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Zhang SY. Integrating disulfidptosis-related long noncoding RNAs in colorectal cancer prognosis: A path to precision medicine. World J Clin Oncol 2024; 15:664-666. [DOI: 10.5306/wjco.v15.i5.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/05/2024] [Accepted: 04/09/2024] [Indexed: 05/21/2024] Open
Abstract
This commentary explores the burgeoning field of disulfidptosis-related long noncoding RNAs (lncRNAs) in the prognosis and therapeutic targeting of colorectal cancer (CRC). By evaluating recent research, including the pivotal study "Predicting colorectal cancer prognosis based on long noncoding RNAs of disulfidptosis genes" by Wang et al, this analysis underscores the critical role of lncRNAs in deciphering the molecular complexities of CRC. Highlighting the innovative methodologies and significant findings, I discuss the implications for patient survival, therapeutic response, and the potential of lncRNAs as biomarkers for precision medicine. The integration of bioinformatics, clinical databases, and molecular biology in these studies offers a promising avenue for advancing CRC treatment strategies and improving patient outcomes.
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Affiliation(s)
- Shi-Yan Zhang
- Department of Clinical Laboratory, Fuding Hospital, Fujian University of Traditional Chinese Medicine, Fuding 355200, Fujian Province, China
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2
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Cheng X, Shihabudeen Haider Ali MS, Baki VB, Moran M, Su H, Sun X. Multifaceted roles of Meg3 in cellular senescence and atherosclerosis. Atherosclerosis 2024; 392:117506. [PMID: 38518516 PMCID: PMC11088985 DOI: 10.1016/j.atherosclerosis.2024.117506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 02/11/2024] [Accepted: 03/05/2024] [Indexed: 03/24/2024]
Abstract
BACKGROUND AND AIMS Long noncoding RNAs are involved in the pathogenesis of atherosclerosis. As long noncoding RNAs maternally expressed gene 3 (Meg3) prevents cellular senescence of hepatic vascular endothelium and obesity-induced insulin resistance, we decided to examine its role in cellular senescence and atherosclerosis. METHODS AND RESULTS By analyzing our data and human and mouse data from the Gene Expression Omnibus database, we found that Meg3 expression was reduced in humans and mice with cardiovascular disease, indicating its potential role in atherosclerosis. In Ldlr-/- mice fed a Western diet for 12 weeks, Meg3 silencing by chemically modified antisense oligonucleotides attenuated the formation of atherosclerotic lesions by 34.9% and 20.1% in male and female mice, respectively, revealed by en-face Oil Red O staining, which did not correlate with changes in plasma lipid profiles. Real-time quantitative PCR analysis of cellular senescence markers p21 and p16 revealed that Meg3 deficiency aggravates hepatic cellular senescence but not cellular senescence at aortic roots. Human Meg3 transgenic mice were generated to examine the role of Meg3 gain-of-function in the development of atherosclerosis induced by PCSK9 overexpression. Meg3 overexpression promotes atherosclerotic lesion formation by 29.2% in Meg3 knock-in mice independent of its effects on lipid profiles. Meg3 overexpression inhibits hepatic cellular senescence, while it promotes aortic cellular senescence likely by impairing mitochondrial function and delaying cell cycle progression. CONCLUSIONS Our data demonstrate that Meg3 promotes the formation of atherosclerotic lesions independent of its effects on plasma lipid profiles. In addition, Meg3 regulates cellular senescence in a tissue-specific manner during atherosclerosis. Thus, we demonstrated that Meg3 has multifaceted roles in cellular senescence and atherosclerosis.
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Affiliation(s)
- Xiao Cheng
- Department of Biochemistry, University of Nebraska - Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA
| | | | - Vijaya Bhaskar Baki
- Department of Biochemistry, University of Nebraska - Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA
| | - Matthew Moran
- Department of Biochemistry, University of Nebraska - Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA; Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska - Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA; Nebraska Center for the Prevention of Obesity Diseases Through Dietary Molecules, University of Nebraska - Lincoln, USA.
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3
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Long Q, Li Z, Yang W, Huang K, Du G. Necroptosis-related lncRNA-based novel signature to predict the prognosis and immune landscape in soft tissue sarcomas. J Cancer Res Clin Oncol 2024; 150:203. [PMID: 38635069 PMCID: PMC11026213 DOI: 10.1007/s00432-024-05682-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Necroptosis-related long noncoding RNAs (lncRNAs) play crucial roles in cancer initiation and progression. Nevertheless, the role and mechanism of necroptosis-related lncRNAs in soft tissue sarcomas (STS) is so far unknown and needs to be explored further. METHODS Clinical and genomic data were obtained from the UCSC Xena database. All STS patients' subclusters were performed by unsupervised consensus clustering method based on the prognosis-specific lncRNAs, and then assessed their survival advantage and immune infiltrates. In addition, we explored the pathways and biological processes in subclusters through gene set enrichment analysis. At last, we established the necroptosis-related lncRNA-based risk signature (NRLncSig) using the least absolute shrinkage and selection operator (LASSO) method, and explored the prediction performance and immune microenvironment of this signature in STS. RESULTS A total of 911 normal soft tissue samples and 259 STS patients were included in current study. 39 prognosis-specific necroptosis-related lncRNAs were selected. Cluster 2 had a worse survival than the cluster 1 and characterized by different immune landscape in STS. A worse outcome in the high-risk group was observed by survival analysis and indicated an immunosuppressive microenvironment. The ROC curve analyses illustrated that the NRLncSig performing competitively in prediction of prognosis for STS patients. In addition, the nomogram presents excellent performance in predicting prognosis, which may be more beneficial towards STS patients' treatment. CONCLUSIONS Our result indicated that the NRLncSig could be a good independent predictor of prognosis, and significantly connected with immune microenvironment, thereby providing new insights into the roles of necroptosis-related lncRNAs in STS.
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Affiliation(s)
- Qiuzhong Long
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhengtian Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wenkang Yang
- Guangxi Medical University, Nanning, Guangxi, China
| | - Ke Huang
- Wuming Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
| | - Gang Du
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Alhajlah S. The molecular mechanisms of various long non-coding RNA (lncRNA) in human lung tumors: Shedding light on the molecular mechanisms. Pathol Res Pract 2024; 256:155253. [PMID: 38513578 DOI: 10.1016/j.prp.2024.155253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Although it is still mostly incomplete, unraveling the gene expression networks controlling the initiation and progression of cancer is crucial. The rapid identification and characterization of long noncoding RNAs (lncRNAs) is made possible by advancements in computational biology and RNA-seq technology. According to recent research, lncRNAs are involved in several stages in the genesis of lung cancer. These lncRNAs interact with DNA, RNA, protein molecules, and/or their combinations. They play a crucial role in transcriptional and post-transcriptional regulation, as well as chromatin architecture. Their misexpression gives cancer cells the ability to start, grow, and spread tumors. This review will focus on their abnormal expression and function in lung cancer, as well as their involvement in cancer therapy and diagnosis.
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Affiliation(s)
- Sharif Alhajlah
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra 11961, Saudi Arabia.
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5
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Jiang X, Zhang M. The roles of long noncoding RNA NEAT1 in cardiovascular diseases. Hypertens Res 2024; 47:735-746. [PMID: 38177287 DOI: 10.1038/s41440-023-01551-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024]
Abstract
The morbidity of cardiovascular diseases (CVDs) gradually increases worldwide. Long noncoding RNAs (lncRNAs) are a large class of non-(protein)-coding RNAs with lengths beyond 200 nucleotides. Increasing evidence suggests that lncRNA NEAT1 plays important roles in the pathogenesis of CVDs, such as myocardial infarction, heart failure, myocardial ischemia-reperfusion (I/R) injury, atherosclerosis, hypertension, cardiomyopathy, and others. We summarized the current studies of NEAT1 in CVDs, which shed light on the understanding of the molecular mechanisms of CVDs and understanding the therapeutic potential of NEAT1.
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Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
| | - Mingjuan Zhang
- Department of Cardiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
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Abu-Alghayth MH, Khan FR, Belali TM, Abalkhail A, Alshaghdali K, Nassar SA, Almoammar NE, Almasoudi HH, Hessien KBG, Aldossari MS, Binshaya AS. The emerging role of noncoding RNAs in the PI3K/AKT/mTOR signalling pathway in breast cancer. Pathol Res Pract 2024; 255:155180. [PMID: 38330621 DOI: 10.1016/j.prp.2024.155180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Breast cancer persists as a major problem for the world's healthcare, thus it is essential to fully understand the complex molecular processes that cause its growth and development. ncRNAs had been discovered to serve critical roles in a variety of cellular functions, including the regulation of signalling pathways. Within different pathways, the AKT/PI3K/mTOR signalling cascade has received a lot of interest because of its role in cancer. A complex interaction between ncRNAs, notably miRNAs, lncRNAs, and circRNAs, and the AKT/PI3K/mTOR signalling pathway exerts both oncogenic and tumor-suppressive activities by targeting critical components of the pathway directly or indirectly. Through miRNA-mediated post-transcriptional regulation, lncRNA-guided chromatin remodelling, and circRNA sequestration, ncRNAs modulate the activity of PI3K, AKT, and mTOR, influencing cell proliferation, survival, and metastasis. Furthermore, ncRNAs can serve as promising biomarkers for breast cancer prognosis, diagnosis, and treatment response, as their dysregulation is commonly observed in breast cancer patients. Harnessing the potential of ncRNAs as therapeutic targets or tools for restoring pathway homeostasis holds promise for innovative treatment strategies in breast cancer. Understanding the intricate regulatory networks orchestrated by ncRNAs in this context may pave the way for novel diagnostic approaches, therapeutic interventions, and a deeper comprehension of breast cancer's molecular landscape, ultimately improving patient outcomes. This abstract underscores the emerging significance of ncRNAs in the AKT/PI3K/mTOR signaling pathway in breast cancer.
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Affiliation(s)
- Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Tareg M Belali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Khalid Alshaghdali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, P.O Box 2440, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Nasser Eissa Almoammar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Khater Balatone G Hessien
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | | | - Abdulkarim S Binshaya
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
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Chen J, Zhong G, Qiu M, Ke W, Xue J, Chen J. Exploring lncRNA Expression Patterns in Patients With Hypertrophied Ligamentum Flavum. Neurospine 2024; 21:330-341. [PMID: 38291747 PMCID: PMC10992663 DOI: 10.14245/ns.2346994.497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 02/01/2024] Open
Abstract
OBJECTIVE Hypertrophy ligamentum flavum (LFH) is a common cause of lumbar spinal stenosis, resulting in significant disability and morbidity. Although long noncoding RNAs (lncRNAs) have been associated with various biological processes and disorders, their involvement in LFH remains not fully understood. METHODS Human ligamentum flavum samples were analyzed using lncRNA sequencing followed by validation through quantitative real-time polymerase chain reaction. To explore the potential biological functions of differentially expressed lncRNA-associated genes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. We also studied the impact of lncRNA PARD3-AS1 on the progression of LFH in vitro. RESULTS In the LFH tissues when compared to that in the nonhypertrophic ligamentum flavum (LFN) tissues, a total of 1,091 lncRNAs exhibited differential expression, with 645 upregulated and 446 downregulated. Based on GO analysis, the differentially expressed transcripts primarily participated in metabolic processes, organelles, nuclear lumen, cytoplasm, protein binding, nucleic acid binding, and transcription factor activity. Moreover, KEGG pathway analysis indicated that the differentially expressed lncRNAs were associated with the hippo signaling pathway, nucleotide excision repair, and nuclear factor-kappa B signaling pathway. The expression of PARD3-AS1, RP11-430G17.3, RP1-193H18.3, and H19 was confirmed to be consistent with the sequencing analysis. Inhibition of PARD3-AS1 resulted in the suppression of fibrosis in LFH cells, whereas the overexpression of PARD3-AS1 promoted fibrosis in LFH cells in vitro. CONCLUSION This study identified distinct expression patterns of lncRNAs that are linked to LFH, providing insights into its underlying mechanisms and potential prognostic and therapeutic interventions. Notably, PARD3-AS1 appears to play a significant role in the pathophysiology of LFH.
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Affiliation(s)
- Junling Chen
- Department of Orthopedics, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guibin Zhong
- Department of Orthopedics, Ren Ji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Manle Qiu
- Department of Orthopedics, Ren Ji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Wei Ke
- Department of Orthopedics, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingsong Xue
- Department of Orthopedics, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianwei Chen
- Department of Orthopedics, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Orthopedics, Ren Ji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
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He YX, Wang T, Li WX, Chen YX. Long noncoding RNA protein-disulfide isomerase-associated 3 regulated high glucose-induced podocyte apoptosis in diabetic nephropathy through targeting miR-139-3p. World J Diabetes 2024; 15:260-274. [PMID: 38464366 PMCID: PMC10921158 DOI: 10.4239/wjd.v15.i2.260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/13/2023] [Accepted: 01/15/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Podocyte apoptosis plays a vital role in proteinuria pathogenesis in diabetic nephropathy (DN). The regulatory relationship between long noncoding RNAs (lncRNAs) and podocyte apoptosis has recently become another research hot spot in the DN field. AIM To investigate whether lncRNA protein-disulfide isomerase-associated 3 (Pdia3) could regulate podocyte apoptosis through miR-139-3p and revealed the underlying mechanism. METHODS Using normal glucose or high glucose (HG)-cultured podocytes, the cellular functions and exact mechanisms underlying the regulatory effects of lncRNA Pdia3 on podocyte apoptosis and endoplasmic reticulum stress (ERS) were explored. LncRNA Pdia3 and miR-139-3p expression were measured through quantitative real-time polymerase chain reaction. Relative cell viability was detected through the cell counting kit-8 colorimetric assay. The podocyte apoptosis rate in each group was measured through flow cytometry. The interaction between lncRNA Pdia3 and miR-139-3p was examined through the dual luciferase reporter assay. Finally, western blotting was performed to detect the effect of lncRNA Pdia3 on podocyte apoptosis and ERS via miR-139-3p. RESULTS The expression of lncRNA Pdia3 was significantly downregulated in HG-cultured podocytes. Next, lncRNA Pdia3 was involved in HG-induced podocyte apoptosis. Furthermore, the dual luciferase reporter assay confirmed the direct interaction between lncRNA Pdia3 and miR-139-3p. LncRNA Pdia3 overexpression attenuated podocyte apoptosis and ERS through miR-139-3p in HG-cultured podocytes. CONCLUSION Taken together, this study demonstrated that lncRNA Pdia3 overexpression could attenuate HG-induced podocyte apoptosis and ERS by acting as a competing endogenous RNA of miR-139-3p, which might provide a potential therapeutic target for DN.
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Affiliation(s)
- Yin-Xi He
- Department of Orthopaedic Trauma, The Third Hospital of Shijiazhuang, Shijiazhuang 050000, Hebei Province, China
| | - Ting Wang
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei Province, China
| | - Wen-Xian Li
- Department of Endocrinology, The First Hospital of Zhangjiakou, Zhangjiakou 075000, Hebei Province, China
| | - Yan-Xia Chen
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei Province, China
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Ouyang S, Zhou ZX, Liu HT, Ren Z, Liu H, Deng NH, Tian KJ, Zhou K, Xie HL, Jiang ZS. LncRNA-mediated Modulation of Endothelial Cells: Novel Progress in the Pathogenesis of Coronary Atherosclerotic Disease. Curr Med Chem 2024; 31:1251-1264. [PMID: 36788688 DOI: 10.2174/0929867330666230213100732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/06/2022] [Accepted: 11/17/2022] [Indexed: 02/16/2023]
Abstract
Coronary atherosclerotic disease (CAD) is a common cardiovascular disease and an important cause of death. Moreover, endothelial cells (ECs) injury is an early pathophysiological feature of CAD, and long noncoding RNAs (lncRNAs) can modulate gene expression. Recent studies have shown that lncRNAs are involved in the pathogenesis of CAD, especially by regulating ECs. In this review, we summarize the novel progress of lncRNA-modulated ECs in the pathogenesis of CAD, including ECs proliferation, migration, adhesion, angiogenesis, inflammation, apoptosis, autophagy, and pyroptosis. Thus, as lncRNAs regulate ECs in CAD, lncRNAs will provide ideal and novel targets for the diagnosis and drug therapy of CAD.
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Affiliation(s)
- Shao Ouyang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
- Key Laboratory of Heart Failure Prevention & Treatment of Hengyang, Department of Cardiovascular Medicine, Hengyang Medical School, The Second Affiliated Hospital, Clinical Medicine Research Center of Arteriosclerotic Disease of Hunan Province, University of South China, Hunan 421001, China
| | - Zhi-Xiang Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hui-Ting Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhong Ren
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Huan Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Nian-Hua Deng
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kai-Jiang Tian
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kun Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hai-Lin Xie
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhi-Sheng Jiang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
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Mohan S, Hakami MA, Dailah HG, Khalid A, Najmi A, Zoghebi K, Halawi MA. The emerging role of noncoding RNAs in the EGFR signaling pathway in lung cancer. Pathol Res Pract 2024; 253:155016. [PMID: 38070221 DOI: 10.1016/j.prp.2023.155016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/24/2024]
Abstract
Noncoding ribonucleic acids (ncRNAs) have surfaced as essential orchestrators within the intricate system of neoplastic biology. Specifically, the epidermal growth factor receptor (EGFR) signalling cascade shows a central role in the etiological underpinnings of pulmonary carcinoma. Pulmonary malignancy persists as a preeminent contributor to worldwide mortality attributable to malignant neoplasms, with non-small cell lung carcinoma (NSCLC) emerging as the most predominant histopathological subcategory. EGFR is a key driver of NSCLC, and its dysregulation is frequently associated with tumorigenesis, metastasis, and resistance to therapy. Over the past decade, researchers have unveiled a complex network of ncRNAs, encompassing microRNAs, long noncoding RNAs, and circular RNAs, which intricately regulate EGFR signalling. MicroRNAs, as versatile post-transcriptional regulators, have been shown to target various components of the EGFR pathway, influencing cancer cell proliferation, migration, and apoptosis. Additionally, ncRNAs have emerged as critical modulators of EGFR signalling, with their potential to act as scaffolds, decoys, or guides for EGFR-related proteins. Circular RNAs, a relatively recent addition to the ncRNA family, have also been implicated in EGFR signalling regulation. The clinical implications of ncRNAs in EGFR-driven lung cancer are substantial. These molecules exhibit diagnostic potential as robust biomarkers for early cancer detection and personalized treatment. Furthermore, their predictive value extends to predicting disease progression and therapeutic outcomes. Targeting ncRNAs in the EGFR pathway represents a novel therapeutic approach with promising results in preclinical and early clinical studies. This review explores the increasing evidence supporting the significant role of ncRNAs in modulating EGFR signalling in lung cancer, shedding light on their potential diagnostic, prognostic, and therapeutic implications.
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Affiliation(s)
- Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; School of Health Sciences, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India; Center for Global health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Hamad Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Maryam A Halawi
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
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Liu M, Song X, Sun Y, Zhang T. LncRNA OIP5-AS1 Targets the miR-140-5p/UBR5 Cascade to Promote the Development of Gastric Cancer. Mol Biotechnol 2023:10.1007/s12033-023-00958-x. [PMID: 38112962 DOI: 10.1007/s12033-023-00958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/23/2023] [Indexed: 12/21/2023]
Abstract
Gastric cancer (GC) is a malignant tumor with the highest incidence among all kinds of malignant tumors in China. Long noncoding RNAs (LncRNAs) have been reported to act as microRNA (miRNAs) sponges and thus play key roles in biological processes and pathogenesis. Thus, this study aimed to investigate the functional effects and the regulatory mechanism of lncRNA opa interacting protein 5-antisense 1 (OIP5-AS1) in gastric cancer cells. The expression of OIP5-AS1, miR-140-5p, Ubiquitin protein ligase E3 component n-recognin 5 (UBR5) was detected using quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation, apoptosis, migration, and invasion were assessed using Cell-Counting Kit-8 (CCK-8), Flow cytometry, and Transwell assays. UBR5 protein level was detected by Western blot. Binding between miR-140-5p and OIP5-AS1 or UBR5 was predicted by Starbasev2.0 and TargetScan, and verified using Dual-luciferase reporter assays and RNA pull-down assay. A xenograft mice model was used to evaluate the effects of OIP5-AS1 on tumor growth in vivo. OIP5-AS1 was upregulated in GC cancer and cells. OIP5-AS1 knockdown inhibited cell proliferation, migration, invasion, but induced cell apoptosis in GC. In mechanism, OIP5-AS1 might serve as a sponge for miR-140-5p to enhance UBR5 expression. Moreover, overexpression of miR-140-5p or UBR5 partly reversed the effects of OIP5-AS1 depletion on the progression of GC cells. Furthermore, OIP5-AS1 depletion also suppressed tumor growth in vivo. OIP5-AS1 silencing might suppress proliferation, migration, invasion, and induced apoptosis in GC cells by regulating the miR-140-5p/UBR5 axis.
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Affiliation(s)
- Mei Liu
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng District, Xiangyang City, 441000, Hubei Province, China
| | - Xiujun Song
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng District, Xiangyang City, 441000, Hubei Province, China
| | - Yinyin Sun
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng District, Xiangyang City, 441000, Hubei Province, China.
| | - Tieshan Zhang
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng District, Xiangyang City, 441000, Hubei Province, China.
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12
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Wu Z, Yin H, Guo Y, Yin H, Li Y. Detection of cell-type-enriched long noncoding RNAs in atherosclerosis using single-cell techniques: A brief review. Life Sci 2023; 333:122138. [PMID: 37805167 DOI: 10.1016/j.lfs.2023.122138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Cardiovascular diseases are the leading causes of mortality and morbidity worldwide. Atherosclerotic plaque underlies the predominant factors and is composed of various cell types, including structure cells, such as endothelial and smooth muscle cells, and immune cells, such as macrophages and T cells. Single-cell RNA sequencing (scRNA-seq) has been extensively applied to decipher these cellular heterogeneities to expand our understanding on the mechanisms of atherosclerosis (AS) and to facilitate identifying cell-type-specific long noncoding RNAs (LncRNAs). LncRNAs have been demonstrated to deeply regulate biological activities at the transcriptional and post-transcriptional levels. A group of well-documented functional lncRNAs in AS have been studied. In our review, we selectively described several lncRNAs involved in the critical process of AS. We highlighted four novel lncRNAs (lncRNA CARMN, LINC00607, PCAT19, LINC01235) detected in scRNA-seq datasets and their functions in AS. We also reviewed open web source and bioinformatic tools, as well as the latest methods to perform an in-depth study of lncRNAs. It is fundamental to annotate functional lncRNAs in the various biological activities of AS, as lncRNAs may represent promising targets in the future for treatment and diagnosis in clinical practice.
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Affiliation(s)
- Zhiyuan Wu
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
| | - Huarun Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongsheng Guo
- Peking University Health Science Center, 100191 Beijing, PR China
| | - Hongchao Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongjun Li
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China; Peking University Health Science Center, 100191 Beijing, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
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13
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Jiang X. The mechanisms and therapeutic potential of long noncoding RNA NEAT1 in fibrosis. Clin Exp Med 2023; 23:3339-3347. [PMID: 37740135 DOI: 10.1007/s10238-023-01191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
Fibrosis is the excess deposition of extracellular matrix involved in the pathogenesis of chronic diseases and finally leads to the disruption of tissue architecture and failure of organ function. Long noncoding RNAs (lncRNAs) are a class of RNAs with lengths greater than 200 nucleotides and do not code proteins, which regulate gene expression at multiple levels. Nuclear-enriched abundant transcript 1 (NEAT1) is a long noncoding RNA that is widely expressed in mammalian cells and known as essential architectural scaffold for the formation of paraspeckles. Recently, the accumulating studies demonstrated that lncRNA NEAT1 was remarkable upregulated in the development of fibrosis in different organs, such as liver fibrosis, renal fibrosis, cardiac fibrosis, and lung fibrosis. More importantly, knockdown of NEAT1 remarkably alleviated fibrosis in vitro and in vivo. In this review, we summarized current studies of NEAT1 in fibrosis and hopefully aid in a better understanding of the mechanisms of fibrosis and the potential of NEAT1 as novel therapeutic target for fibrosis.
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Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China.
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14
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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15
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Chu Q, Yu J, Zhou J. Long noncoding RNA LTCONS4500 promotes antibacterial immune responses via targeting miR-3570-5p in teleost fish Miichthys miiuy. Dev Comp Immunol 2023; 147:104764. [PMID: 37356679 DOI: 10.1016/j.dci.2023.104764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/23/2023] [Indexed: 06/27/2023]
Abstract
There is accumulating evidence demonstrated that long noncoding RNAs (lncRNA) act as gene regulators in various biological processes, including innate immunity, in which lncRNAs could play their regulatory roles by interacting with miRNAs. Compared with mammals, there is little attention paid to the mechanism of the lncRNA-miRNA regulatory network in teleost fish. Herein, we found a long noncoding RNAs LTCONS4500 that could function as a positive regulator of the immune response in miiuy croaker (Miichthys miiuy). Specifically, we found that the expression of LTCONS4500 could be upregulated by gram-negative bacteria, such as Vibrio anguillarum and Vibrio harveyi. Upregulated LTCONS4500 could promote the expression of inflammatory cytokines. Further study showed that LTCONS4500 could act as a competing endogenous RNA (ceRNA) to interact with miR-3570-5p to facilitate MyD88 expression and thus enhance antibacterial immune responses. Our data suggests the function and mechanism of lncRNAs in antibacterial immune responses of teleost fish, which will enrich the gene regulatory network of vertebrates.
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Affiliation(s)
- Qing Chu
- School of Agriculture, Ludong University, Yantai, China.
| | - Jingyao Yu
- School of Agriculture, Ludong University, Yantai, China
| | - Jiale Zhou
- School of Agriculture, Ludong University, Yantai, China
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16
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Karger A, Mansouri S, Leisegang MS, Weigert A, Günther S, Kuenne C, Wittig I, Zukunft S, Klatt S, Aliraj B, Klotz LV, Winter H, Mahavadi P, Fleming I, Ruppert C, Witte B, Alkoudmani I, Gattenlöhner S, Grimminger F, Seeger W, Pullamsetti SS, Savai R. ADPGK-AS1 long noncoding RNA switches macrophage metabolic and phenotypic state to promote lung cancer growth. EMBO J 2023; 42:e111620. [PMID: 37545364 PMCID: PMC10505917 DOI: 10.15252/embj.2022111620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 08/08/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) influence the transcription of gene networks in many cell types, but their role in tumor-associated macrophages (TAMs) is still largely unknown. We found that the lncRNA ADPGK-AS1 was substantially upregulated in artificially induced M2-like human macrophages, macrophages exposed to lung cancer cells in vitro, and TAMs from human lung cancer tissue. ADPGK-AS1 is partly located within mitochondria and binds to the mitochondrial ribosomal protein MRPL35. Overexpression of ADPGK-AS1 in macrophages upregulates the tricarboxylic acid cycle and promotes mitochondrial fission, suggesting a phenotypic switch toward an M2-like, tumor-promoting cytokine release profile. Macrophage-specific knockdown of ADPGK-AS1 induces a metabolic and phenotypic switch (as judged by cytokine profile and production of reactive oxygen species) to a pro-inflammatory tumor-suppressive M1-like state, inhibiting lung tumor growth in vitro in tumor cell-macrophage cocultures, ex vivo in human tumor precision-cut lung slices, and in vivo in mice. Silencing ADPGK-AS1 in TAMs may thus offer a novel therapeutic strategy for lung cancer.
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Affiliation(s)
- Annika Karger
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
| | - Siavash Mansouri
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Medical FacultyGoethe University FrankfurtFrankfurtGermany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of MedicineGoethe University FrankfurtFrankfurtGermany
- Frankfurt Cancer Institute (FCI)Goethe University FrankfurtFrankfurtGermany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
| | - Carsten Kuenne
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
| | - Ilka Wittig
- Functional Proteomics, Medical SchoolGoethe University FrankfurtFrankfurtGermany
| | - Sven Zukunft
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Stephan Klatt
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Blerina Aliraj
- Institute of Biochemistry I, Faculty of MedicineGoethe University FrankfurtFrankfurtGermany
| | - Laura V Klotz
- Translational Lung Research Center (TLRC), Member of the DZLHeidelbergGermany
- Department of Thoracic SurgeryThoraxklinik at the University Hospital HeidelbergHeidelbergGermany
| | - Hauke Winter
- Translational Lung Research Center (TLRC), Member of the DZLHeidelbergGermany
- Department of Thoracic SurgeryThoraxklinik at the University Hospital HeidelbergHeidelbergGermany
| | - Poornima Mahavadi
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular MedicineGoethe UniversityFrankfurtGermany
| | - Clemens Ruppert
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Biruta Witte
- Department of General and Thoracic SurgeryUniversity Hospital GiessenGiessenGermany
| | - Ibrahim Alkoudmani
- Department of General and Thoracic SurgeryUniversity Hospital GiessenGiessenGermany
| | | | - Friedrich Grimminger
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung ResearchMember of the German Center for Lung Research (DZL), Member of the Cardio‐Pulmonary Institute (CPI)Bad NauheimGermany
- Institute for Lung Health (ILH)Justus Liebig UniversityGiessenGermany
- Frankfurt Cancer Institute (FCI)Goethe University FrankfurtFrankfurtGermany
- Department of Internal MedicineMember of the DZL, Member of CPI, Justus Liebig UniversityGiessenGermany
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17
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Guo B, Li T, Wang L, Liu F, Chen B. Long non-coding RNAs regulate heavy metal-induced apoptosis in embryo-derived cells. Environ Pollut 2023; 333:121956. [PMID: 37271361 DOI: 10.1016/j.envpol.2023.121956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/14/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
Heavy metal pollution has been a worldwide prevalent problem, and particularly a threat to ecosystem integrity and animals' health. Previous studies on the mechanisms of heavy metal toxicity have focused on protein-coding genes, whereas most genomic transcripts are long non-coding RNAs (lncRNAs). Although lncRNAs are known to play important regulatory roles in biological processes, their role in heavy metal stress regulation is still not fully understood. We here developed an insect embryo cell model for studying metal toxicity and the underlying regulatory mechanisms. We performed genome-wide screening and functional characterization of lncRNAs induced by two essential and two non-essential heavy metals in Drosophila embryo-derived S2 cells. We identified 4894 lncRNAs, of which 1410 were novel. Forty-one lncRNAs, together with 328 mRNAs, were induced by all the four heavy metals. LncRNA-mRNA co-expression network and pathway enrichment analysis showed that detoxification metabolism, circadian rhythm, and apoptosis regulation pathways were activated in response to heavy metal stress. LncRNA CR44138 was remarkably upregulated in cells exposed to the four heavy metals and was associated with the apoptosis pathway. Expression interference confirmed that CR44138 aggravated cytotoxicity-induced apoptosis in cells under heavy metals stress. This study highlights the important role of lncRNAs in regulating the cellular response to heavy metals. This study also lays the foundation for discovering the novel regulatory mechanisms and developing diagnostic biomarkers of the toxic effects of heavy metal pollutants on organisms.
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Affiliation(s)
- Boyang Guo
- College of Life Science, Hebei University, Baoding 071002, China
| | - Ting Li
- School of Life Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, 271016, Shandong Province, China
| | - Lingyan Wang
- College of Life Science, Hebei University, Baoding 071002, China
| | - Fengsong Liu
- College of Life Science, Hebei University, Baoding 071002, China
| | - Bing Chen
- College of Life Science, Hebei University, Baoding 071002, China.
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18
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Song GY, Guo XN, Yao J, Lu ZN, Xie JH, Wu F, He J, Fu ZL, Han J. Differential expression profiles and functional analysis of long non-coding RNAs in calcific aortic valve disease. BMC Cardiovasc Disord 2023; 23:326. [PMID: 37369992 DOI: 10.1186/s12872-023-03311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
AIM To evaluate the expression profile of long non-coding RNAs (lncRNAs) in calcific aortic valve disease (CAVD) and explore their potential mechanism of action. METHODS The gene expression profiles (GSE153555, GSE148219, GSE199718) were downloaded from the Gene Expression Omnibus (GEO) database and FastQC was run for quality control checks. After filtering and classifying candidate lncRNAs by differentially expressed genes (DEGs) and weighted co-expression networks (WGCNA) in GSE153555, we predicted the potential cis- or trans-regulatory target genes of differentially expressed lncRNAs (DELs) by using FEELnc and established the competitive endogenous RNA (ceRNA) network by miRanda, more over functional enrichment was analyzed using the ClusterProfiler package in R Bioconductor. The hub cis- or trans-regulatory genes were verified in GSE148219 and GSE199718 respectively. RESULTS There were 340 up-regulated lncRNAs identified in AS group compared with the control group (|log2Fold Change| ≥ 1.0 and Padj ≤ 0.05), and 460 down-regulated lncRNAs. Based on target gene prediction and co-expression network construction, twelve Long non-coding RNAs (CDKN2B-AS1, AC244453.2, APCDD1L-DT, SLC12A5-AS1, TGFB3, AC243829.4, MIR4435-2HG, FAM225A, BHLHE40-AS1, LINC01614, AL356417.2, LINC01150) were identified as the hub cis- or trans-regulatory genes in the pathogenesis of CAVD which were validated in GSE148219 and GSE19971. Additionally, we found that MIR4435-2HG was the top hub trans-acting lncRNA which also plays a crucial role by ceRNA pattern. CONCLUSION LncRNAs may play an important role in CAVD and may provide a new perspective on the pathogenesis, diagnosis, and treatment of this disease. Further studies are required to illuminate the underlying mechanisms and provide potential therapeutic targets.
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Affiliation(s)
- Guang-Yuan Song
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China.
| | - Xu-Nan Guo
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jing Yao
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhi-Nan Lu
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jia-Hong Xie
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Fang Wu
- Department of Cardiac Surgery, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jing He
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhao-Lin Fu
- Interventional Center of Valvular Heart Disease, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jie Han
- Department of Cardiac Surgery, Beijing Anzhen Hospital Affiliated to Capital Medical University, Beijing, China.
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19
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Plaisance I, Chouvardas P, Sun Y, Nemir M, Aghagolzadeh P, Aminfar F, Shen S, Shim WJ, Rochais F, Johnson R, Palpant N, Pedrazzini T. A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovasc Res 2023; 119:1361-1376. [PMID: 36537036 PMCID: PMC10262180 DOI: 10.1093/cvr/cvac191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 03/25/2024] Open
Abstract
AIMS The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The human lncRNA CARMEN, which is known to dictate specification toward the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced isoforms. METHODS AND RESULTS The CARMEN locus can be manipulated to direct human primary cardiac precursor cells (CPCs) into specific cardiovascular fates. Investigating CARMEN isoform usage in differentiating CPCs represents therefore a unique opportunity to uncover isoform-specific functions in lncRNAs. Here, we identify one CARMEN isoform, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. CONCLUSIONS These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA. They further demonstrated the crucial importance of the lncRNA isoform CARMEN-201 in SMC specification during heart development.
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Affiliation(s)
- Isabelle Plaisance
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Yuliangzi Sun
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Mohamed Nemir
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Farhang Aminfar
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
| | - Sophie Shen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Francesca Rochais
- Aix Marseille University, Marseille Medical Genetics, INSERM, U1251, Marseille, France
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nathan Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, University of Lausanne Medical School, Lausanne, Switzerland
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20
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Duan J, Huang Z, Nice EC, Xie N, Chen M, Huang C. Current advancements and future perspectives of long noncoding RNAs in lipid metabolism and signaling. J Adv Res 2023; 48:105-123. [PMID: 35973552 PMCID: PMC10248733 DOI: 10.1016/j.jare.2022.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The investigation of lncRNAs has provided a novel perspective for elucidating mechanisms underlying diverse physiological and pathological processes. Compelling evidence has revealed an intrinsic link between lncRNAs and lipid metabolism, demonstrating that lncRNAs-induced disruption of lipid metabolism and signaling contribute to the development of multiple cancers and some other diseases, including obesity, fatty liver disease, and cardiovascular disease. AIMOF REVIEW The current review summarizes the recent advances in basic research about lipid metabolism and lipid signaling-related lncRNAs. Meanwhile, the potential and challenges of targeting lncRNA for the therapy of cancers and other lipid metabolism-related diseases are also discussed. KEY SCIENTIFIC CONCEPT OF REVIEW Compared with the substantial number of lncRNA loci, we still know little about the role of lncRNAs in metabolism. A more comprehensive understanding of the function and mechanism of lncRNAs may provide a new standpoint for the study of lipid metabolism and signaling. Developing lncRNA-based therapeutic approaches is an effective strategy for lipid metabolism-related diseases.
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Affiliation(s)
- Jiufei Duan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China.
| | - Mingqing Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079 Wuhan, China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, 610041 Chengdu, China.
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21
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Zhang L, Liu C, Zhang X, Wang C, Liu D. Breast cancer prognosis and immunological characteristics are predicted using the m6A/m5C/m1A/m7G-related long noncoding RNA signature. Funct Integr Genomics 2023; 23:117. [PMID: 37014493 DOI: 10.1007/s10142-023-01026-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/05/2023]
Abstract
According to statistics, breast cancer (BC) has replaced lung cancer as the most common cancer in the world. Therefore, specific detection markers and therapeutic targets need to be explored as a way to improve the survival rate of BC patients. We first identified m6A/m5C/m1A/m7G-related long noncoding RNAs (MRlncRNAs) and developed a model of 16 MRlncRNAs. Kaplan-Meier survival analysis was applied to assess the prognostic power of the model, while univariate Cox analysis and multivariate Cox analysis were used to assess the prognostic value of the constructed model. Then, we constructed a nomogram to illustrate whether the predicted results were in good agreement with the actual outcomes. We tried to use the model to distinguish the difference in sensitivity to immunotherapy between the two groups and performed some analyses such as immune infiltration analysis, ssGSEA and IC50 prediction. To explore the novel anti-tumor drug response, we reclassified the patients into two clusters. Next, we assessed their response to clinical treatment by the R package pRRophetic, which is determined by the IC50 of each BC patient. We finally identified 11 MRlncRNAs and based on them, a risk model was constructed. In this model, we found good agreement between calibration plots and prognosis prediction. The AUC of ROC curves was 0.751, 0.734, and 0.769 for 1-year, 2-year, and 3-year overall survival (OS), respectively. The results showed that the IC50 was significantly different between the risk groups, suggesting that the risk groups can be used as a guide for systemic treatment. We regrouped patients into two clusters based on 11 MRlncRNAs expression. Next, we conducted immune scores for 2 clusters, which showed that cluster 1 had higher stromal scores, immune scores and higher estimated (microenvironment) scores, demonstrating that TME of cluster 1 was different from cluster 2. The results of this study support that MRlncRNAs can predict tumor prognosis and help differentiate patients with different sensitivities to immunotherapy as a basis for individualized treatment for BC patients.
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Affiliation(s)
- Lina Zhang
- Department of Health Examination Center, Xingtai People's Hospital, Xingtai, 054001, Hebei, China
| | - Chengyu Liu
- Graduate School of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Xiaochong Zhang
- Key Laboratory of Cancer Prevention and Treatment, Xingtai People's Hospital, Xingtai, 054001, Hebei, China
| | - Changjing Wang
- Department of Gastrointestinal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Dengxiang Liu
- Institute of Cancer Control, Xingtai People's Hospital, Xingtai, 054001, Hebei, China.
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22
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Ghorbaninejad M, Abdollahpour-Alitappeh M, Shahrokh S, Fayazzadeh S, Asadzadeh-Aghdaei H, Meyfour A. TGF-β receptor I inhibitor may restrict the induction of EMT in inflamed intestinal epithelial cells. Exp Biol Med (Maywood) 2023; 248:665-676. [PMID: 36775873 PMCID: PMC10408554 DOI: 10.1177/15353702231151959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/15/2022] [Indexed: 02/14/2023] Open
Abstract
Despite the extensive body of research, understanding the exact molecular mechanisms governing inflammatory bowel diseases (IBDs) still demands further investigation. Transforming growth factor-β1 (TGF-β1) signaling possesses a multifacial effect on a broad range of context-dependent cellular responses. However, long-term TGF-β1 activity may trigger epithelial-mesenchymal transition (EMT), followed by fibrosis. This study aimed to determine the role of epithelial TGF-β1 signaling in inflammatory bowel disease (IBD) pathogenesis. The expression of TGF-β1 signaling components and EMT-related and epithelial tight junction markers was examined in IBD patients (n = 60) as well as LPS-induced Caco-2/RAW264.7 co-culture model using quantitative real-time polymerase chain reaction (qRT-PCR), Western blotting, and immunofluorescence staining. Furthermore, the effect of A83-01, as a TGF-β receptor I (TβRI) inhibitor, on the inflamed epithelial cells was evaluated in vitro. To evaluate the cytotoxic effects of the TβRI inhibitor, a cell viability assay was performed by the MTS method. Considering the activation of canonical and non-canonical TGF-β1 signaling pathways in IBD patients, expression results indicated that administering A83-01 in inflamed Caco-2 cells substantially blocked the expression level of TGF-β1, SMAD4, and PI3K and the phosphorylation of p-SMAD2/3, p-AKT, and p-RPS6 as well as prevented downregulation of LncGAS5 and LncCDKN2B. Further analysis revealed that the inhibition of TGF-β1 signaling in inflamed epithelial cells by the small molecule could suppress the EMT-related markers as well as improve the expression of epithelial adherens and tight junctions. Collectively, these findings indicated that the inhibition of the TGF-β1 signaling could suppress the induction of EMT in inflamed epithelial cells as well as exert a protective effect on preserving tight junction integrity. There is a pressing need to determine the exact cellular mechanisms by which TGF-β1 exerts its effect on IBD pathogenesis.
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Affiliation(s)
- Mahsa Ghorbaninejad
- 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
| | | | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717413, Iran
| | - Sara Fayazzadeh
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, 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
| | - Anna Meyfour
- 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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23
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Li QY, Gong T, Huang YK, Kang L, Warner CA, Xie H, Chen LM, Duan XQ. Role of noncoding RNAs in liver fibrosis. World J Gastroenterol 2023; 29:1446-1459. [PMID: 36998425 PMCID: PMC10044853 DOI: 10.3748/wjg.v29.i9.1446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/27/2022] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Liver fibrosis is a wound-healing response following chronic liver injury caused by hepatitis virus infection, obesity, or excessive alcohol. It is a dynamic and reversible process characterized by the activation of hepatic stellate cells and excess accumulation of extracellular matrix. Advanced fibrosis could lead to cirrhosis and even liver cancer, which has become a significant health burden worldwide. Many studies have revealed that noncoding RNAs (ncRNAs), including microRNAs, long noncoding RNAs and circular RNAs, are involved in the pathogenesis and development of liver fibrosis by regulating signaling pathways including transforming growth factor-β pathway, phosphatidylinositol 3-kinase/protein kinase B pathway, and Wnt/β-catenin pathway. NcRNAs in serum or exosomes have been reported to tentatively applied in the diagnosis and staging of liver fibrosis and combined with elastography to improve the accuracy of diagnosis. NcRNAs mimics, ncRNAs in mesenchymal stem cell-derived exosomes, and lipid nanoparticles-encapsulated ncRNAs have become promising therapeutic approaches for the treatment of liver fibrosis. In this review, we update the latest knowledge on ncRNAs in the pathogenesis and progression of liver fibrosis, and discuss the potentials and challenges to use these ncRNAs for diagnosis, staging and treatment of liver fibrosis. All these will help us to develop a comprehensive understanding of the role of ncRNAs in liver fibrosis.
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Affiliation(s)
- Qing-Yuan Li
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Tao Gong
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yi-Ke Huang
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
| | - Lan Kang
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
| | - Charlotte A Warner
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - He Xie
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xi’an 710077, Shaanxi Province, China
| | - Li-Min Chen
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xi’an 710077, Shaanxi Province, China
| | - Xiao-Qiong Duan
- Center for Transfusion-transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu 610052, Sichuan Province, China
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24
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Tang W, Xu J, Xu C. Noncoding RNAs in the crosstalk between multiple myeloma cells and bone marrow microenvironment. Cancer Lett 2023; 556:216081. [PMID: 36739065 DOI: 10.1016/j.canlet.2023.216081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy; however, it remains incurable, and the underlying pathogenesis and mechanisms of drug resistance remain unclear. It is widely recognized that the bone marrow microenvironment plays a crucial role in regulating the immune response, inducing drug resistance, and promoting tumor proliferation and invasion in MM, and thus serves as a potential therapeutic target. Among the various signaling loops between myeloma cells and components of the microenvironment, noncoding RNAs are emerging as crucial regulators of intercellular communication within the microenvironment. Noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and PIWI-interacting RNAs, have been associated with numerous biological processes involved in myeloma cell growth, survival, migration, invasion, and drug resistance. This review summarizes recent advances in the regulatory mechanisms of noncoding RNAs involved in the interaction between the MM bone marrow microenvironment and discusses the therapeutic potential of noncoding RNAs in MM.
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Affiliation(s)
- Wenjiao Tang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Juan Xu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Caigang Xu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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25
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Han YC, Shen ZJ, Xiang RL, Lu B, Qian H, Li JY, Xie HZ. Long Noncoding RNA and mRNA Expression Profiles in Rats with LPS-induced Myocardial Dysfunction. Curr Genomics 2023; 23:412-423. [PMID: 37920555 PMCID: PMC10173418 DOI: 10.2174/1389202924666230119160258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/09/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Background Sepsis is an uncontrolled systemic inflammatory response. Long noncoding RNAs (lncRNAs) are involved in the pathogenesis of sepsis. However, little is known about the roles of lncRNAs in sepsis-induced myocardial dysfunction. Objective We aimed to determine the regulatory mechanism of lncRNAs in sepsis-induced myocardial dysfunction. Methods In this study, we analysed the lncRNA and mRNA expression profiles using microarray analysis. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, protein-protein interaction network, and gene set enrichment analysis were used to evaluate the data. We also constructed coding and noncoding coexpression and competing endogenous RNA networks to investigate the mechanisms. Results In vivo lipopolysaccharide -induced sepsis rat model was established. A total of 387 lncRNAs and 1,952 mRNAs were identified as significantly changed in the left ventricle. Kyoto Encyclopedia of Genes and Genomes analysis of mRNAs showed that the upregulated genes were mainly enriched in the "complement and coagulation cascade pathway" and "immune-related biological processes" terms. Eight significantly changed lncRNAs detected by RT-qPCR may be responsible for these processes. A competing endogenous RNA network was generated, and the results indicated that eight lncRNAs were related to the "calcium ion binding" process. Conclusion These results demonstrate that crosstalk between lncRNAs and mRNAs may play important roles in the development of sepsis-induced myocardial dysfunction.
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Affiliation(s)
- Ye-Chen Han
- Department of Cardiology, Peking Union Medical College Hospital, No. 1 North Street, Dongdan, Beijing, 100032, China
| | - Zhu-Jun Shen
- Department of Cardiology, Peking Union Medical College Hospital, No. 1 North Street, Dongdan, Beijing, 100032, China
| | - Ruo-Lan Xiang
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Bo Lu
- Department of Gastroenterology, Peking Union Medical College Hospital, Beijing, China
| | - Hao Qian
- Department of Cardiology, Peking Union Medical College Hospital, No. 1 North Street, Dongdan, Beijing, 100032, China
| | - Jing-Yi Li
- Department of Cardiology, Peking Union Medical College Hospital, No. 1 North Street, Dongdan, Beijing, 100032, China
| | - Hong-Zhi Xie
- Department of Cardiology, Peking Union Medical College Hospital, No. 1 North Street, Dongdan, Beijing, 100032, China
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Deng P, Zhang H, Wang L, Jie S, Zhao Q, Chen F, Yue Y, Wang H, Tian L, Xie J, Chen M, Luo Y, Yu Z, Pi H, Zhou Z. Long-term cadmium exposure impairs cognitive function by activating lnc-Gm10532/m6A/FIS1 axis-mediated mitochondrial fission and dysfunction. Sci Total Environ 2023; 858:159950. [PMID: 36336035 DOI: 10.1016/j.scitotenv.2022.159950] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Cadmium (Cd), a ubiquitous environmental contaminant, is deemed a possible aetiological cause of cognitive disorders in humans. Nevertheless, the exact mechanism by which chronic exposure to Cd causes neurotoxicity is not fully understood. In this study, mouse neuroblastoma cells (Neuro-2a cells) and primary hippocampal neurons were exposed to low-dose (1, 2, and 4 μM for Neuro-2a cells or 0.5, 1, and 1.5 μM for hippocampal neurons) cadmium chloride (CdCl2) for 72 h (h), and male mice (C57BL/6J, 8 weeks) were orally administered CdCl2 (0.6 mg/L, approximately equal to 2.58 μg/kg·bw/d) for 6 months to investigate the effects and mechanism of chronic Cd-induced neurotoxicity. Here, chronic exposure to Cd impaired mitochondrial function by promoting excess reactive oxygen species (ROS) production, altering mitochondrial membrane potential (Δψm) and reducing adenosine triphosphate (ATP) content, contributing to neuronal cell death. Specifically, microarray analysis revealed that the long noncoding RNA Gm10532 (lnc-Gm10532) was most highly expressed in Neuro-2a cells exposed to 4 μM CdCl2 for 72 h compared with controls, and inhibition of lnc-Gm10532 significantly antagonized CdCl2-induced mitochondrial dysfunction and neurotoxicity. Mechanistically, lnc-Gm10532 increased Fission 1 (FIS1) expression and mitochondrial fission by recruiting the m6A writer methyltransferase-like 14 (METTL14) and enhancing m6A modification of Fis1 mRNA. Moreover, lnc-Gm10532 was also required for chronic Cd-induced mitochondrial dysfunction and memory deficits in a rodent model. Therefore, data of this study reveal a new epigenetic mechanism of chronic Cd neurotoxicity.
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Affiliation(s)
- Ping Deng
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Huadong Zhang
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China
| | - Liting Wang
- Biomedical Analysis Center, Third Military Medical University, Chongqing 400038, China
| | - Sheng Jie
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Qi Zhao
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China
| | - Fengqiong Chen
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China
| | - Yang Yue
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Hui Wang
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Li Tian
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Jia Xie
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Mengyan Chen
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Yan Luo
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Zhengping Yu
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China
| | - Huifeng Pi
- Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing 400038, China.
| | - Zhou Zhou
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China; Department of Environmental Medicine, School of Public Health, and Department of Emergency Medicine, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China.
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27
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Zhang Y, Guo J, Gao Y, Li S, Pan T, Xu G, Li X, Li Y, Yang J. Dynamic transcriptome analyses reveal m 6A regulated immune non-coding RNAs during dengue disease progression. Heliyon 2023; 9:e12690. [PMID: 36685392 PMCID: PMC9850062 DOI: 10.1016/j.heliyon.2022.e12690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Dengue infection is one of the most prevalent arthropod-borne viral diseases, which can result in severe complications. Identification of genes and long non-coding RNAs (lncRNAs) involved in dengue infection would help in deciphering potential mechanisms responsible for the disease progression. We comprehensively analyzed the dynamic transcriptome during dengue disease progression and identified critical genes and lncRNAs with expression perturbations. Our findings revealed that the expression of genes (i.e., CCR10 and GNG7) and lncRNAs (i.e., CTBP1-AS and MAFG-AS1) were potentially regulated by m6A RNA methylation. Interestingly, dengue viral proteins prevalently interact with genes or lncRNAs with expression perturbations, which are involved in cell cycle, inflammation signaling pathways and immune response. Dynamically expressed genes and lncRNAs were likely to locate in the central regions of human protein-protein network, which play crucial roles in mediating signaling spread and helping viral replication. Immune microenvironments analysis revealed that plasma cells levels were increased and T cells infiltrations were decreased during dengue disease progression. Dynamically expressed genes and lncRNAs were correlated with immune cell infiltrations. Moreover, network analysis reveals the associations between dengue viral infections and human complex diseases (i.e., digestive diseases and neoplasms). Our comprehensive transcriptome analysis of dengue disease progression identified potential gene and lncRNA biomarkers, providing novel insights for understanding the pathogenesis of and developing effective therapeutic strategies for dengue infection.
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Affiliation(s)
- Ya Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Jing Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Yueying Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Si Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Tao Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Gang Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China,Corresponding author.Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China.
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,Corresponding author.
| | - Jun Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children’s Medical Center, Hainan Medical University, Haikou 571199, China,Corresponding author.
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Yan X, Liu H, Li T. Lncrna NEAT1 Regulates Th1/Th2 in Pediatric Asthma by Targeting MicroRNA-217/GATA3. Iran J Public Health 2023; 52:106-117. [PMID: 36824247 PMCID: PMC9941437 DOI: 10.18502/ijph.v52i1.11671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/18/2022] [Indexed: 01/18/2023]
Abstract
Background The imbalance of immune response between helper Th1 and Th2 cells is the direct cause of asthma. It was closely related to abnormal expression of lncRNAs. However, whether lncRNAs can regulate Th1/Th2 balance in pediatric asthma remains to be investigated. Methods Peripheral blood samples were collected from children with asthma and normal volunteers at the Children's Hospital of Shaanxi Provincial People's Hospital (Xi'an, China) in 2020. The qRT-PCR was used to detect the expression of lncRNA NEAT1, miR-217 and GATA3 in peripheral blood samples. The effects of lncRNA NEAT1, miR-217, and GATA3 on CD4+T cell population were detected in vitro. Meanwhile, the regulatory effect of lncRNA NEAT1/miR-217/GATA3 was evaluated through the dual luciferase report assay, functional assays and animal experiments. Results We investigated that lncRNA NEAT1 and GATA3 was significantly up-regulated in CD4+T cells in peripheral blood of children with asthma (P<0.001). Knockdown of lncRNA NEAT1 or GATA3 significantly reduced Th2-related cytokines (P<0.05), but had no effect on Th1 cells. Importantly, the interactions of lncRNA NEAT1 with miR-217 and miR-217 with GATA3 were confirmed by dual luciferase report assay. Meanwhile, functional assays and animal experiments demonstrated that lncRNA NEAT1 regulated GATA3 expression through sponge miR-217, thereby regulating Th1/Th2 balance in CD4+T cells in pediatric asthma. Conclusion lncRNA NEAT1/miR-217/GATA3 axis may reveal the immunological mechanism of pediatric asthma, which has potential clinical application value in the future.
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Affiliation(s)
- Xianpeng Yan
- Children’s Hospital of Shaanxi Provincial People’s Hospital, Xi’an 710068, PR China
| | - Hong Liu
- Children’s Hospital of Shaanxi Provincial People’s Hospital, Xi’an 710068, PR China,Corresponding Author:
| | - Ting Li
- Children’s Hospital of Shaanxi Provincial People’s Hospital, Xi’an 710068, PR China
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Guzmán-Martín CA, Juárez-Vicuña Y, Domínguez-López A, González-Ramírez J, Amezcua-Guerra LM, Martínez-Martínez LA, Sánchez-Muñoz F. lncRNAs dysregulation in monocytes from primary antiphospholipid syndrome patients: a bioinformatic and an experimental proof-of-concept approach. Mol Biol Rep 2023; 50:937-41. [PMID: 36367661 DOI: 10.1007/s11033-022-08080-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Antiphospholipid syndrome (APS) is the main cause of acquired thrombophilia where peripheral circulating cells such as monocytes have a key role. Currently, several studies have linked long non-coding RNAs (lncRNAs) in different inflammatory and autoimmune processes, including lupus. However, the role of lncRNAs in antiphospholipid syndrome is unknown, therefore, we aimed to select and measure expression levels of three lncRNAs based on its abundance in monocytes from APS patients. METHODS Selection of lncRNAs candidates were carried out based on its abundance in monocytes and their relationship with Perez-Sanchez miRNA signature by using miRNet 2.0 bioinformatic tool, then lncRNAs expression levels was measured in monocytes by RT-qPCR. RESULTS This is the first study to report that lncRNAs: FGD5-AS1, OIP5-AS1 and GAS5 are promising candidates for play a role on APS monocytes and they are expressed differently between patients and controls. CONCLUSIONS OIP5-AS1, FGD5-AS1 and GAS5 are downregulated on monocytes from APS patients.
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30
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Yang X, Liu L, Shen X, Shi L, Liu W. Dysregulation and implications of lncRNAs and miRNAs in oral tongue squamous cell carcinoma: In reply with emphasis on the role of ceRNAs. Oral Oncol 2023; 136:106277. [PMID: 36508884 DOI: 10.1016/j.oraloncology.2022.106277] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
Increasing evidence indicates that long noncoding RNAs (lncRNAs) as competing endogenous RNAs (ceRNAs) competitively sequestering microRNAs (miRNAs) participate in biological processes of oral tongue squamous cell carcinoma (TSCC). In this Letter, the ceRNA regulatory networks consisting of lncRNA/miRNA/mRNA axes in TSCC were summarized. Dysregulated profiles containing 33 lncRNAs and 31 miRNAs were identified by cancer-associated phenotypes verification. Almost all the lncRNAs could exert the oncogenic roles to sponge miRNAs and regulate targeting mRNA expression, thereby modulating cell proliferation, cell cycle, apoptosis, invasion, migration, metastasis, epithelial-mesenchymal transition, as well as chemoresistance. Significantly, the implications of functional ceRNAs deactivated in tumor cells contribute to the exploitation of novel diagnostic and therapeutic strategies for TSCC.
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Affiliation(s)
- Xi Yang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Fengcheng Hospital of Fengxian District, Shanghai Ninth People's Hospital Fengcheng Branch Hospital, Shanghai, China; Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lijun Liu
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China; Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, e Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuemin Shen
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China; Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, e Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linjun Shi
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China; Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, e Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Wei Liu
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China.
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Zhu L, Chen D, Lin X, Liu L. Gene expression profile for different susceptibilities to sound stimulation: a comparative study on brainstems between two inbred laboratory mouse strains. BMC Genomics 2022; 23:783. [PMID: 36451107 PMCID: PMC9710100 DOI: 10.1186/s12864-022-09016-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND DBA/1 mice have a higher susceptibility to generalized audiogenic seizures (AGSz) and seizure-induced respiratory arrest (S-IRA) than C57/BL6 mice. The gene expression profile might be potentially related to this difference. This study aimed to investigate the susceptibility difference in AGSz and S-IRA between DBA/1 and C57BL/6 mice by profiling long noncoding RNAs (lncRNAs) and mRNA expression. METHODS We compared lncRNAs and mRNAs from the brainstem of the two strains with Arraystar Mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD). Gene Ontology (GO) and pathway analyses were performed to determine the potentially related biological functions and pathways based on differentially expressed mRNAs. qRT-PCR was carried out to validate the results. RESULTS A total of 897 lncRNAs and 438 mRNAs were differentially expressed (fold change ≥2, P < 0.05), of which 192 lncRNAs were upregulated and 705 lncRNAs were downregulated. A total of 138 mRNAs were upregulated, and 300 mRNAs were downregulated. In terms of specific mRNAs, Htr5b, Gabra2, Hspa1b and Gfra1 may be related to AGSz or S-IRA. Additionally, lncRNA Neat1 may participate in the difference in susceptibility. GO and pathway analyses suggested that TGF-β signaling, metabolic process and MHC protein complex could be involved in these differences. Coexpression analysis identified 9 differentially expressed antisense lncRNAs and 115 long intergenic noncoding RNAs (lincRNAs), and 2010012P19Rik and its adjacent RNA Tnfsf12-Tnfsf13 may have participated in S-IRA by regulating sympathetic neuron function. The results of the qRT-PCR of five selected lncRNAs (AK038711, Gm11762, 1500004A13Rik, AA388235 and Neat1) and four selected mRNAs (Hspa1b, Htr5b, Gabra2 and Gfra1) were consistent with those obtained by microarray. CONCLUSION We concluded that TGF-β signaling and metabolic process may contribute to the differential sensitivity to AGSz and S-IRA. Among mRNAs, Htr5b, Gabra2, Hspa1b and Gfra1 could potentially influence the susceptibility. LncRNA Neat1 and 2010012P19Rik may also contribute to the different response to sound stimulation. Further studies should be carried out to explore the underlying functions and mechanisms of differentially expressed RNAs.
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Affiliation(s)
- Lina Zhu
- grid.412901.f0000 0004 1770 1022Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Lane 37 #, Chengdu, 610041 Sichuan China
| | - Deng Chen
- grid.412901.f0000 0004 1770 1022Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Lane 37 #, Chengdu, 610041 Sichuan China
| | - Xin Lin
- grid.412901.f0000 0004 1770 1022Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Lane 37 #, Chengdu, 610041 Sichuan China
| | - Ling Liu
- grid.412901.f0000 0004 1770 1022Department of Neurology, West China Hospital, Sichuan University, Wai Nan Guo Xue Lane 37 #, Chengdu, 610041 Sichuan China
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Lin J, Xie Z, Zhang Z, Li M, Ye G, Yu W, Li J, Ye F, Su Z, Che Y, Xu P, Zeng C, Wang P, Wu Y, Shen H. LncRNA MRF drives the regulatory function on monocyte recruitment and polarization through HNRNPD-MCP1 axis in mesenchymal stem cells. J Biomed Sci 2022; 29:73. [PMID: 36127734 PMCID: PMC9490984 DOI: 10.1186/s12929-022-00858-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background Mesenchymal stem cells (MSCs) exhibit two bidirectional immunomodulatory abilities: proinflammatory and anti-inflammatory regulatory effects. Long noncoding RNAs (lncRNAs) have important functions in the immune system. Previously, we performed high-throughput sequencing comparing lncRNA expression profiles between MSCs cocultured with or without CD14+ monocytes and screened out a new lncRNA termed lncRNA MCP1 regulatory factor (MRF). However, the mechanism of MRF in MSCs is still unknown. Methods MRF expression was quantified via qRT–PCR. RNA interference and lentiviruses were used to regulate MRF expression. The immunomodulatory effects of MSCs on monocytes were evaluated via monocyte migration and macrophage polarization assays. RNA pull-down and mass spectrometry were utilized to identify downstream factors of MRF. A dual-luciferase reporter assay was applied to analyze the transcription factors regulating MRF. qRT–PCR, western blotting and ELISAs were used to assess MCP1 expression. A human monocyte adoptive transfer mouse model was applied to verify the function of MRF in vivo. Results MRF was upregulated in MSCs during coculture with CD14+ monocytes. MRF increased monocyte recruitment by upregulating the expression of monocyte chemotactic protein (MCP1). Knockdown of MRF enhanced the regulatory effect of MSCs on restraining M1 polarization and facilitating M2 polarization. Mechanistically, MRF bound to the downstream protein heterogeneous nuclear ribonucleoprotein D (HNRNPD) to upregulate MCP1 expression, and the transcription factor interferon regulatory factor 1 (IRF1) activated MRF transcription early during coculture. The human monocyte adoptive transfer model showed that MRF downregulation in MSCs inhibited monocyte chemotaxis and enhanced the effects of MSCs to inhibit M1 macrophage polarization and promote M2 polarization in vivo. Conclusion We identified the new lncRNA MRF, which exhibits proinflammatory characteristics. MRF regulates the ability of MSCs to accelerate monocyte recruitment and modulate macrophage polarization through the HNRNPD-MCP1 axis and initiates the proinflammatory regulatory process in MSCs, suggesting that MRF is a potential target to improve the clinical effect of MSC-based therapy or correct MSC-related immunomodulatory dysfunction under pathological conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00858-3.
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Affiliation(s)
- Jiajie Lin
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Zhongyu Xie
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Zhaoqiang Zhang
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Ming Li
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Guiwen Ye
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Wenhui Yu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Jinteng Li
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Feng Ye
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Zepeng Su
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Yunshu Che
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Peitao Xu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Chenying Zeng
- Center for Biotherapy, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China
| | - Peng Wang
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China.
| | - Yanfeng Wu
- Center for Biotherapy, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China.
| | - Huiyong Shen
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, China.
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Su H, Hailin Z, Dongdong L, Jiang Y, Shuncheng H, Shun Z, Dan L, Biao P. Long non-coding RNA LINC01018 inhibits human glioma cell proliferation and metastasis by directly targeting miRNA-182-5p. J Neurooncol 2022. [PMID: 36094613 DOI: 10.1007/s11060-022-04113-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/04/2022] [Indexed: 10/14/2022]
Abstract
AIM Accumulating evidence suggests that lncRNAs are potential biomarkers and key regulators of tumor development and progression. However, the precise function of most lncRNAs in glioma remains unknown. In this study, we explored the role of long intergenic non-protein coding RNA 1018 (LINC01018) in human glioma. METHODS Expression levels of LINC01018 and miR-182-5p in clinical glioma tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR). Cell proliferation, migration, and invasion were determined by Cell Counting Kit-8 (CCK-8) assay and Transwell assay. Epithelial-mesenchymal transition (EMT) related proteins were measured by Western blotting. Direct relationship between LINC01018 and miR-182-5p was tested by dual-luciferase reporter assay, RNA immunoprecipitation assay (RIP), and rescue assays. Lastly, bioinformatics analyses were conducted to predict the downstream factors of LINC01018/miR-182-5p axis in glioma. RESULTS LINC01018 was significantly down-regulated in glioma tissues and cell lines. Overexpression of LINC01018 dramatically inhibited cell proliferation, migration, and invasion and reverse EMT process in glioma. LINC01018 directly target to miR-182-5p. Forced up-regulation of miR-182-5p reversed the inhibitory effects on proliferative and metastatic abilities of glioma cells with LINC01018 overexpression. Lastly, the bioinformatics analyses revealed that LINC01018/miR-182-5p axis mediated a cluster of downstream genes (ADRA2C, RAB6B, RAB27B, RAPGEF5, STEAP2, TAGLN3, and UNC13C), which were potential key factors in the development of glioma. CONCLUSION LINC01018 inhibits cell proliferation and metastasis in human glioma by targeting miR-182-5p, and should be considered as a potential therapeutic target in this cancer.
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Liang Z, Fan W, Chen H, Huang ZP, Fang R, Dong B, Chen C, Li J, Dai G, Xue R, Dong Y, Liu C. Identification of a long noncoding RNA Gm17501 as a novel negative regulator of cardiac hypertrophy. Exp Cell Res 2022; 418:113262. [PMID: 35714940 DOI: 10.1016/j.yexcr.2022.113262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/26/2022] [Accepted: 06/12/2022] [Indexed: 11/28/2022]
Abstract
Pathological cardiac hypertrophy is an independent risk factor for the development of heart failure. Long noncoding RNAs (lncRNAs), an emerging class of non-protein-coding transcripts, are involved in regulation of multiple cardiac diseases through diverse molecular mechanism, whereas the role of cytoplasmic lncRNAs in regulating cardiac hypertrophy remains unclear. In this study, we identified a novel and functional long noncoding RNA Gm17501, which was predominantly expressed in the cytoplasm of cardiomyocytes. The expression level of lncRNA Gm17501 was altered in cardiac hypertrophy induced by pressure overload and phenylephrine treatment. Moreover, lncRNA Gm17501 expression was decreased in the heart tissue of patients with heart failure. Silencing lncRNA Gm17501 aggravated cardiac hypertrophy under pathological stress. Inhibition of lncRNA Gm17501 did not alter the expression of nearby genes but decreased mRNA level of calcium handling proteins which were involved in cardiac contraction. Therefore, the cytoplasmic lncRNA Gm17501 might protect cardiomyocytes against hypertrophy, possibly by maintaining calcium signaling pathway.
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Affiliation(s)
- Zhuomin Liang
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Wendong Fan
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Hao Chen
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Zhan-Peng Huang
- NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China; Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Rong Fang
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Bin Dong
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Chen Chen
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Jiayong Li
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Gang Dai
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Ruicong Xue
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China
| | - Yugang Dong
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China.
| | - Chen Liu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China; NHC Key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou, Guangdong, 510080, China.
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Abstract
Several diverse long noncoding RNAs (lncRNAs) have been identified to be involved in hepatitis B virus (HBV) replication and oncogenesis, especially those dysregulated in HBV-related hepatocellular carcinoma (HCC). Most of these dysregulated lncRNAs are modulated by the HBV X protein. The regulatory mechanisms of some lncRNAs in HBV replication and oncogenesis have been characterized. Genetic polymorphisms of several lncRNAs affecting HBV replication or oncogenesis have also been studied. The prognosis of HCC remains poor. It is important to identify novel tumor markers for early diagnosis and find more therapeutic targets for effective treatments of HCC. Some dysregulated lncRNAs in HBV-related HCC may become biomarkers for early diagnosis and/or the therapeutic targets of HCC. This mini-review summarizes these findings briefly, focusing on recent developments.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
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Quintero D, Rodriguez HC, Potty AG, Kouroupis D, Gupta A. Long noncoding RNAs in mesenchymal stromal/stem cells osteogenic differentiation: Implications in osteoarthritis pathogenesis. World J Stem Cells 2022; 14:429-434. [PMID: 35949395 PMCID: PMC9244951 DOI: 10.4252/wjsc.v14.i6.429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/27/2022] [Accepted: 05/22/2022] [Indexed: 02/06/2023] Open
Abstract
This letter focuses on a recently published article that provided an exceptional description of the effect of epigenetic modifications on gene expression patterns related to skeletal system remodeling. Specifically, it discusses a novel modality of epigenetic regulation, the long noncoding RNAs (lncRNAs), and provides evidence of their involvement in mesenchymal stromal/stem cells osteo-/adipo-genic differentiation balance. Despite focus on lncRNAs, there is an emerging cross talk between lncRNAs and miRNAs interaction as a novel mechanism in the regulation of the function of the musculoskeletal system, by controlling bone homeostasis and bone regeneration, as well as the osteogenic differentiation of stem cells. Thus, we touched on some examples to demonstrate this interaction. In addition, we believe there is still much to discover from the effects of lncRNAs on progenitor and non-progenitor cell differentiation. We incorporated data from other published articles to review lncRNAs in normal progenitor cell osteogenic differentiation, determined lncRNAs involved in osteoarthritis pathogenesis in progenitor cells, and provided a review of lncRNAs in non-progenitor cells that are differentially regulated in osteoarthritis. In conclusion, we really enjoyed reading this article and with this information we hope to further our understanding of lncRNAs and mesenchymal stromal/stem cells regulation.
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Affiliation(s)
- Daniel Quintero
- Department of Orthopaedics, Division of Sports Medicine, University of Miami, Miller School of Medicine, Miami, FL 33136, United States
| | - Hugo C Rodriguez
- Holy Cross Orthopedic Institute: Fort Lauderdale Practice, Oakland Park, FL 33334, United States
| | - Anish G Potty
- South Texas Orthopedic Research Institute, Laredo, TX 78045 United States
| | - Dimitrios Kouroupis
- Diabetes Research Institute, Cell Transplant Center, University of Miami, Miller School of Medicine, Miami, FL 33136, United States
| | - Ashim Gupta
- South Texas Orthopedic Research Institute, Laredo, TX 78045 United States
- BioIntegrate, Lawrenceville, GA 30043, United States
- Future Biologics, Lawrenceville, GA 30043, United States
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Karimi B, Dehghani Firoozabadi A, Peymani M, Ghaedi K. Circulating long noncoding RNAs as novel bio-tools: Focus on autoimmune diseases. Hum Immunol 2022; 83:618-627. [PMID: 35717260 DOI: 10.1016/j.humimm.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs that do not encode proteins. These RNAs have various essential regulatory functions. Irregular expression of lncRNAs has been related to the pathological process of varied diseases, and are considered promising diagnostic biomarkers. LncRNAs can release into the circulation and be stable in body fluids as circulating lncRNAs. A subset of circulating lncRNAs that exist in exosomes are referred to as exosomal lncRNA molecules. These lncRNAs are highly stable and resist RNases. Exosomes have captured a great deal of attention due to their involvement in regulating communications between cells. In conditions of autoimmune disease, exosomes play critical roles in the pathological processes. In this context, circulating lncRNAs have been shown to modulate the immune response and indicated as prognosis and diagnostic biomarkers for autoimmune diseases. This review highlights the role of circulating lncRNAs (particularly exosomal) as diagnostic biomarkers for autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, psoriasis, and Sjögren's syndrome.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kamran Ghaedi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Dai T, Li J, Ye L, Yu H, Deng M, Liu W, Li H, Yang Y, Wang G. Prognostic Role and Potential Mechanisms of N6-methyladenosine-related Long Noncoding RNAs in Hepatocellular Carcinoma. J Clin Transl Hepatol 2022; 10:308-320. [PMID: 35528973 PMCID: PMC9039697 DOI: 10.14218/jcth.2021.00096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS Numerous studies have explored the important role of N6-methyladenosine (m6A) in cancer. Nonetheless, the interaction between m6A and long noncoding RNAs (lncRNAs) is poorly investigated. Herein, we systematically analyzed the role and prognostic value of m6A-related lncRNAs in hepatocellular carcinoma (HCC). METHODS The m6A-related lncRNAs were identified based on the correlation coefficients with m6A-related genes in HCC from The Cancer Genome Atlas. Subsequently, a novel risk score model was determined using the least absolute shrinkage and selection operator Cox regression analyses. Univariate and multivariate Cox analyses were used to identify independent prognostic factors for overall survival (OS) of HCC; thereafter, a prognostic nomogram was constructed. RESULTS A total of 259 lncRNAs showed significant correlations with m6A in HCC, while 29 lncRNAs had prognostic significance. Further, six critical m6A-related lncRNAs (NRAV, SNHG3, KDM4A-AS1, AC074117.1, AC025176.1, and AL031985.3) were screened out to construct a novel risk score model which classified HCC patients into high- and low-risk groups. Survival analyses revealed that patients in the high-risk group exhibited worse OS, both in the training and validation groups. The risk score was also identified as an independent prognostic factor of OS, and a nomogram was established and verified with superior prediction capacity. Besides, the risk score significantly correlated with the expression of immune checkpoint genes and immune subtypes. CONCLUSIONS These findings indicated the significant role of m6A-related lncRNAs in HCC and the potential application of the novel risk score model for prognostic prediction.
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Affiliation(s)
- Tianxing Dai
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jing Li
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Linsen Ye
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Haoyuan Yu
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Mingbin Deng
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hua Li
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yang Yang
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Correspondence to: Guoying Wang and Yang Yang, Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, Guangdong 510630, China. ORCID: https://orcid.org/0000-0002-0304-0986 (GW), https://orcid.org/0000-0003-4981-4745 (YY). Tel: +86-020-8525-2177, Fax: +86-020-8525-2276, E-mail: (GW), (YY)
| | - Guoying Wang
- Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Correspondence to: Guoying Wang and Yang Yang, Department of Hepatic Surgery and Liver Transplant Program, The Third Affiliated Hospital of Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, Guangdong 510630, China. ORCID: https://orcid.org/0000-0002-0304-0986 (GW), https://orcid.org/0000-0003-4981-4745 (YY). Tel: +86-020-8525-2177, Fax: +86-020-8525-2276, E-mail: (GW), (YY)
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Long D, Tian XD, Yang YM. Emerging Role of Exosomal-Derived Long Noncoding RNAs in Human PDAC. Visc Med 2022; 38:30-36. [PMID: 35295891 PMCID: PMC8874243 DOI: 10.1159/000520947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023] Open
Abstract
Background The incidence and mortality of pancreatic ductal adenocarcinoma (PDAC) are increasing recently. Most patients with PDAC are diagnosed at advanced stage because of the high invasiveness of cancer cells and the lack of typical early symptoms. Therefore, early diagnosis of PDAC is very important to improve the prognosis. Exosomes play crucial role in intercellular communication and deliver the contents to recipient cells to regulate their biological behaviors. Recent evidence suggests emerging role of exosomes in the carcinogenesis of a variety of cancers including PDAC. Long noncoding RNAs (LncRNAs) have been reported to be involved in the development of PDAC. It has been proved that LncRNAs have the potential to be biomarkers and therapeutic targets for PDAC. Moreover, increasing number of studies focus on the role of exosomal LncRNAs in PDAC. Summary In this review, we summarize the current status on our understanding of the role of exosomal-derived LncRNAs in the progression and metastasis of PDAC. Key Messages We focus on challenges in the potential of exosomal-derived LncRNAs as novel diagnostic and prognostic markers and therapeutic targets of PDAC. In addition, we provide an overview about the demonstrated important role of exosomal LncRNAs in the progression of PDAC.
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Zheng W, Shen GL, Xu KY, Yin QQ, Hui TC, Zhou ZW, Xu CA, Wang SH, Wu WH, Shi LF, Pan HY. Lnc524369 promotes hepatocellular carcinoma progression and predicts poor survival by activating YWHAZ-RAF1 signaling. World J Gastrointest Oncol 2022; 14:253-264. [PMID: 35116115 PMCID: PMC8790426 DOI: 10.4251/wjgo.v14.i1.253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Liver cancer is one of the most highly malignant cancers, characterized by easy metastasis and chemoradiotherapy resistance. Emerging evidence indicates that long noncoding RNAs (LncRNAs), including Lnc524369, are highly involved in the initiation, progression, radioresistance, and chemoresistance of hepatocellular carcinoma (HCC). However, the function of Lnc524369 remains unclear.
AIM To explore the function of Lnc524369 in HCC.
METHODS To investigate the effect of Lnc524369, tissue from 41 HCC patients were analyzed using CCK8, migration, and invasion assays. Lnc524369 and YWHAZ (also named 14-3-3ζ) mRNA were detected by qPCR, and YWHAZ and RAF1 proteins were detected by western blot in liver cancer cell lines and human HCC tissues. The Cancer Cell Line Encyclopedia (CCLE) databases, STRING database, Human Protein Atlas database, and the TCGA database were used for bioinformatic analysis.
RESULTS Lnc524369 was significantly upregulated in the nucleus of liver cancer cells and human HCC tissues. Overexpression of Lnc524369 was associated with the proliferation, migration, and invasion of liver cancer cells. YWHAZ and RAF1 proteins and YWHAZ mRNA were overexpressed in liver cancer, which could be attenuated by overexpression of Lnc524369. Lnc524369 and its downstream target YWHAZ and RAF1 proteins were negatively associated with overall survival time.
CONCLUSION Lnc524369 might be a promising target of HCC as it can enhance liver cancer progression and decrease the overall survival time of HCC by activating the YWHAZ/RAF1 pathway.
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Affiliation(s)
- Wei Zheng
- Department of Clinical Medicine, Medical College of Soochow University, Suzhou 215006, Jiangsu Province, China
- Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang Province, China
| | - Guo-Liang Shen
- Department of Hepatobiliary & Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang Province, China
| | - Ke-Yang Xu
- School of Chinese Medicine, Hongkong Baptist university, Hong Kong 999777, China
| | - Qiao-Qiao Yin
- Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang Province, China
| | - Tian-Chen Hui
- Department of Graduate School, Bengbu Medical College, Bengbu 233030, Anhui Province, China
| | - Zhe-Wen Zhou
- Department of Graduate School, Bengbu Medical College, Bengbu 233030, Anhui Province, China
| | - Cheng-An Xu
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Shou-Hao Wang
- Medical Department of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China
| | - Wen-Hao Wu
- Medical Department of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China
| | - Ling-Fei Shi
- Diagnosis and Treatment Center of Osteoporosis, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hang Zhou 310014, Zhejiang Province, China
| | - Hong-Ying Pan
- Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang Province, China
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Peng Y, Wang H, Huang Q, Wu J, Zhang M. A prognostic model based on immune-related long noncoding RNAs for patients with epithelial ovarian cancer. J Ovarian Res 2022; 15:8. [PMID: 35031063 PMCID: PMC8760785 DOI: 10.1186/s13048-021-00930-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are important regulators of gene expression and can affect a variety of physiological processes. Recent studies have shown that immune-related lncRNAs play an important role in the tumour immune microenvironment and may have potential application value in the treatment and prognosis prediction of tumour patients. Epithelial ovarian cancer (EOC) is characterized by a high incidence and poor prognosis. However, there are few studies on immune-related lncRNAs in EOC. In this study, we focused on immune-related lncRNAs associated with survival in EOC. METHODS We downloaded mRNA data for EOC patients from The Cancer Genome Atlas (TCGA) database and mRNA data for normal ovarian tissue from the Genotype-Tissue Expression (GTEx) database and identified differentially expressed genes through differential expression analysis. Immune-related lncRNAs were obtained through intersection and coexpression analysis of differential genes and immune-related genes from the Immunology Database and Analysis Portal (ImmPort). Samples in the TCGA EOC cohort were randomly divided into a training set, validation set and combination set. In the training set, Cox regression analysis and LASSO regression were performed to construct an immune-related lncRNA signature. Kaplan-Meier survival analysis, time-dependent ROC curve analysis, Cox regression analysis and principal component analysis were performed for verification in the training set, validation set and combination set. Further studies of pathways and immune cell infiltration were conducted through Gene Set Enrichment Analysis (GSEA) and the Timer data portal. RESULTS An immune-related lncRNA signature was identified in EOC, which was composed of six immune-related lncRNAs (KRT7-AS, USP30-AS1, AC011445.1, AP005205.2, DNM3OS and AC027348.1). The signature was used to divide patients into high-risk and low-risk groups. The overall survival of the high-risk group was lower than that of the low-risk group and was verified to be robust in both the validation set and the combination set. The signature was confirmed to be an independent prognostic biomarker. Principal component analysis showed the different distribution patterns of high-risk and low-risk groups. This signature may be related to immune cell infiltration (mainly macrophages) and differential expression of immune checkpoint-related molecules (PD-1, PDL1, etc.). CONCLUSIONS We identified and established a prognostic signature of immune-related lncRNAs in EOC, which will be of great value in predicting the prognosis of clinical patients and may provide a new perspective for immunological research and individualized treatment in EOC.
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Affiliation(s)
- Yao Peng
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China.,Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, P.R. China
| | - Hui Wang
- Department of Oncology, Lu'an People's Hospital of Anhui Province, No. 21, West Anhui Road, Lu'an, 237006, Anhui, P.R. China
| | - Qi Huang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China
| | - Jingjing Wu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China
| | - Mingjun Zhang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei, 230601, Anhui, P.R. China. .,Anhui Medical University, No. 81, Meishan Road, Hefei, 230032, Anhui, P.R. China.
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Abstract
Recently an explosion in the discovery of long noncoding RNAs (lncRNAs) was obtained by high-throughput sequencing. Genome-wide transcriptome analyses, in conjugation with research for epigenetic modifications of chromatins, identified a novel type of non-protein coding transcripts longer than 200 nucleotides named lncRNAs . They are gradually emerging as functional and critical participants in many physiological processes. Here we gave an overview of the characteristics, biological functions, and working mechanism for this new class of noncoding RNA molecules.
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Xia M, Zu X, Chen Z, Wen G, Zhong J. Noncoding RNAs in triple negative breast cancer: Mechanisms for chemoresistance. Cancer Lett 2021; 523:100-110. [PMID: 34601022 DOI: 10.1016/j.canlet.2021.09.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype among breast cancers with high recurrence and this condition is partly due to chemoresistance. Therefore, fully understanding the mechanism of TNBC-resistance is the key to overcoming chemoresistance, which will be an effective strategy for TNBC therapy. Various potential mechanisms involved in the chemoresistance of TNBC have been investigated and indicated that noncoding RNAs (ncRNAs) especially microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) take part in most TNBC resistance. The ncRNA-induced chemoresistance process is involved in the alteration of many activities. here, we mainly summarize the mechanisms of ncRNAs in the chemoresistance of TNBC and discuss the potential clinical application of ncRNAs in the treatment of TNBC, indicating that targeting ncRNAs might be a promising strategy for resensitization to chemotherapies.
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Affiliation(s)
- Min Xia
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Xuyu Zu
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China; Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Zuyao Chen
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China
| | - Gebo Wen
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China; Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.
| | - Jing Zhong
- Institute of Clinical Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China; Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, PR China.
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Yang N, Yang J, He X, Zhang W, Xing Y. Construction and analysis of mRNA, lncRNA, and transcription factor regulatory networks after retinal ganglion cell injury. Exp Eye Res 2021; 215:108915. [PMID: 34971620 DOI: 10.1016/j.exer.2021.108915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/11/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Retinal ganglion cell (RGC) injury is a critical pathological feature of several optic neurodegenerative diseases. The regulatory mechanisms underlying RGC injury remain poorly understood. Recent evidence has highlighted the important roles of long noncoding RNAs (lncRNAs) in degenerative neuropathy but few studies have focused on lncRNAs associated with RGC injury. In this study, we analyzed dysregulated lncRNAs associated with RGC injury, their potential regulatory functions, and the molecular mechanisms underlying the regulation of lncRNAs and transcription factors (TFs). We analyzed lncRNA and mRNA profiles in the GSE142881 dataset associated with RGC injury and identified 1049 differentially expressed genes (DEGs), with 18 differentially expressed (DE) TFs among 883 DE mRNAs and 312 DE lncRNAs. The predicted DE lncRNAs and DE mRNAs were used to construct a lncRNA-mRNA co-expression network. Functional enrichment analysis was performed to explore the functions of the lncRNAs and mRNAs. The co-expression network between DE lncRNAs and DE mRNAs was highly enriched in inflammatory and immune-related pathways, indicating that they play role in the process of RGC injury. Among the DE mRNAs, we screened 18 DE TFs, including activating transcription factor 3 (ATF3), associated with RGC injury. Co-expression analysis predicted that 13 lncRNAs were potential binding targets of ATF3. The screening of the potential targets of these 13 lncRNAs showed that they were also significantly enriched in functional pathways associated with inflammation and apoptosis. After analysis, we constructed the mRNA-ATF3-lncRNA regulatory network after RGCs injury. In summary, we identified the gene module associated with immune and inflammatory responses after optic nerve injury and constructed a regulatory network of lncRNA-TF-mRNA. The results indicate that lncRNAs, by binding to TFs, can regulate downstream genes and function during RGC injury. The results provide a foundation for further studies of the mechanism of RGC injury and provide insight into the clinical diagnosis and investigation direction of neurodegenerative diseases such as traumatic optic neuropathy and glaucoma.
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Kang YJ, Li JY, Ke L, Jiang S, Yang DC, Hou M, Gao G. Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells. Brief Bioinform 2021; 23:6445106. [PMID: 34849565 DOI: 10.1093/bib/bbab483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
Gene transcription and protein translation are two key steps of the 'central dogma.' It is still a major challenge to quantitatively deconvolute factors contributing to the coding ability of transcripts in mammals. Here, we propose ribosome calculator (RiboCalc) for quantitatively modeling the coding ability of RNAs in human genome. In addition to effectively predicting the experimentally confirmed coding abundance via sequence and transcription features with high accuracy, RiboCalc provides interpretable parameters with biological information. Large-scale analysis further revealed a number of transcripts with a variety of coding ability for distinct types of cells (i.e. context-dependent coding transcripts), suggesting that, contrary to conventional wisdom, a transcript's coding ability should be modeled as a continuous spectrum with a context-dependent nature.
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Affiliation(s)
- Yu-Jian Kang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jing-Yi Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lan Ke
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuai Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - De-Chang Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Mei Hou
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ge Gao
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), and State Key Laboratory of Protein and Plant Gene Research at School of Life Sciences, Peking University, Beijing, 100871, China
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Wang Y, Ma J, Li R, Gao X, Wang H, Jiang G. LncRNA TMPO-AS1 serves as a sponge for miR-4731-5p modulating breast cancer progression through FOXM1. Am J Transl Res 2021; 13:11094-11106. [PMID: 34786045 PMCID: PMC8581887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To investigate the function of IncRNA-TMPO-AS1 in breast cancer (BC) and to further explore its molecular mechanism. METHODS TMPO-AS1, miR-4731-5p and FOXM1 were quantitatively determined using qRT-PCR. CCK-8 assays, plate cloning experiments, wound healing and Transwell assays, and flow cytometry were used to assess the biological behaviors of BC cells. Dual-luciferase reporter assays were used to assess the interactions between TMPO-AS1 and its downstream targets. The apoptosis and cell cycle-related proteins were quantitatively determined using Western blot. RESULTS In the BC tissues and cells, TMPO-AS1 was significantly increased (P<0.05). Functional studies suggest that the knockdown of TMPO-AS1 tremendously restrains tumor cell growth and migration (P<0.05). Mechanically, TMPO-AS1 negatively regulates miR-4731-5p and influences the progression of BC through the miR-4731-5p/FOXM1 axis. CONCLUSION LncRNA TMPO-AS1spongess miR-4731-5p to modulate BC progression through FOXM1.
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Affiliation(s)
- Ying Wang
- Department of Surgery, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu Province, China
- Department of General Surgery, The Affiliated Hospital of Yangzhou UniversityYangzhou 225012, Jiangsu Province, China
| | - Jun Ma
- Department of Surgery Oncology, The Anqing Municipal HospitalAnqing 246003, Anhui Province, China
| | - Ruiqing Li
- Department of General Surgery, The Affiliated Hospital of Yangzhou UniversityYangzhou 225012, Jiangsu Province, China
| | - Xiaokang Gao
- Department of General Surgery, The Affiliated Hospital of Yangzhou UniversityYangzhou 225012, Jiangsu Province, China
| | - Hongli Wang
- Department of General Surgery, The Affiliated Hospital of Yangzhou UniversityYangzhou 225012, Jiangsu Province, China
| | - Guoqin Jiang
- Department of Surgery, The Second Affiliated Hospital of Soochow UniversitySuzhou 215004, Jiangsu Province, China
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He S, Arikin A, Chen J, Huang T, Wu Z, Wang L, Yang F, Li Y, Yang Y, Wang R, Lian M, Zhong Q, Fang J. Transcriptome Analysis Identified 2 New lncRNAs Associated with the Metastasis of Papillary Thyroid Carcinoma. ORL J Otorhinolaryngol Relat Spec 2021; 84:247-254. [PMID: 34818244 DOI: 10.1159/000518085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/20/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Papillary thyroid microcarcinoma (PTMC) is a specific subgroup of papillary thyroid carcinoma and defined with the dimension ≤1 cm by the WHO. Although it shows a relatively high 10-year livability, the metastasis of PTMC into other tissues and organs seriously affects the daily life of patients with relatively high mortality. Therefore, the genetic basis for the metastasis of PTMC needs to be explored for effective therapeutic targets. Here, we conducted a series of comparative analysis of the transcriptional expression profile between PTMC patients with and without lymph node metastasis. METHODS Gene expression profile and gene function were analyzed using RNA extracted from pathological tissues of 12 patients with PTMC, and the core biomarkers closely related to its metastasis were identified. RESULTS Our results showed that 7,507 genes and 42 RNAs showed remarkably different expression patterns. More sophisticated analysis showed that the high expression of 2 lncRNAs (T077499 and T004533) resulted in the metastasis of PTMC, which suggests that the expression pattern of the 2 lncRNAs may act as a potential biomarker for pathogenesis and prognosis of PTMC metastasis. CONCLUSION Our findings preliminarily reveal the molecular mechanisms for PTMC metastasis, which will provide vital reference for subsequent studies about the genetic basis and molecular targeted therapy for PTMC metastasis.
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Affiliation(s)
- Shizhi He
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Abdeyrim Arikin
- Department of Otorhinolaryngology Head and Neck Surgery, The People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Jiaming Chen
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Tianqiao Huang
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Lingwa Wang
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Fan Yang
- Department of Otolaryngology Head Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Yunxia Li
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yifan Yang
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ru Wang
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Meng Lian
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qi Zhong
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jugao Fang
- Department of Otolaryngology Head Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Hua Q, Wang D, Zhao L, Hong Z, Ni K, Shi Y, Liu Z, Mi B. AL355338 acts as an oncogenic lncRNA by interacting with protein ENO1 to regulate EGFR/AKT pathway in NSCLC. Cancer Cell Int 2021; 21:525. [PMID: 34627260 PMCID: PMC8502354 DOI: 10.1186/s12935-021-02232-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is a malignancy with considerable morbidity and mortality. Abnormal metabolism is a hallmark of cancer; however, the mechanism of glycolysis regulation in NSCLC progression is not completely understood. Recent studies suggest that some dysregulated long non-coding RNAs (lncRNAs) play important roles in tumor metabolic reprogramming. METHODS To identify glycolysis-associated-lncRNAs in NSCLC, we compared RNA-sequencing results between high 18F-fluorodeoxyglucose (FDG)-uptake NSCLC tissues and paired paratumor tissues. The transcript abundance of AL355338 in 80 pairs of clinical samples was evaluated by quantitative real-time PCR assay and fluorescence in situ hybridization. The biological role of AL355338 on NSCLC cells were evaluated by functional experiments in vitro and in vivo. Moreover, RNA pull-down, mass spectrometry and RNA immunoprecipitation (RIP) assays were used to identify the protein interacted with AL355338. Co-immunoprecipitation, in situ proximity ligation assays and western blotting were applied to define the potential downstream pathways of AL355338. RESULTS AL355338 was an upregulated glycolysis-associated lncRNA in NSCLC. Functional assays revealed that AL355338 was critical for promoting aerobic glycolysis and NSCLC progression. Mechanistic investigations showed that AL355338 directly bound with alpha-enolase (ENO1) and enhanced the protein's stability by modulating its degradation and ubiquitination. A positive correlation was observed between AL355338 and ENO1 in NSCLC, and ENO1 was subsequently confirmed to be responsible for the oncogenic role of AL355338. Furthermore, AL355338 was capable of modulating ENO1/EGFR complex interaction and further activating EGFR-AKT signaling. CONCLUSIONS This study indicates that AL355338 confers an aggressive phenotype to NSCLC, and targeting it might be an effective therapeutic strategy.
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Affiliation(s)
- Qian Hua
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Dongliang Wang
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Lin Zhao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Zhihui Hong
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Kairu Ni
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Yizhen Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Zengli Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
| | - Baoming Mi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
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Abstract
The mammalian brain expresses several classes of noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). These ncRNAs play vital roles in regulating cellular processes by RNA/protein scaffolding, sponging and epigenetic modifications during the pathophysiological conditions, thereby controlling transcription and translation. Some of these functions are the result of crosstalk between ncRNAs to form a competitive endogenous RNA network. These intricately organized networks comprise lncRNA/miRNA, circRNA/miRNA, or lncRNA/miRNA/circRNA, leading to crosstalk between coding and ncRNAs through miRNAs. The miRNA response elements predominantly mediate the ncRNA crosstalk to buffer the miRNAs and thereby fine-tune and counterbalance the genomic changes and regulate neuronal plasticity, synaptogenesis and neuronal differentiation. The perturbed levels and interactions of the ncRNAs could lead to pathologic events like apoptosis and inflammation. Although the regulatory landscape of the ncRNA crosstalk is still evolving, some well-known examples such as lncRNA Malat1 sponging miR-145, circRNA CDR1as sponging miR-7, and lncRNA Cyrano and the circRNA CDR1as regulating miR-7, has been shown to affect brain function. The ability to manipulate these networks is crucial in determining the functional outcome of central nervous system (CNS) pathologies. The focus of this review is to highlights the interactions and crosstalk of these networks in regulating pathophysiologic CNS function.
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Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA; William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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Kay M, Soltani BM, Nemir M, Aghagolzadeh P, Pezzuto I, Chouvardas P, Ruberto F, Movahedi F, Ansari H, Baharvand H, Pedrazzini T. The conserved long noncoding RNA CARMA regulates cardiomyocyte differentiation. Cardiovasc Res 2021; 118:2339-2353. [PMID: 34459880 DOI: 10.1093/cvr/cvab281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
AIMS Production of functional cardiomyocytes from pluripotent stem cells requires tight control of the differentiation process. Long noncoding RNAs (lncRNAs) exert critical regulatory function in cell specification during development. In this study, we designed an integrated approach to identify lncRNAs implicated in cardiogenesis in differentiating human embryonic stem cells (ESCs). METHODS AND RESULTS We identified CARMA (CARdiomyocyte Maturation-Associated lncRNA), a conserved lncRNA controlling cardiomyocyte differentiation and maturation in human ESCs. CARMA is located adjacent to MIR-1-1HG, the host gene for two cardiogenic miRNAs: MIR1-1 and MIR-133a2, and transcribed in an antisense orientation. The expression of CARMA and the miRNAs is negatively correlated, and CARMA knockdown increases MIR1-1 and MIR-133a2 expression. In addition, CARMA possesses MIR-133a2 binding sites, suggesting the lncRNA could be also a target of miRNA action. Upon CARMA downregulation, MIR-133a2 target protein-coding genes are coordinately downregulated. Among those, we found RBPJ, the gene encoding the effector of the NOTCH pathway. NOTCH has been shown to control a binary cell fate decision between the mesoderm and the neuroectoderm lineages, and NOTCH inhibition leads to enhanced cardiomyocyte differentiation at the expense of neuroectodermal derivatives. Interestingly, two lncRNAs, linc1230 and linc1335, which are known repressors of neuroectodermal specification, were found upregulated upon Notch1 silencing in ESCs. Forced expression of either linc1230 or linc1335 improved ESC-derived cardiomyocyte production. These two lncRNAs were also found upregulated following CARMA knockdown in ESCs. CONCLUSIONS Altogether, these data suggest the existence of a network, implicating three newly identified lncRNAs, the two myomirs MIR1-1 and MIR-133a2 and the NOTCH signaling pathway, for the coordinated regulation of cardiogenic differentiation in ESCs. TRANSLATIONAL PERSPECTIVE Cardiac dysfunction and heart failure develop secondary to a massive loss of cardiomyocytes in the damaged myocardium. Several avenues have been evaluated to promote regeneration following injury. Cell therapy for heart disease envisages the production of functional cardiomyocytes from differentiating pluripotent stem cells prior transfer into the injured heart muscle. Here, we report the functional characterization of CARMA, a lncRNA implicated in cardiogenesis. CARMA knockdown in differentiating human embryonic stem cells (ESCs) promotes cardiogenic commitment and cardiomyocyte differentiation. CARMA represents therefore a novel target for improving human ESC-derived cardiomyocyte production, and cell-based regenerative strategies for heart disease.
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Affiliation(s)
- Maryam Kay
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Bahram M Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohamed Nemir
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Parisa Aghagolzadeh
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Iole Pezzuto
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | | | - Francesco Ruberto
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Fatemeh Movahedi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Hassan Ansari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Divison of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
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