabolism of hepatoma cells, laying the foundation for further clarifying the roles of lncRNAs in tumor metabolic reprogramming.
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Affiliation(s)
- Yijing Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tingge Sun
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xueli Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Ying Meng
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Mengmeng Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jialin Xiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Lingyu Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew R. Hoffman
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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12
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Xue W, Zheng Y, Shen Z, Li L, Fan Z, Wang W, Zhu Z, Zhai Y, Zhao J, Kan Q. Involvement of long non-coding RNAs in the progression of esophageal cancer. Cancer Commun (Lond) 2021; 41:371-388. [PMID: 33605567 PMCID: PMC8118593 DOI: 10.1002/cac2.12146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/12/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Esophageal cancer (EC) is one of the most common malignant tumors of the digestive system with high incidence and mortality rate worldwide. Therefore, exploring the pathogenesis of EC and searching for new targeted therapies are the current research hotspot for EC treatment. Long non‐coding RNAs (lncRNAs) are endogenous RNAs with more than 200 nucleotides, but without protein‐coding function. In recent years, lncRNAs have gradually become the focuses in the field of non‐coding RNA. Some lncRNAs have been proved to be closely related to the pathogenesis of EC. Many lncRNAs are abnormally expressed in EC and participate in many biological processes including cell proliferation, apoptosis, and metastasis by inhibiting or promoting target gene expression. LncRNAs can also regulate the progression of EC through epithelial‐mesenchymal transformation (EMT), which is closely related to the occurrence, development, and prognosis of EC. In this article, we review and discuss the involvement of lncRNAs in the progression of EC.
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Affiliation(s)
- Wenhua Xue
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Yuanyuan Zheng
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Zhibo Shen
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Lifeng Li
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Zhirui Fan
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Wenbin Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Zijia Zhu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
| | - Yunkai Zhai
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Jie Zhao
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, Henan, 450052, P. R. China
| | - Quancheng Kan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, Henan, 450052, P. R. China
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13
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Metabolic Reprogramming by Malat1 Depletion in Prostate Cancer. Cancers (Basel) 2020; 13:cancers13010015. [PMID: 33375130 PMCID: PMC7801945 DOI: 10.3390/cancers13010015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is one of the most common cancers in developed countries, being the second leading cause of cancer death among men. Surgery is the primary therapeutic option, but about one-third of patients develop a recurrence within ten years, for which successful therapy is unavailable. Based on these observations, it has become urgent to develop novel molecular tools for predicting clinical outcome. Here, we focus on one of the best characterized cancer-associated long non-coding transcripts, namely metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). This study highlighted a novel role for MALAT1 as a controller of prostate cancer metabolism. MALAT1 silencing caused a metabolic rewire in both experimental models adopted, prostate cancer cell lines, and organotypic slice cultures derived from surgical specimens. PCa cells upon MALAT1 silencing revert their phenotype towards glycolysis, which is characteristic of normal prostate cells. In this regard, MALAT1 targeting may represent a promising diagnostic tool and a novel therapeutic option. Abstract The lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) promotes growth and progression in prostate cancer (PCa); however, little is known about its possible impact in PCa metabolism. The aim of this work has been the assessment of the metabolic reprogramming associated with MALAT1 silencing in human PCa cells and in an ex vivo model of organotypic slice cultures (OSCs). Cultured cells and OSCs derived from primary tumors were transfected with MALAT1 specific gapmers. Cell growth and survival, gene profiling, and evaluation of targeted metabolites and metabolic enzymes were assessed. Computational analysis was made considering expression changes occurring in metabolic markers following MALAT1 targeting in cultured OSCs. MALAT1 silencing reduced expression of some metabolic enzymes, including malic enzyme 3, pyruvate dehydrogenase kinases 1 and 3, and choline kinase A. Consequently, PCa metabolism switched toward a glycolytic phenotype characterized by increased lactate production paralleled by growth arrest and cell death. Conversely, the function of mitochondrial succinate dehydrogenase and the expression of oxidative phosphorylation enzymes were markedly reduced. A similar effect was observed in OSCs. Based on this, a predictive algorithm was developed aimed to predict tumor recurrence in a subset of patients. MALAT1 targeting by gapmer delivery restored normal metabolic energy pathway in PCa cells and OSCs.
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14
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Liu PF, Farooqi AA, Peng SY, Yu TJ, Dahms HU, Lee CH, Tang JY, Wang SC, Shu CW, Chang HW. Regulatory effects of noncoding RNAs on the interplay of oxidative stress and autophagy in cancer malignancy and therapy. Semin Cancer Biol 2020; 83:269-282. [PMID: 33127466 DOI: 10.1016/j.semcancer.2020.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) regulation of various diseases including cancer has been extensively studied. Reactive oxidative species (ROS) elevated by oxidative stress are associated with cancer progression and drug resistance, while autophagy serves as an ROS scavenger in cancer cells. However, the regulatory effects of ncRNAs on autophagy and ROS in various cancer cells remains complex. Here, we explore how currently investigated ncRNAs, mainly miRNAs and lncRNAs, are involved in ROS production through modulating antioxidant genes. The regulatory effects of miRNAs and lncRNAs on autophagy-related (ATG) proteins to control autophagy activity in cancer cells are discussed. Moreover, differential expression of ncRNAs in tumor and normal tissues of cancer patients are further analyzed using The Cancer Genome Atlas (TCGA) database. This review hypothesizes links between ATG genes- or antioxidant genes-modulated ncRNAs and ROS production, which might result in tumorigenesis, malignancy, and cancer recurrence. A better understanding of the regulation of ROS and autophagy by ncRNAs might advance the use of ncRNAs as diagnostic and prognostic markers as well as therapeutic targets in cancer therapy.
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Affiliation(s)
- Pei-Feng Liu
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Ammad Ahmad Farooqi
- Department of Molecular Oncology, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
| | - Sheng-Yao Peng
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Tzu-Jung Yu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
| | - Cheng-Hsin Lee
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Sheng-Chieh Wang
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Chih-Wen Shu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan; Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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15
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Shi Y, Zheng X, Zheng M, Wang L, Chen Y, Shen Y. Identification of mitochondrial function-associated lncRNAs in septic mice myocardium. J Cell Biochem 2020; 122:53-68. [PMID: 32786114 DOI: 10.1002/jcb.29831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 05/30/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
The present study aimed to analyze long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in septic mice heart and to identify potential lncRNAs and mRNAs that be responsible for cardiac mitochondrial dysfunction during sepsis. Mice were treated with 10 mg/kg of lipopolysaccharides to induce sepsis. LncRNAs and mRNAs expression were evaluated by using lncRNA and mRNA microarray or real-time polymerase chain reaction technique. LncRNA-mRNA coexpression network assay, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed. The results showed that 1275 lncRNAs were differentially expressed in septic myocardium compared with those in the control group. A total of 2769 mRNAs were dysregulated in septic mice heart, most of which are mainly related to the process of inflammation, mitochondrial metabolism, oxidative stress, and apoptosis. Coexpression network analysis showed that 14 lncRNAs were highly correlated with 11 mitochondria-related differentially expressed mRNA. Among all lncRNAs and their cis-acting mRNAs, 41 lncRNAs-mRNA pairs (such as NONMMUG004378 and Apaf1 gene) were enriched in GO terms and KEGG pathways. In summary, we gained some specific lncRNAs and their potential target mRNAs that might be involved in mitochondrial dysfunction in septic myocardium. These findings provide a panoramic view of lncRNA and might allow developing new treatment strategies for sepsis.
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Affiliation(s)
- Yingzhou Shi
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohe Zheng
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingzhi Zheng
- Department of Pharmacology, Hangzhou Medical College, Hangzhou, China
| | - Linlin Wang
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou, China.,Department of Orthopaedics of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingying Chen
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou, China.,Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yueliang Shen
- Department of Basic Medicine Sciences, Zhejiang University School of Medicine, Hangzhou, China
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16
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Lin W, Huang Z, Xu Y, Chen X, Chen T, Ye Y, Ding J, Chen Z, Chen L, Qiu X, Qiu S. A three-lncRNA signature predicts clinical outcomes in low-grade glioma patients after radiotherapy. Aging (Albany NY) 2020; 12:9188-9204. [PMID: 32453707 PMCID: PMC7288909 DOI: 10.18632/aging.103189] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Although radiation therapy (RT) plays a critical role in the treatment of low-grade glioma (LGG), many patients suffer from adverse effects without experiencing survival benefits. In various carcinomas, long non-coding RNAs (lncRNAs) contribute to pathogenic processes, including tumorigenesis, metastasis, chemoresistance, and radioresistance. Currently, the role of lncRNAs in the radiosensitivity of LGG is largely unknown. Here, we downloaded clinical data for 167 LGG patients from The Cancer Genome Atlas database and divided them between radiosensitive and radioresistant groups based on their clinical outcomes after receiving radiotherapy. We identified 37 lncRNAs that were differentially expressed (DElncRNAs) between the groups. Functional enrichment analysis revealed that their potential target mRNAs were mainly enriched in the PI3K-Akt and MAPK signaling pathways and in DNA damage response. Kaplan-Meier survival analysis revealed that increased expression of six lncRNAs was significantly associated with radiosensitivity. We then developed a risk signature based on three of the DElncRNAs that served as an independent biomarker for predicting LGG patient outcomes after radiotherapy. In vitro experiments further validated the biological function of these lncRNAs on low-grade glioma radiation response.
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Affiliation(s)
- Wanzun Lin
- Department of Radiation Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Zongwei Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Yanyan Xu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaochuan Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Ting Chen
- Department of Chemotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuling Ye
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Jianming Ding
- Department of Radiation Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Zhangjie Chen
- Department of Chemotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Long Chen
- Division of Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
| | - Xianxin Qiu
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Shanghai, China
| | - Sufang Qiu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
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17
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Zhao L, Bi M, Zhang H, Shi M. Downregulation of NEAT1 Suppresses Cell Proliferation, Migration, and Invasion in NSCLC Via Sponging miR-153-3p. Cancer Biother Radiopharm 2020; 35:362-370. [PMID: 32380843 DOI: 10.1089/cbr.2019.3119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Long noncoding RNA nuclear enriched abundant transcript 1 (NEAT1) has been reported to play a promotive role in nonsmall cell lung cancer (NSCLC) progression through microRNAs (miRNAs). However, the exact influence and mechanism of NEAT1 were unsatisfied. Methods: Quantitative real-time polymerase chain reaction was applied to examine the expression of NEAT1 and miR-153-3p. The cell proliferation ability, apoptosis rate, migration, and invasion were measured by Cell Counting Kit-8 (CCK8) assay, flow cytometry, and transwell assay, respectively. The epithelial-mesenchymal transition process and Wnt/β-catenin signaling pathway were verified by Western blot. The interaction between NEAT1 and miR-153-3p was confirmed by dual-luciferase reporter assay and RNA immunoprecipitation assay. Results: These data showed that NEAT1 is highly expressed in NSCLC tissues and cell lines. Knockdown of NEAT1 suppresses cell proliferation, invasion, migration, and induces the cell apoptosis in NSCLC cell lines. At the same time, NEAT1 directly interacts with miR-153-3p in NSCLC. In addition, upregulation of miR-153-3p inhibits the cell progression, and miR-153-3p inhibitor recovers the inhibition effect of si-NEAT1 in NSCLC cell lines. Subsequently, si-NEAT1 inhibits Wnt/β-catenin signaling pathway, which is reactivated by miR-153-3p inhibitor. Conclusions: Knockdown of NEAT1 could suppress cell proliferation, migration, and invasion of NSCLC while promoting cell apoptosis through sponging miR-153-3p.
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Affiliation(s)
- Lun Zhao
- Department of Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Minghong Bi
- Department of Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Haoran Zhang
- Department of Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Mohan Shi
- Department of Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
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18
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Chaleshi V, Irani S, Alebouyeh M, Mirfakhraie R, Aghdaei HA. Association of lncRNA-p53 regulatory network (lincRNA-p21, lincRNA-ROR and MALAT1) and p53 with the clinicopathological features of colorectal primary lesions and tumors. Oncol Lett 2020; 19:3937-3949. [PMID: 32391102 PMCID: PMC7204634 DOI: 10.3892/ol.2020.11518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/10/2019] [Indexed: 01/20/2023] Open
Abstract
Colorectal cancer (CRC) is a common intestinal cancer with a high mortality rate. Early detection of this type of cancer is fundamental to the prevention of the disease, which results in improved survival rates. In the human colon tissue, transition from normal epithelium to adenoma is considered to be caused by unknown molecular incidents occurring over 5-10 years. The detection of CRC has proved problematic when in the early stages of disease. In addition, identifying suitable biomarkers for the detection of CRC progress in patients remains one of the most significant challenges. Long non-coding RNAs have been demonstrated to contribute to the promotion of CRC. The aim of the present study was to investigate the clinical and biological significance of long intergenic non-coding (linc)RNA-p21, lincRNA-regulator of reprogramming (ROR) and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in the colon tumor and polyp tissue, and the association that these have with the expression of p53 at the mRNA level. Neoplastic and paired adjacent normal tissue samples were obtained from 72 patients (46 polyps and 26 tumors). Reverse transcription-quantitative PCR was performed to determine the relative fold changes in the expression of lincRNA-p21, lincRNA-RoR, MALAT1 and p53 in the samples. A significant association was observed between the levels of MALAT1 and p53 in neoplasm tissues (R=0.073; P<0.05). The relative expression of the MALAT1 gene revealed a statistically significant difference between the different polyp types and number of polyps (P=0.0028 and 0.022, respectively). Adjuvant therapy in patients with tumors revealed an association between the levels of lincRNA-ROR and lincRNA-p21 expression (P=0.015 and 0.038, respectively). MALAT1 may be selected as an early detection biomarker for CRC. Furthermore, lincRNA-ROR and lincRNA-p21 may serve as prognostic and therapeutic biomarkers in patients with CRC.
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Affiliation(s)
- Vahid Chaleshi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717413, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717413, Iran
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19
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Klinge CM. Estrogenic control of mitochondrial function. Redox Biol 2020; 31:101435. [PMID: 32001259 PMCID: PMC7212490 DOI: 10.1016/j.redox.2020.101435] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Sex-based differences in human disease are caused in part by the levels of endogenous sex steroid hormones which regulate mitochondrial metabolism. This review updates a previous review on how estrogens regulate metabolism and mitochondrial function that was published in 2017. Estrogens are produced by ovaries and adrenals, and in lesser amounts by adipose, breast stromal, and brain tissues. At the cellular level, the mechanisms by which estrogens regulate diverse cellular functions including reproduction and behavior is by binding to estrogen receptors α, β (ERα and ERβ) and G-protein coupled ER (GPER1). ERα and ERβ are transcription factors that bind genomic and mitochondrial DNA to regulate gene transcription. A small proportion of ERα and ERβ interact with plasma membrane-associated signaling proteins to activate intracellular signaling cascades that ultimately alter transcriptional responses, including mitochondrial morphology and function. Although the mechanisms and targets by which estrogens act directly and indirectly to regulate mitochondrial function are not fully elucidated, it is clear that estradiol regulates mitochondrial metabolism and morphology via nuclear and mitochondrial-mediated events, including stimulation of nuclear respiratory factor-1 (NRF-1) transcription that will be reviewed here. NRF-1 is a transcription factor that interacts with coactivators including peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PGC-1α) to regulate nuclear-encoded mitochondrial genes. One NRF-1 target is TFAM that binds mtDNA to regulate its transcription. Nuclear-encoded miRNA and lncRNA regulate mtDNA-encoded and nuclear-encoded transcripts that regulate mitochondrial function, thus acting as anterograde signals. Other estrogen-regulated mitochondrial activities including bioenergetics, oxygen consumption rate (OCR), and extracellular acidification (ECAR), are reviewed.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, 40292, KY, USA.
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20
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Gusic M, Prokisch H. ncRNAs: New Players in Mitochondrial Health and Disease? Front Genet 2020; 11:95. [PMID: 32180794 PMCID: PMC7059738 DOI: 10.3389/fgene.2020.00095] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/28/2020] [Indexed: 12/19/2022] Open
Abstract
The regulation of mitochondrial proteome is unique in that its components have origins in both mitochondria and nucleus. With the development of OMICS technologies, emerging evidence indicates an interaction between mitochondria and nucleus based not only on the proteins but also on the non-coding RNAs (ncRNAs). It is now accepted that large parts of the non‐coding genome are transcribed into various ncRNA species. Although their characterization has been a hot topic in recent years, the function of the majority remains unknown. Recently, ncRNA species microRNA (miRNA) and long-non coding RNAs (lncRNA) have been gaining attention as direct or indirect modulators of the mitochondrial proteome homeostasis. These ncRNA can impact mitochondria indirectly by affecting transcripts encoding for mitochondrial proteins in the cytoplasm. Furthermore, reports of mitochondria-localized miRNAs, termed mitomiRs, and lncRNAs directly regulating mitochondrial gene expression suggest the import of RNA to mitochondria, but also transcription from the mitochondrial genome. Interestingly, ncRNAs have been also shown to hide small open reading frames (sORFs) encoding for small functional peptides termed micropeptides, with several examples reported with a role in mitochondria. In this review, we provide a literature overview on ncRNAs and micropeptides found to be associated with mitochondrial biology in the context of both health and disease. Although reported, small study overlap and rare replications by other groups make the presence, transport, and role of ncRNA in mitochondria an attractive, but still challenging subject. Finally, we touch the topic of their potential as prognosis markers and therapeutic targets.
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Affiliation(s)
- Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
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21
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Enchill Z, Lantz C, Thorp EB. Select Macrophage Noncoding RNAs of Interest in Cardiovascular Disease. J Lipid Atheroscler 2020; 9:153-161. [PMID: 32821728 PMCID: PMC7379065 DOI: 10.12997/jla.2020.9.1.153] [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: 12/05/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 12/24/2022] Open
Abstract
Cardiovascular disease remains a leading cause of morbidity and mortality worldwide. Aspects of disease severity that are associated with heightened inflammation, such as during atherosclerosis or after myocardial infarction, are correlated with macrophage activation and macrophage polarization of the transcriptome and secretome. In this setting, non-coding RNAs (ncRNAs) may be as abundant as protein-coding genes and are increasingly recognized as significant modulators of macrophage gene expression and cytokine secretion, although the functions of most ncRNAs—and in particular, long non-coding RNAs—remain unknown. Herein, we discuss a subset of specific ncRNAs of interest in macrophages in atherosclerosis and during myocardial inflammation.
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Affiliation(s)
- Zenaida Enchill
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Connor Lantz
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edward B Thorp
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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22
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Smith-Sonneborn J. Telomerase Biology Associations Offer Keys to Cancer and Aging Therapeutics. Curr Aging Sci 2020; 13:11-21. [PMID: 31544708 PMCID: PMC7403649 DOI: 10.2174/1874609812666190620124324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/07/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although telomerase has potential for age-related disease intervention, the overexpression of telomerase in about 90% of cancers, and in HIV virus reservoirs, cautions against se in anti-aging telomerase therapeutics. While multiple reviews document the canonical function of telomerase for maintenance of telomeres, as well as an increasing numbers of reviews that reveal new non-canonical functions of telomerase, there was no systematic review that focuses on the array of associates of the subunit of Telomerase Reverse transcriptase protein (TERT) as pieces of the puzzle to assemble a picture of the how specific TERT complexes uniquely impact aging and age-related diseases and more can be expected. METHODS A structured search of bibliographic data on TERT complexes was undertaken using databases from the National Center for Biotechnology Information Pubmed with extensive access to biomedical and genomic information in order to obtain a unique documented and cited overview of TERT complexes that may uniquely impact aging and age-related diseases. RESULTS The TERT associations include proper folding, intracellular TERT transport, metabolism, mitochondrial ROS (Reactive Oxygen Species) regulation, inflammation, cell division, cell death, and gene expression, in addition to the well-known telomere maintenance. While increase of cell cycle inhibitors promote aging, in cancer, the cell cycle check-point regulators are ambushed in favor of cell proliferation, while cytoplasmic TERT protects a cell cycle inhibitor in oxidative stress. The oncogene cMyc regulates gene expression for overexpression of TERT, and reduction of cell cycle inhibitors-the perfect storm for cancer promotion. TERT binds with the oncogene RMRP RNA, and TERT-RMRP function can regulate levels of that oncogene RNA, and TERT in a TBN complex can regulate heterochromatin. Telomerase benefit and novel function in neurology and cardiology studies open new anti- aging hope. GV1001, a 16 amino acid peptide of TERT that associates with Heat Shock Proteins (HSP's), bypasses the cell membrane with remarkable anti disease potential. CONCLUSIONS TERT "associates" are anti-cancer targets for downregulation, but upregulation in antiaging therapy. The overview revealed that unique TERT associations that impact all seven pillars of aging identified by the Trans-NIH Geroscience Initiative that influence aging and urge research for appropriate targeted telomerase supplements/ stimulation, and inclusion in National Institute on Aging Intervention Testing Program. The preference for use of available "smart drugs", targeted to only cancer, not off-target anti- aging telomerase is implied by the multiplicity of TERT associates functions.
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Affiliation(s)
- Joan Smith-Sonneborn
- Department Zoology and Physiology, University of Wyoming, Laramie, Wyoming, WY, USA
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23
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Devadoss D, Long C, Langley RJ, Manevski M, Nair M, Campos MA, Borchert G, Rahman I, Chand HS. Long Noncoding Transcriptome in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2019; 61:678-688. [PMID: 31486667 PMCID: PMC6890411 DOI: 10.1165/rcmb.2019-0184tr] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Chronic airway inflammation from recurring exposures to noxious environmental stimuli results in a progressive and irreversible airflow limitation and the lung parenchymal damage that characterizes chronic obstructive pulmonary disease (COPD). The large variability observed in the onset and progression of COPD is primarily driven by complex gene-environment interactions. The transcriptomic and epigenetic memory potential of lung epithelial and innate immune cells drive responses, such as mucus hyperreactivity and airway remodeling, that are tightly regulated by various molecular mechanisms, for which several candidate susceptibility genes have been described. However, the recently described noncoding RNA species, in particular the long noncoding RNAs, may also have an important role in modulating pulmonary responses to chronic inhalation of toxic substances and the development of COPD. This review outlines the features of long noncoding RNAs that have been implicated in regulating the airway inflammatory responses to cigarette smoke exposure and their possible association with COPD pathogenesis. As COPD continues to debilitate the increasingly aging population and contribute to higher morbidity and mortality rates worldwide, the search for better biomarkers and alternative therapeutic options is pivotal.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Christopher Long
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Raymond J. Langley
- Department of Pharmacology, University of South Alabama, Mobile, Alabama
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Michael A. Campos
- Pulmonary Section, Miami Veterans Administration Medical Center, Miami, Florida
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Coral Gables, Florida; and
| | - Glen Borchert
- Department of Pharmacology, University of South Alabama, Mobile, Alabama
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
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Gong W, Yang L, Wang Y, Xian J, Qiu F, Liu L, Lin M, Feng Y, Zhou Y, Lu J. Analysis of Survival-Related lncRNA Landscape Identifies A Role for LINC01537 in Energy Metabolism and Lung Cancer Progression. Int J Mol Sci 2019; 20:ijms20153713. [PMID: 31374807 PMCID: PMC6696180 DOI: 10.3390/ijms20153713] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023] Open
Abstract
Many long non-coding RNAs (lncRNAs) have emerged as good biomarkers and potential therapeutic targets for various cancers. We aimed to get a detailed understanding of the lncRNA landscape that is associated with lung cancer survival. A comparative analysis between our RNA sequencing (RNA-seq) data and TCGA datasets was conducted to reveal lncRNAs with significant correlations with lung cancer survival and then the association of the most promising lncRNA was validated in a cohort of 243 lung cancer patients. Comparing RNA-seq data with TCGA ones, 84 dysregulated lncRNAs were identified in lung cancer tissues, among which 10 lncRNAs were significantly associated with lung cancer survival. LINC01537 was the most significant one (p = 2.95 × 10−6). Validation analysis confirmed the downregulation of LINC01537 in lung cancer. LINC01537 was observed to inhibit tumor growth and metastasis. It also increased cellular sensitivity to nilotinib. PDE2A (phosphodiesterase 2A) was further identified to be a target of LINC01537 and it was seen that LINC01537 promoted PDE2A expression via RNA–RNA interaction to stabilize PDE2A mRNA and thus echoed effects of PDE2A on energy metabolism including both Warburg effect and mitochondrial respiration. Other regulators of tumor energy metabolism were also affected by LINC01537. These results elucidate a suppressed role of LINC01537 in lung cancer development involving tumor metabolic reprogramming, and we believe that it might be a biomarker for cancer survival prediction and therapy.
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Affiliation(s)
- Wei Gong
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China.
| | - Yuanyuan Wang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Jianfeng Xian
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Li Liu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Mingzhu Lin
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Yingyi Feng
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, 1 Shizi Road, Suzhou 215123, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China.
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Long non-coding RNA MEG3 inhibits chondrogenic differentiation of synovium-derived mesenchymal stem cells by epigenetically inhibiting TRIB2 via methyltransferase EZH2. Cell Signal 2019; 63:109379. [PMID: 31376524 DOI: 10.1016/j.cellsig.2019.109379] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 01/05/2023]
Abstract
Osteoarthritis (OA) is a highly prevalent skeletal disease. Mesenchymal stem cell-derived cartilage tissue engineering is a clinical method used for OA treatment. Investigations on the molecular regulatory mechanisms of the chondrogenic differentiation of synovium-derived mesenchymal stem cells(SMSCs) will help promote its clinical applications. In this study, bioinformatics analysis from three different databases indicated that the long non-coding RNA (lncRNA) MEG3 may regulate the chondrogenic differentiation of SMSCs by targeting TRIB2. We then performed assays and found that both knockdown of MEG3 or overexpression of TRIB2 can stimulate the chondrogenic differentiation of SMSCs and increase Col2A1 and aggrecan expression. Knockdown of MEG3 can induce the expression of TRIB2; conversely, overexpression of MEG3 can inhibit the expression of TRIB2. Futhermore, knockdown of the TRIB2 can rescue the MEG3 silencing-mediated promotion of chondrogenic differentiation. Moreover, RNA immunoprecipitation(RIP) and RNA pull-down assays demonstrated that MEG3 can interact with EZH2, thus recruiting it to induce H3K27me3, which promotes the methylation of TRIB2 by binding with the promoter of TRIB2 in SMSCs. Additionally, EZH2 silencing significantly rescued the MEG3 overexpression-mediated inhibition of TRIB2 expression and chondrogenic differentiation of SMSCs. Taken together, these data indicated that MEG3 regulates chondrogenic differentiation by inhibiting TRIB2 expression through EZH2-mediated H3K27me3.
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26
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Tang L, Wang Y, Wang H, Xu B, Ji H, Xu G, Ge X, Li Q, Miao L. Long noncoding-RNA component of mitochondrial RNA processing endoribonuclease is involved in the progression of cholangiocarcinoma by regulating microRNA-217. Cancer Sci 2019; 110:2166-2179. [PMID: 31111617 PMCID: PMC6609814 DOI: 10.1111/cas.14074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/08/2019] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a malignant tumor originating from bile duct epithelium and its incidence is increasing year by year. In recent years, long noncoding RNAs (lncRNAs) have been found to play an important role in the occurrence and progression of malignant tumors. In the present study, for the first time, abnormal expression of lnc‐RNA component of mitochondrial RNA processing endoribonuclease (RMRP) and its possible role in CCA were found. We explored the effects of RMRP on various behaviors of CCA cells in vitro and in vivo. In addition, by second‐generation sequencing, we explored the microRNA expression profiles that RMRP may affect in the HCCC‐9810 cell line. We also validated and explored the role of microRNA‐217 (miR‐217) with high differential expression by in vitro experiments. Our findings indicated that RMRP can play a part in promoting cancer by regulating the expression of miR‐217. RMRP is involved in the progression of CCA and can be a novel indicator of poor prognosis in patients with CCA.
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Affiliation(s)
- Lingyu Tang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yuting Wang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Huishan Wang
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Boming Xu
- Department of Gastroenterology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Hao Ji
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guolong Xu
- Department of Immunology, Nanjing Medical University, Nanjing, China
| | - Xianxiu Ge
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Quanpeng Li
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Digestive Diseases Kizilsu Kirghiz, The People's Hospital of Kizilsu Kirghiz Autonomous Prefecture, Xinjiang, China
| | - Lin Miao
- Medical Centre for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
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27
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Li P, Zhao S, Hu Y. SFRP2 modulates non‑small cell lung cancer A549 cell apoptosis and metastasis by regulating mitochondrial fission via Wnt pathways. Mol Med Rep 2019; 20:1925-1932. [PMID: 31257495 DOI: 10.3892/mmr.2019.10393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/20/2019] [Indexed: 11/05/2022] Open
Abstract
The secreted frizzled‑related protein 2 (SFRP2) has been reported to inhibit non‑small cell lung cancer (NSCLC) cell survival and metastasis; however, the underlying mechanisms are yet to be fully determined. The present study focused on mitochondrial fission and the Wnt signaling pathway. The results demonstrated that SFRP2 was downregulated in the NSCLC cell line A549 compared with in a normal pulmonary epithelial cell line using western blotting, reverse transcription‑quantitative PCR and immunofluorescence. Subsequently, it was demonstrated that SFRP2 overexpression promoted the apoptosis, and inhibited the proliferation and metastasis of A549 cells using MTT assays, TUNEL staining and 5‑ethynyl‑2'‑deoxyuridine labeling. At the molecular level, the overexpression of SFRP2 in A549 cells led to the activation of mitochondrial fission by inhibiting the Wnt signal pathway. Excessive mitochondrial fission induced low ATP generation, impaired mitochondrial respiratory function, induced mitochondrial potential depolarization, and increased mitochondrial permeability transition pore opening, and imbalances in pro‑ and antiapoptotic protein expression. Furthermore, mitochondrial fission was involved in the inhibition of A549 cell proliferation and metastasis. Thus, SFRP2 may inhibit the survival and metastasis of NSCLC cells via the Wnt/mitochondrial fission pathway.
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Affiliation(s)
- Peng Li
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Shu Zhao
- Department of Oncology, Τhe Second Medical Center, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Yi Hu
- Department of Oncology, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing 100853, P.R. China
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28
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Wen L, Zhang Z, Peng R, Zhang L, Liu H, Peng H, Sun Y. Whole transcriptome analysis of diabetic nephropathy in the db/db mouse model of type 2 diabetes. J Cell Biochem 2019; 120:17520-17533. [PMID: 31106482 DOI: 10.1002/jcb.29016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Whole-transcriptome analysis using RNA sequencing (RNA-seq) affords broader insights about gene expression regulatory networks in diabetic nephropathy (DN). To better explore the molecular basis of DN, kidney tissue from db/db DN model mice and control mice were submitted to RNA-seq analysis. Thousands of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) were found to be significantly differentially expressed in the DN group relative to the control group. To research the regulatory mechanism of these lncRNAs and mRNAs, the integrated co-expression networks were constructed for 322 mRNAs and 27 lncRNAs that revealed significantly correlated expression patterns in DN. The potential roles of these co-expressed mRNAs were classified by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The co-expression networks involved 27 lncRNAs interacting with 38 key mRNAs related to metabolic processes, including ND4/4L, Ndufa2/5, Ndufb4/7, Ndufs3, Uqcrc1, Aco2, Alad, Alas1, Alpl, Atp5j2, Coq5, Coq6, Cth, and CytB, all of which are highly related to encoding subunits of the mitochondrial complexes. Thus, mitochondrial dysfunction could result in renal function decline in DN. Seven dysregulated lncRNAs and nine dysregulated mRNAs in the DN model were confirmed by quantitative real-time polymerase chain reaction. The lncRNA-mRNA co-expression network provides novel evidence to support the contention that metabolic changes are associated with metabolic reprogramming in the kidneys, and that these changes play a critical role during the progression of DN.
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Affiliation(s)
- Li Wen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China.,Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Zhang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing, China
| | - Luyu Zhang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Handeng Liu
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Huimin Peng
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, China
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29
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Gao C, Wu X, Zhai J, Shen J, Wang S, Shen L. Long non-coding RNA SNHG17 promotes gastric cancer progression by inhibiting P15 and P16. Transl Cancer Res 2019; 8:520-531. [PMID: 35116784 PMCID: PMC8798068 DOI: 10.21037/tcr.2019.04.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND The dysregulated long non-coding RNA (lncRNA) small nucleolar RNA host genes (SNHGs) have been demonstrated to be involved in gastric carcinogenesis and progression; however, the role of SNHG17 in gastric carcinoma remains to be investigated. We aimed to ascertain the expression of SNHG17 in gastric carcinoma tissues and cell lines, and to investigate its mechanistic role in this malignancy. METHODS The expression levels of SNHG17, P15, P16, P18, P19 and cyclin dependent kinases-4 (CDK4) were determined by real-time quantitative polymerase chain reaction (RT-qPCR) and/or western blotting in human gastric cancer tissues and cell lines. Correlations between SNHG17 levels and clinicopathological features were evaluated. siRNAs were used to silence SNHG17 in cell lines, and then Cell Counting Kit-8, colony formation, and transwell migration assays were used to assess proliferation, clonogenic potential, and migration, respectively. Flow cytometry was used to analyze cell cycle distributions and apoptosis. In vivo tumorigenicity was evaluated using xenografts in nude mice. RESULTS Analysis of The Cancer Genome Atlas (TCGA) database revealed that SNHG17 expression was remarkably higher in gastric carcinoma tissues than normal stomach mucosae (P=4.85×10-10). We confirmed that SNHG17 was overexpressed in gastric cancer tissues (P<0.0001) and cell lines (P<0.01) compared with corresponding noncancerous tissues and gastric epithelial cell line, respectively. Furthermore, SNHG17 levels in tumor tissues were associated with lymph node metastasis (P=0.0006), pTNM stage (P=0.0061), and lymphovascular invasion (P=0.0005), but were not associated with overall survival (OS) (P=0.888). Loss-of-function studies indicated that SNHG17 promoted gastric carcinoma cell proliferation in vitro and in vivo (P<0.01), and that SNHG17 enhanced gastric cancer cell migration (P<0.01). Mechanistically, we found that SNHG17 inhibited P15 and P16, and enhanced CDK4 expression, resulting in a G0/G1 cell cycle arrest, and that SNHG17 inhibited cell apoptosis. CONCLUSIONS These preliminary findings highlight the role of SNHG17 in gastric cancer, and suggest that it may be a novel indicator and/or a potential therapeutic target for diagnosing and/or treating gastric cancer.
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Affiliation(s)
- Cheng Gao
- Division of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.,Department of General Surgery, Affiliated Hai'an Hospital, Nantong University, Nantong 226600, China
| | - Xinqian Wu
- Division of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Jing Zhai
- Division of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.,Department of Surgical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Jiajia Shen
- Division of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Shoulin Wang
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Lizong Shen
- Division of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.,Department of Surgical Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
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30
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De Paepe B. Sporadic Inclusion Body Myositis: An Acquired Mitochondrial Disease with Extras. Biomolecules 2019; 9:biom9010015. [PMID: 30621041 PMCID: PMC6359202 DOI: 10.3390/biom9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
The sporadic form of inclusion body myositis (IBM) is the most common late-onset myopathy. Its complex pathogenesis includes degenerative, inflammatory and mitochondrial aspects. However, which of those mechanisms are cause and which effect, as well as their interrelations, remain partly obscured to this day. In this review the nature of the mitochondrial dysregulation in IBM muscle is explored and comparison is made with other muscle disorders. Mitochondrial alterations in IBM are evidenced by histological and serum biomarkers. Muscular mitochondrial dynamics is disturbed, with deregulated organelle fusion leading to subsequent morphological alterations and muscle displays abnormal mitophagy. The tissue increases mitochondrial content in an attempt to compensate dysfunction, yet mitochondrial DNA (mtDNA) alterations and mild mtDNA depletion are also present. Oxidative phosphorylation defects have repeatedly been shown, most notably a reduction in complex IV activities and levels of mitokines and regulatory RNAs are perturbed. Based on the cumulating evidence of mitochondrial abnormality as a disease contributor, it is therefore warranted to regard IBM as a mitochondrial disease, offering a feasible therapeutic target to be developed for this yet untreatable condition.
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Affiliation(s)
- Boel De Paepe
- Neuromuscular Reference Centre, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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31
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Klinge CM. Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication. Noncoding RNA 2018; 4:E40. [PMID: 30545127 PMCID: PMC6316884 DOI: 10.3390/ncrna4040040] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are regulators of intracellular and intercellular signaling in breast cancer. ncRNAs modulate intracellular signaling to control diverse cellular processes, including levels and activity of estrogen receptor α (ERα), proliferation, invasion, migration, apoptosis, and stemness. In addition, ncRNAs can be packaged into exosomes to provide intercellular communication by the transmission of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) to cells locally or systemically. This review provides an overview of the biogenesis and roles of ncRNAs: small nucleolar RNA (snRNA), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), miRNAs, and lncRNAs in breast cancer. Since more is known about the miRNAs and lncRNAs that are expressed in breast tumors, their established targets as oncogenic drivers and tumor suppressors will be reviewed. The focus is on miRNAs and lncRNAs identified in breast tumors, since a number of ncRNAs identified in breast cancer cells are not dysregulated in breast tumors. The identity and putative function of selected lncRNAs increased: nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), steroid receptor RNA activator 1 (SRA1), colon cancer associated transcript 2 (CCAT2), colorectal neoplasia differentially expressed (CRNDE), myocardial infarction associated transcript (MIAT), and long intergenic non-protein coding RNA, Regulator of Reprogramming (LINC-ROR); and decreased levels of maternally-expressed 3 (MEG3) in breast tumors have been observed as well. miRNAs and lncRNAs are considered targets of therapeutic intervention in breast cancer, but further work is needed to bring the promise of regulating their activities to clinical use.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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32
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Zhao Y, Sun L, Wang RR, Hu JF, Cui J. The effects of mitochondria-associated long noncoding RNAs in cancer mitochondria: New players in an old arena. Crit Rev Oncol Hematol 2018; 131:76-82. [DOI: 10.1016/j.critrevonc.2018.08.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/06/2018] [Accepted: 08/22/2018] [Indexed: 12/17/2022] Open
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The nonsense-mediated mRNA decay (NMD) pathway differentially regulates COX17, COX19 and COX23 mRNAs. Curr Genet 2018; 65:507-521. [PMID: 30317392 PMCID: PMC6420912 DOI: 10.1007/s00294-018-0892-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/12/2023]
Abstract
The differential regulation of COX17, COX19 and COX23 mRNAs by the nonsense-mediated mRNA decay (NMD) pathway was investigated. The NMD pathway regulates mRNAs that aberrantly terminate translation. This includes mRNAs harboring premature translation termination codons and natural mRNAs. Most natural mRNAs regulated by NMD encode fully functional proteins involved in various cellular processes. However, the cause and targeting of most of these mRNAs by the pathway is not understood. Analysis of a set of mRNAs involved in copper homeostasis showed that a subset of these mRNAs function in mitochondrial copper homeostasis. Here, we examined the regulation of COX17, COX19 and COX23 mRNAs by NMD. These mRNAs encode homologous mitochondrial proteins involved in metallation of cytochrome c oxidase. We found that COX17, COX19 and COX23 mRNAs are differentially regulated by NMD depending on environmental copper levels. A long 3'-UTR contributes to the direct regulation of COX19 mRNA by the pathway. Alternatively, COX23 mRNA contains a long 3'-UTR, but is indirectly regulated by the pathway under two conditions tested here. Analysis of the functionality of the NMD targeting features in COX23 mRNA showed that the COX23 3'-UTR is sufficient to trigger NMD. The regulation of mRNAs involved in mitochondrial copper metabolism by NMD is physiologically significant because excess copper enhances growth of NMD mutants on a non-fermentable carbon source. These findings suggest that regulation of mRNAs encoding homologous proteins by NMD can be differential depending on environmental copper levels. Furthermore, these findings suggest copper ion homeostatic mechanisms in the mitochondria occur at the mRNA level via the NMD pathway.
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He Z, You C, Zhao D. Long non-coding RNA UCA1/miR-182/PFKFB2 axis modulates glioblastoma-associated stromal cells-mediated glycolysis and invasion of glioma cells. Biochem Biophys Res Commun 2018; 500:569-576. [DOI: 10.1016/j.bbrc.2018.04.091] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/12/2018] [Indexed: 02/09/2023]
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Cahoon AB, Qureshi AA. Leaderless mRNAs are circularized in Chlamydomonas reinhardtii mitochondria. Curr Genet 2018; 64:1321-1333. [DOI: 10.1007/s00294-018-0848-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 11/28/2022]
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Weikard R, Hadlich F, Hammon HM, Frieten D, Gerbert C, Koch C, Dusel G, Kuehn C. Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets. Oncotarget 2018; 9:21052-21069. [PMID: 29765519 PMCID: PMC5940403 DOI: 10.18632/oncotarget.24898] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/25/2018] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves’ intestinal mucosa. Nine lncRNA loci were differentially expressed (DE lncRNAs) between both calf groups. To elucidate their biological function, we applied a systems biology approach that combines weighted gene co-expression network analysis with functional enrichment and biological pathway analysis. Four DE lncRNAs were found to be strongly correlated with a gene network module (GNM) enriched for genes from canonical pathways of remodeling of epithelial adherens junction, tight junction and integrin signaling. Another DE lncRNA was strongly correlated with a GNM enriched for genes associated with energy metabolism and maintaining of cellular homeostasis with a focus on mitochondrial processes. Our data suggest that these DE lncRNAs may play potential regulatory roles in modulating biological processes associated with energy metabolism pathways and cellular signaling processes affecting the barrier function of intestinal epithelial cells of calves in response to different feeding regimens in the pre-weaning period.
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Affiliation(s)
- Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | - Caroline Gerbert
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler, Germany
| | - Christian Koch
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler, Germany
| | - Georg Dusel
- University of Applied Sciences, Bingen, Germany
| | - Christa Kuehn
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
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Zhang J, Yuan Y, Wei Z, Ren J, Hou X, Yang D, Cai S, Chen C, Tan M, Chen GG, Wu K, He Y. Crosstalk between prognostic long noncoding RNAs and messenger RNAs as transcriptional hallmarks in gastric cancer. Epigenomics 2018; 10:433-443. [PMID: 29402138 DOI: 10.2217/epi-2017-0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIM Our study investigated the significance of the crosstalk between long noncoding RNAs (lncRNAs) and mRNAs in gastric cancer (GC). METHODS lncRNA and mRNA expression profiling data in 671 GC tumors and 77 nontumorous gastric tissues were retrieved from the gene expression omnibus database: GSE54129, GSE13911, GSE19826, GSE79973, GSE15459 and GSE66229. Differentially expressed analysis, RNA coexpression network construction, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted in this study. RESULTS Using differentially expressed and prognostic lncRNAs or mRNAs in GC, we constructed the lncRNA-mRNA coexpression networks. This network involved with vital GO and KEGG pathways. CONCLUSION Our study reveals coexpressed lncRNAs and mRNAs as transcriptional hallmarks in GC patients which provide interesting information regarding the incidence and outcome of GC.
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Affiliation(s)
- Jian Zhang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yujie Yuan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Zhewei Wei
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Jianwei Ren
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Xun Hou
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Dongjie Yang
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Sirong Cai
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Chuangqi Chen
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Min Tan
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - George Gong Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.,Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, PR China
| | - Kaiming Wu
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yulong He
- Division of Gastrointestinal Surgery & Gastric Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
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