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Li L, Hongying C, Heng G. Autophagy-related LncRNA PRDM10-DT responds to UVB radiation in keratinocytes. Biochem Biophys Res Commun 2023; 677:105-112. [PMID: 37566921 DOI: 10.1016/j.bbrc.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/01/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023]
Abstract
Ultraviolet (UV)-B radiation is a major environmental risk factor that is responsible for the development and progression of many skin disorders. Autophagy is the process of degradation and recycling of damaged cytoplasmic organelles, macromolecular aggregates, and long-lived proteins. Previously, we found that the autophagy inducer apigenin restored UVB-impaired autophagy and the cellular response by downregulating the expression of autophagy-related genes such as ATG5. To explore long noncoding RNAs (lncRNAs) involved in regulating these autophagy-related genes, in this study, we assessed the expression profiles of lncRNAs and mRNAs using a microarray in human epidermal keratinocytes (HEKs) treated with or without apigenin after UVB radiation. The expression levels of 80 selected autophagy-related genes and related lncRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT‒PCR). The lncRNA PRDM10-DT was proposed to regulate IRGM based on the ceRNA and coexpression pattern and was demonstrated to be involved in autophagy regulation, proliferation and migration of HEKs by qRT‒PCR, Western blotting, colony formation and scratch wound assays, respectively. These findings suggest an autophagy-related lncRNA in response to UVB radiation that promotes the proliferation and migration of HEKs through inducing autophagy by competing microRNAs for IRGM.
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Affiliation(s)
- Li Li
- Central Laboratory, Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, 210042, China.
| | - Chen Hongying
- Department of Physical Therapy, Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, 210042, China
| | - Gu Heng
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Nanjing, 210042, China.
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2
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Wang P, Chen W, Zhao S, Cheng F. The role of LncRNA-regulated autophagy in AKI. Biofactors 2023; 49:1010-1021. [PMID: 37458310 DOI: 10.1002/biof.1980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/16/2023] [Indexed: 10/04/2023]
Abstract
Acute kidney injury (AKI) is a complex clinical syndrome involving a series of pathophysiological processes regulated by multiple pathways at the molecular and cellular level. Long noncoding RNAs (lncRNAs) play an important role in the regulation of epigenetics, and their regulation of autophagy-related genes in AKI has attracted increasing attention. However, the role of lncRNA-regulated autophagy in AKI has not been fully elucidated. Evidence indicated that lncRNAs play regulatory roles in most factors that induce AKI. LncRNAs can regulate autophagy in AKI via a complex network of regulatory pathways to affect the development and prognosis of AKI. This article reviewed and analyzed the pathways of lncRNA regulation of autophagy in AKI in recent years. The results provide new ideas for further study of the pathophysiological process and targeted therapy for AKI.
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Affiliation(s)
- Peihan Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wu Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Sheng Zhao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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Huang X, Chi H, Gou S, Guo X, Li L, Peng G, Zhang J, Xu J, Nian S, Yuan Q. An Aggrephagy-Related LncRNA Signature for the Prognosis of Pancreatic Adenocarcinoma. Genes (Basel) 2023; 14:124. [PMID: 36672865 PMCID: PMC9859148 DOI: 10.3390/genes14010124] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is a common, highly malignant, and aggressive gastrointestinal tumor. The conventional treatment of PAAD shows poor results, and patients have poor prognosis. The synthesis and degradation of proteins are essential for the occurrence and development of tumors. Aggrephagy is a type of autophagy that selectively degrades aggregated proteins. It decreases the formation of aggregates by degrading proteins, thus reducing the harm to cells. By breaking down proteins, it decreases the formation of aggregates; thus, minimizing damage to cells. For evaluating the response to immunotherapy and prognosis in PAAD patients, in this study, we developed a reliable signature based on aggrephagy-related genes (ARGs). We obtained 298 AGGLncRNAs. Based on the results of one-way Cox and LASSO analyses, the lncRNA signature was constructed. In the risk model, the prognosis of patients in the low-risk group was noticeably better than that of the patients in the high-risk group. Additionally, the ROC curves and nomograms validated the capacity of the risk model to predict the prognosis of PAAD. The patients in the low-risk and high-risk groups showed considerable variations in functional enrichment and immunological analysis. Regarding drug sensitivity, the low-risk and high-risk groups had different half-maximal inhibitory concentrations (IC50).
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Affiliation(s)
- Xueyuan Huang
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Siqi Gou
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Xiyuan Guo
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lin Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Gaoge Peng
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou 646000, China
| | - Jiayu Xu
- Statistics Department, School of Science, Minzu University of China, Beijing 100081, China
| | - Siji Nian
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Qing Yuan
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, Public Center of Experimental Technology, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
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Luo L, Liang Y, Fu Y, Liang Z, Zheng J, Lan J, Shen F, Huang Z. Toosendanin Induces Hepatocyte Damage by Inhibiting Autophagic Flux via TFEB-Mediated Lysosomal Dysfunction. Pharmaceuticals (Basel) 2022; 15:ph15121509. [PMID: 36558960 PMCID: PMC9781622 DOI: 10.3390/ph15121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
Toosendanin (TSN) is a triterpenoid from the fruit or bark of Melia toosendan Sieb et Zucc, which has clear antitumor and insecticidal activities, but it possesses limiting hepatotoxicity in clinical application. Autophagy is a degradation and recycling mechanism to maintain cellular homeostasis, and it also plays an essential role in TSN-induced hepatotoxicity. Nevertheless, the specific mechanism of TSN on autophagy-related hepatotoxicity is still unknown. The hepatotoxicity of TSN in vivo and in vitro was explored in this study. It was found that TSN induced the upregulation of the autophagy-marker microtubule-associated proteins 1A/1B light chain 3B (LC3B) and P62, the accumulation of autolysosomes, and the inhibition of autophagic flux. The middle and late stages of autophagy were mainly studied. The data showed that TSN did not affect the fusion of autophagosomes and lysosomes but significantly inhibited the acidity, the degradation capacity of lysosomes, and the expression of hydrolase cathepsin B (CTSB). The activation of autophagy could alleviate TSN-induced hepatocyte damage. TSN inhibited the expression of transcription factor EB (TFEB), which is a key transcription factor for many genes of autophagy and lysosomes, such as CTSB, and overexpression of TFEB alleviated the autophagic flux blockade caused by TSN. In summary, TSN caused hepatotoxicity by inhibiting TFEB-lysosome-mediated autophagic flux and activating autophagy by rapamycin (Rapa), which could effectively alleviate TSN-induced hepatotoxicity, indicating that targeting autophagy is a new strategy to intervene in the hepatotoxicity of TSN.
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Affiliation(s)
- Li Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yonghong Liang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyuan Fu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiyuan Liang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jinfen Zheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Lan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Feihai Shen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Correspondence: (F.S.); (Z.H.)
| | - Zhiying Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Correspondence: (F.S.); (Z.H.)
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Ming S, Tian J, Ma K, Pei C, Li L, Wang Z, Fang Z, Liu M, Dong H, Li W, Zeng J, Peng Y, Gao X. Oxalate-induced apoptosis through ERS-ROS-NF-κB signalling pathway in renal tubular epithelial cell. Mol Med 2022; 28:88. [PMID: 35922749 PMCID: PMC9347104 DOI: 10.1186/s10020-022-00494-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
Background Kidney stones are composed of approximately 70–80% calcium oxalate. However, the exact mechanism of formation of calcium oxalate kidney stones remains unclear. In this study, we investigated the roles of endoplasmic reticulum stress (ERS), reactive oxygen species (ROS), and the NF-κB signalling pathway in the pathogenesis of oxalate-induced renal tubular epithelial cell injury and its possible molecular mechanisms. Methods We established a model to evaluate the formation of kidney stones by intraperitoneal injection of glyoxylic acid solution into mice and assessed cell morphology, apoptosis, and the expression levels of ERS, ROS, and NF-κB signalling pathway-related proteins in mouse renal tissues. Next, we treated HK-2 cells with potassium oxalate to construct a renal tubular epithelial cell injury model. We detected the changes in autophagy, apoptosis, and mitochondrial membrane potential and investigated the ultrastructure of the cells by transmission electron microscopy. Western blotting revealed the expression levels of apoptosis and autophagy proteins; mitochondrial structural and functional proteins; and ERS, ROS, and NF-κB (p65) proteins. Lastly, we studied the downregulation of NF-κB activity in HK-2 cells by lentivirus interference and confirmed the interaction between the NF-κB signalling and ERS/ROS pathways. Results We observed swelling of renal tissues, increased apoptosis of renal tubular epithelial cells, and activation of the ERS, ROS, and NF-κB signalling pathways in the oxalate group. We found that oxalate induced autophagy, apoptosis, and mitochondrial damage in HK-2 cells and activated the ERS/ROS/NF-κB pathways. Interestingly, when the NF-κB signalling pathway was inhibited, the ERS/ROS pathway was also inhibited. Conclusion Oxalate induces HK-2 cell injury through the interaction between the NF-κB signalling and ERS/ROS pathways.
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Affiliation(s)
- Shaoxiong Ming
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Jia Tian
- Department of Human Sperm Bank of Ningxia, General Hospital of Ningxia Medical University, Ningxia Medical University, No. 804 Shengli South Street, Xingqing District, Yinchuan, 750001, Ningxia Hui Autonomous Region, China
| | - Ke Ma
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Chengbin Pei
- Department of Human Sperm Bank of Ningxia, General Hospital of Ningxia Medical University, Ningxia Medical University, No. 804 Shengli South Street, Xingqing District, Yinchuan, 750001, Ningxia Hui Autonomous Region, China
| | - Ling Li
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Zeyu Wang
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Ziyu Fang
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Min Liu
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Hao Dong
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China
| | - Weijian Li
- Department of Urology, Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People's Hospital), B24, Yinquan Road, XinchengDistrict, Qingyuan, 511518, Guangdong Province, China
| | - Jianwen Zeng
- Department of Urology, Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People's Hospital), B24, Yinquan Road, XinchengDistrict, Qingyuan, 511518, Guangdong Province, China
| | - Yonghan Peng
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China.
| | - Xiaofeng Gao
- Department of Urology, Changhai Hospital of Shanghai, No. 168, Changhai Road, Yangpu District, Shanghai, 200433, China.
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Bahrami T, Sheikhesmaeili F, Ebadi N, Karimipoor M, Omrani MA, Omrani MD. Lnc-HNF1A-AS1 and its target gene ATG5 is dysregulated in HLA-DRB1*15:01-negative female patients with multiple sclerosis. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Shen L, Li N, Zhou Q, Li Z, Shen L. Development and Validation of an Autophagy-Related LncRNA Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Oncol 2021; 11:743611. [PMID: 34660307 PMCID: PMC8517509 DOI: 10.3389/fonc.2021.743611] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/08/2021] [Indexed: 01/23/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the greatest public challenges because of delayed diagnosis and poor prognosis. In this study, we established an autophagy-associated long non-coding (Lnc)RNA prognostic signature to assess the prognosis of HNSCC patients. The LncRNA expression profiles and clinical information of 499 HNSCC samples were available in The Cancer Genome Atlas. Autophagic LncRNAs were analyzed using Pearson correlation. A co-expression network showed the interactions between autophagic genes and LncRNAs. An autophagic LncRNAs prognostic signature, consisting of MYOSLID, AL139287.1, AC068580.1, AL022328.2, AC104083.1, AL160006.1, AC116914.2, LINC00958, and AL450992.2, was developed through uni- and multivariate Cox regressions. High- and low-risk groups were classified based on the median risk scores. The high-risk group had significantly worse overall survival according to Kaplan–Meier curve analysis. Multivariate Cox regression demonstrated that risk scores were a significant independent prognostic factor (hazard ratio = 1.739, 95% confidence interval: 1.460–2.072), with an area under the curve of 0.735. Principal component analysis distinguished two categories based on the nine-LncRNA prognostic signature. In conclusion, this novel autophagic LncRNA signature is an independent prognostic factor and may suggest novel therapeutic targets for HNSCC.
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Affiliation(s)
- Lin Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Qin Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
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Peng XF, Huang SF, Chen LJ, Xu L, Ye WC. Targeting epigenetics and lncRNAs in liver disease: From mechanisms to therapeutics. Pharmacol Res 2021; 172:105846. [PMID: 34438063 DOI: 10.1016/j.phrs.2021.105846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/19/2022]
Abstract
Early onset and progression of liver diseases can be driven by aberrant transcriptional regulation. Different transcriptional regulation processes, such as RNA/DNA methylation, histone modification, and ncRNA-mediated targeting, can regulate biological processes in healthy cells, as well also under various pathological conditions, especially liver disease. Numerous studies over the past decades have demonstrated that liver disease has a strong epigenetic component. Therefore, the epigenetic basis of liver disease has challenged our knowledge of epigenetics, and epigenetics field has undergone an important transformation: from a biological phenomenon to an emerging focus of disease research. Furthermore, inhibitors of different epigenetic regulators, such as m6A-related factors, are being explored as potential candidates for preventing and treating liver diseases. In the present review, we summarize and discuss the current knowledge of five distinct but interconnected and interdependent epigenetic processes in the context of hepatic diseases: RNA methylation, DNA methylation, histone methylation, miRNAs, and lncRNAs. Finally, we discuss the potential therapeutic implications and future challenges and ongoing research in the field. Our review also provides a perspective for identifying therapeutic targets and new hepatic biomarkers of liver disease, bringing precision research and disease therapy to the modern era of epigenetics.
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Affiliation(s)
- Xiao-Fei Peng
- Department of General Surgery, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Shi-Feng Huang
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Ling-Juan Chen
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Lingqing Xu
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Wen-Chu Ye
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China.
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9
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Bi Y, Li Q, Tao W, Tang J, You G, Yu L. Ginsenoside Rg1 and ginsenoside Rh1 prevent liver injury induced by acetaminophen in mice. J Food Biochem 2021; 45:e13816. [PMID: 34155666 DOI: 10.1111/jfbc.13816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/01/2021] [Accepted: 05/23/2021] [Indexed: 12/26/2022]
Abstract
With the development of technology, drugs are being developed for different purposes. Thus, the rate of drug injury considerably increased worldwide. Liver is the largest detoxification organ in the human body, but it is also the organ most vulnerable to drug damage. Ginsenoside Rg1 has been reported to have an extensive protective effect on liver injury. However, no evident results showed whether ginsenoside Rh1 could improve the injury caused by drugs. Therefore, this paper aimed to explore the protective effect in a mouse model with liver injury. Mice administered with acetaminophen (APAP) were used as the negative group, while those administered with Rg1 (10, 20, and 30 mg/kg) and Rh1 (10, 20, and 30 mg/kg) were used as the prevention groups. Results indicated that the treatments increased the levels of GSH and SOD remarkably and decreased that of MDA. In addition, the expression levels of GOT and GPT was remarkably reduced compared with the negative group. Inflammatory agents TNF-α, IL-6, and IL-1β were also decreased by the treatments. Meanwhile, Rg1 and Rh1 not only prevented the expression of Bax but also promoted Bcl-2 levels in mice. All results suggested that ginsenoside Rg1 and ginsenoside Rh1 exerted a preventive effect on APAP-induced liver injury in mice. PRACTICAL APPLICATIONS: With the increasing number of patients suffering from drug-induced liver injury, it is urgent to find alternative natural plant drugs to treat liver injury. This paper focuses on the protective effects of Ginsenoside Rg1 and ginsenoside Rh1 on acetaminophen (APAP) induced liver injury. From the previous studies, we found that there is no sufficient evidence to show that ginsenoside Rh1 has protective effect on liver injury. In this paper, the detection of oxidative stress indicators, liver histopathological analysis and immunoprotein analysis show that both ginsenoside Rg1 and ginsenoside Rh1 have preventive effect on liver injury caused by APAP, which provides a reference for the follow-up experimental research.
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Affiliation(s)
- Yunfeng Bi
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
| | - Qiuyang Li
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
| | - Weiming Tao
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
| | - Jinxin Tang
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
| | - Gaofei You
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
| | - Lei Yu
- College of Food science and Engineering, Jilin Agricultural University, Changchun, China
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Ganguly N, Chakrabarti S. Role of long non‑coding RNAs and related epigenetic mechanisms in liver fibrosis (Review). Int J Mol Med 2021; 47:23. [PMID: 33495817 PMCID: PMC7846421 DOI: 10.3892/ijmm.2021.4856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Liver fibrosis is one of the major liver pathologies affecting patients worldwide. It results from an improper tissue repair process following liver injury or inflammation. If left untreated, it ultimately leads to liver cirrhosis and liver failure. Long non‑coding RNAs (lncRNAs) have been implicated in a wide variety of diseases. They can regulate gene expression and modulate signaling. Some of the lncRNAs promote, while others inhibit liver fibrosis. Similarly, other epigenetic processes, such as methylation and acetylation regulate gene transcription and can modulate gene expression. Notably, there are several regulatory associations of lncRNAs with other epigenetic processes. A major mechanism of action of long non‑coding RNAs is to competitively bind to their target microRNAs (miRNAs or miRs), which in turn affects miRNA availability and bioactivity. In the present review, the role of lncRNAs and related epigenetic processes contributing to liver fibrosis is discussed. Finally, various potential therapeutic approaches targeting lncRNAs and related epigenetic processes, which are being considered as possible future treatment targets for liver fibrosis are identified.
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Affiliation(s)
- Niladri Ganguly
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1, Canada
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De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. Int J Mol Sci 2021; 22:ijms22020941. [PMID: 33477898 PMCID: PMC7833382 DOI: 10.3390/ijms22020941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3′ autonomous untranslated regions (3′UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury.
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Li G, Deng L, Huang N, Sun F. The Biological Roles of lncRNAs and Future Prospects in Clinical Application. Diseases 2021; 9:diseases9010008. [PMID: 33450825 PMCID: PMC7838801 DOI: 10.3390/diseases9010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Chemo and radiation therapies are the most commonly used therapies for cancer, but they can induce DNA damage, resulting in the apoptosis of host cells. DNA double-stranded breaks (DSBs) are the most lethal form of DNA damage in cells, which are constantly caused by a wide variety of genotoxic agents, both environmentally and endogenously. To maintain genomic integrity, eukaryotic organisms have developed a complex mechanism for the repair of DNA damage. Researches reported that many cellular long noncoding RNAs (lncRNAs) were involved in the response of DNA damage. The roles of lncRNAs in DNA damage response can be regulated by the dynamic modification of N6-adenosine methylation (m6A). The cellular accumulation of DNA damage can result in various diseases, including cancers. Additionally, lncRNAs also play roles in controlling the gene expression and regulation of autophagy, which are indirectly involved with individual development. The dysregulation of these functions can facilitate human tumorigenesis. In this review, we summarized the origin and overview function of lncRNAs and highlighted the roles of lncRNAs involved in the repair of DNA damage.
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Affiliation(s)
- Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
| | - Liang Deng
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
- Correspondence: ; Tel.: +86-021-6630-6909
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Four Autophagy-Related lncRNAs Predict the Prognosis of HCC through Coexpression and ceRNA Mechanism. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3801748. [PMID: 33102579 PMCID: PMC7568797 DOI: 10.1155/2020/3801748] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/25/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Abnormally expressed long noncoding RNAs (lncRNAs) have been reported to affect the occurrence and progression of hepatocellular carcinoma (HCC) by modulating the autophagy axis. However, none of studies has explored the clinical significance of these autophagy-related lncRNAs in HCC comprehensively. In this study, the RNA-seq, miRNA-seq, and clinical data of normal and HCC patients from the TCGA database and autophagy genes from the Human Autophagy Database were extracted. Subsequently, we screened out 78 differentially expressed autophagy-related lncRNAs, and four prognostic-related lncRNAs (LUCAT1, AC099850.3, ZFPM2-AS1, and AC009005.1) were eventually used to develop the prognostic model. This signature could be regarded as an independent prognostic signature for HCC patients and has the highest prediction efficiency than other clinicopathological factors for the 1-, 3-, and 5-year survival (AUC = 0.764, 0.738, and 0.717, respectively). Additionally, regardless of whether the clinical information is complete for HCC patients, the autophagy-related lncRNA model shows a good predictive power for the overall survival. Importantly, the coexpression network of 4 lncRNAs and 11 autophagy-related genes was constructed. Moreover, based on the bioinformatic analyses, our results found that LUCAT1 and ZFPM2-AS1 may affect the autophagic activity in HCC through the hsa-miR-495-3p/DLC1 and hsa-miR-515-5p/DAPK2 axis, respectively. In conclusion, we establish an effective prognostic model for HCC patients and shed new light on the autophagy-related regulatory mechanisms of the identified lncRNAs.
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LncRNA KCNQ1OT1 ameliorates the liver injury induced by acetaminophen through the regulation of miR-122-5p/CES2 axis. Mol Cell Biochem 2020; 475:107-118. [PMID: 32779042 DOI: 10.1007/s11010-020-03863-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/28/2020] [Indexed: 12/30/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to be implicated in acetaminophen (APAP)-induced liver injury (AILI). We applied this study to investigate the role and functional mechanism of KCNQ1 overlapping transcript 1 (KCNQ1OT1) in AILI. The AILI model was established by APAP treatment in mice. The liver injury was preliminarily evaluated by ALT and AST activities via the detection kits. The quantitative real-time polymerase chain reaction (qRT-PCR) was exploited for detecting the expression of KCNQ1OT1, microRNA-122-5p (miR-122-5p), and carboxylesterase 2 (CES2). Protein levels were analyzed via Western blot. 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay, and flow cytometry were separately applied to determine cell proliferation and apoptosis rate. Inflammation was assessed by enzyme-linked immunosorbent assay (ELISA). Dual-luciferase reporter assay was implemented to testify the intergenic combination. The function of KCNQ1OT1 in vivo was explored through KCNQ1OT1 knockdown in mice. APAP triggered the downregulation of KCNQ1OT1 and CES2 in mice serums. KCNQ1OT1 upregulation could relieve the AILI in HepaRG cells, which were abrogated by CES2 downregulation. KCNQ1OT1 served as a sponge of miR-122-5p and miR-122-5p directly targeted CES2. KCNQ1OT1 overexpression abated the AILI through the miR-122-5p/CES2 axis in HepaRG cells in vitro and mice in vivo. The collective results clarified that KCNQ1OT1 weakened the AILI in vitro and in vivo by the miR-122-5p/CES2 axis, providing an explicit molecular mechanism and selectable therapeutic strategy of AILI.
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He Z, Yang D, Fan X, Zhang M, Li Y, Gu X, Yang M. The Roles and Mechanisms of lncRNAs in Liver Fibrosis. Int J Mol Sci 2020; 21:ijms21041482. [PMID: 32098245 PMCID: PMC7073061 DOI: 10.3390/ijms21041482] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Many studies have revealed that circulating long noncoding RNAs (lncRNAs) regulate gene and protein expression in the process of hepatic fibrosis. Liver fibrosis is a reversible wound healing response followed by excessive extracellular matrix accumulation. In the development of liver fibrosis, some lncRNAs regulate diverse cellular processes by acting as competing endogenous RNAs (ceRNAs) and binding proteins. Previous investigations demonstrated that overexpression of lncRNAs such as H19, maternally expressed gene 3 (MEG3), growth arrest-specific transcript 5 (GAS5), Gm5091, NR_002155.1, and HIF 1alpha-antisense RNA 1 (HIF1A-AS1) can inhibit the progression of liver fibrosis. Furthermore, the upregulation of several lncRNAs [e.g., nuclear paraspeckle assembly transcript 1 (NEAT1), hox transcript antisense RNA (Hotair), and liver-enriched fibrosis-associated lncRNA1 (lnc-LFAR1)] has been reported to promote liver fibrosis. This review will focus on the functions and mechanisms of lncRNAs, the lncRNA transcriptome profile of liver fibrosis, and the main lncRNAs involved in the signalling pathways that regulate hepatic fibrosis. This review provides insight into the screening of therapeutic and diagnostic markers of liver fibrosis.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (D.Y.); (M.Y.); Tel.: +86-159-2848 7973 (M.Y.)
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China;
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Z.H.); (X.F.); (M.Z.); (Y.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (D.Y.); (M.Y.); Tel.: +86-159-2848 7973 (M.Y.)
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