201
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Yang Y, Chen S, Li P, Jing Y, Cheng B, Hu Y, Zheng Q, Wang C. PFOI stimulates the motility of T24 bladder cancer cells: Possible involvement and activation of lncRNA malat1. CHEMOSPHERE 2022; 287:131967. [PMID: 34438215 DOI: 10.1016/j.chemosphere.2021.131967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Perfluorinated iodine alkanes (PFIs) can serve as an important raw materials for the synthesis of various perfluorinated chemical products through telomerization reaction. The estrogenic effects of PFIs have been reported previously by some in vitro and in vivo screening assays. To explore the potential epigenetic toxicity of PFIs, activation of lncRNAs was screened, and the cell motility changes induced by perfluorooctyl iodide (PFOI) were analyzed in this study. High metastatic bladder cell line (T24) was used to investigate the cellular migration function affected by PFOI. PFOI exposure significantly induced the upregulation of lncRNA anril, thorlnc, hotairm1, meg3, and malat1. The migration and invasion of T24 cells were also enhanced upon PFOI exposure. The transcription level of matrix metalloenzyme genes, epidermal growth factors, cytoskeleton genes, and the upstream factors involved in cell motility pathways were examined to illustrate possible mechanisms. Additionally, the basic role of malat1 in cellular motility was investigated by lncRNA knockdown and migration assays. The knockdown of malat1 inhibited the cellular motility induced by PFOI. The levels of MMP-2/-9 genes were also down-regulated by the treatment of si-malat1. Overall, the perturbation of cytoskeleton genes (E-cadherin/N-cadherin) may account for the impact on the motility of T24 cells. Our studies indicate that perfluorinated chemicals might regulate the lncRNAs, thus promoting the metastasis of the tumor cells.
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Affiliation(s)
- Yuying Yang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China; School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430025, China
| | - Siyi Chen
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Pingdeng Li
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China; School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430025, China
| | - Yingwei Jing
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China; School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430025, China
| | - Bo Cheng
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430025, China
| | - Yeli Hu
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430025, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Jianghan University, Wuhan, 430056, China
| | - Chang Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China.
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202
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Ren J, Jiang C, Zhang H, Shi X, Ai X, Li R, Dong J, Wang J, Zhao X, Yu H. LncRNA-mediated ceRNA networks provide novel potential biomarkers for peanut drought tolerance. PHYSIOLOGIA PLANTARUM 2022; 174:e13610. [PMID: 34888889 DOI: 10.1111/ppl.13610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Drought stress has been the major constraint on peanut yield and quality, and an understanding of the function of long non-coding (lncRNAs) in the peanut drought stress response is still in its infancy. In this study, two peanut varieties with contrasting drought tolerance were used to explore the functions of lncRNAs in the peanut drought response, and the results showed that the drought-tolerant variety presented greater antioxidant enzyme activity, osmotic adjustment ability, and photosynthesis under drought conditions. There were 4329 lncRNAs identified in the two varieties, of which 535 and 663 lncRNAs were differentially expressed in NH5 and FH18, respectively. The cis targets of the differentially expressed lncRNAs were putatively involved in secondary metabolite biosynthesis and other basic metabolic processes. A total of 673 competing endogenous RNA (ceRNA) pairs were selected specifically in NH5, and the associated ceRNA network revealed six lncRNAs, MSTRG.70535.2, MSTRG.86570.2, MSTRG.86570.1, MSTRG.100618.1, MSTRG.81214.2, and MSTRG.30931.1were considered as hub nodes. They were speculated to contribute to enhancing peanut drought tolerance, such as regulating transcription and plant growth processes, thereby improving the drought stress response. In this study, lncRNAs and mRNAs interaction networks were constructed to aid a comprehensive understanding of the peanut drought stress response and form a basis for future research.
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Affiliation(s)
- Jingyao Ren
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Chunji Jiang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - He Zhang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Shi
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xin Ai
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Rengyuan Li
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Jiale Dong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Jing Wang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Xinhua Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Haiqiu Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, China
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203
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Brodnicki TC. A Role for lncRNAs in Regulating Inflammatory and Autoimmune Responses Underlying Type 1 Diabetes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:97-118. [DOI: 10.1007/978-3-030-92034-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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204
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Zhang S, Qin J, Zhao Y, Wang J, Tian Z. Identification of molecular patterns and diagnostic biomarkers in juvenile idiopathic arthritis based on the gene expression of m 6A regulators. Front Pediatr 2022; 10:930119. [PMID: 36160781 PMCID: PMC9497457 DOI: 10.3389/fped.2022.930119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
The role of N 6-methyladenosine modification in immunity is increasingly being appreciated. However, the landscape of m6A regulators in juvenile idiopathic arthritis (JIA) is poorly understood. Thus, this study explored the impact of m6A modification and related lncRNAs in JIA immune microenvironment. Fourteen m6A regulators and eight lncRNAs were identified as potential diagnostic biomarkers for JIA. Two diagnostic models for JIA were also constructed. The putative molecular regulatory mechanism of FTO-mediated m6A modification in JIA was hypothesized. Three distinct m6A patterns mediated by 26 m6A regulators and three diverse lncRNA clusters mediated by 405 lncRNAs were thoroughly investigated. They exhibited dramatically diverse immune microenvironments and expression of HLA genes. The identification of two separate subtypes of enthesitis-related arthritis implies that our work may aid in the establishment of a more precise categorization system for JIA. m6A modification-related genes were obtained, and their underlying biological functions were explored. The m6Ascore system developed for individual JIA patients may be utilized to evaluate the immunological state or molecular pattern, thereby offering therapy recommendations. In short, through the investigation of the m6A regulators in JIA, the current work may contribute to our knowledge of the pathophysiology of JIA.
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Affiliation(s)
- Shibo Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Qin
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuechao Zhao
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jian Wang
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhiliang Tian
- Department of Pediatrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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205
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Xu S, Dong H, Zhao Y, Feng W. Differential Expression of Long Non-Coding RNAs and Their Role in Rodent Neuropathic Pain Models. J Pain Res 2021; 14:3935-3950. [PMID: 35002313 PMCID: PMC8722684 DOI: 10.2147/jpr.s344339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Neuropathic pain, which is accompanied by an unpleasant sensation, affects the patient's quality of life severely. Considering the complexity of the neuropathic pain, there are huge unmet medical needs for it while current effective therapeutics remain far from satisfactory. Accordingly, exploration of mechanisms of neuropathic pain could provide new therapeutic insights. While numerous researches have pointed out the contribution of sensory neuron-immune cell interactions, other mechanisms of action, such as long non-coding RNAs (lncRNAs), also could contribute to the neuropathic pain observed in vivo. LncRNAs have more than 200 nucleotides and were originally considered as transcriptional byproducts. However, recent studies have suggested that lncRNAs played a significant role in gene regulation and disease pathogenesis. A substantial number of long non-coding RNAs were expressed differentially in neuropathic pain models. Besides, therapies targeting specific lncRNAs can significantly ameliorate the development of neuropathic pain, which reveals the contribution of lncRNAs in the generation and maintenance of neuropathic pain and provides a new therapeutic strategy. The primary purpose of this review is to introduce recent studies of lncRNAs on different neuropathic pain models.
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Affiliation(s)
- Songchao Xu
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People’s Republic of China
| | - He Dong
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People’s Republic of China
| | - Yang Zhao
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People’s Republic of China
| | - Wei Feng
- Department of Anesthesiology, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, People’s Republic of China
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206
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Lin Y, Pan X, Chen Z, Lin S, Shen Z, Chen S. Prognostic value and immune infiltration of novel signatures in colon cancer microenvironment. Cancer Cell Int 2021; 21:679. [PMID: 34922547 PMCID: PMC8684099 DOI: 10.1186/s12935-021-02342-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Growing evidence has shown that the prognosis for colon cancer depends on changes in microenvironment. The purpose of this study was to elucidate the prognostic value of long noncoding RNAs (lncRNAs) related to immune microenvironment (IM) in colon cancer. Methods Single sample gene set enrichment analysis (ssGSEA) was used to identify the subtypes of colon cancer based on the immune genomes of 29 immune signatures. Cox regression analysis identified a lncRNA signatures associated with immune infiltration. The Tumor Immune Estimation Resource database was used to analyze immune cell content. Results Colon cancer samples were divided into three subtypes by unsupervised cluster analysis. Cox regression analysis identified an immune infiltration-related 5-lncRNA signature. This signature combined with clinical factors can effectively improve the predictive ability for the overall survival (OS) of colon cancer. At the same time, we found that the expression of H19 affects the content of B cells and macrophages in the microenvironment of colon cancer and affects the prognosis of colon cancer. Finally, we constructed the H19 regulatory network and further analyzed the possible mechanisms. We found that knocking down the expression of H19 can significantly inhibit the expression of CCND1 and VEGFA. At the same time, the immunohistochemical assay found that the expression of CCND1 and VEGFA protein was significantly positively correlated with the infiltration of M2 type macrophages. Conclusion The findings may help to formulate clinical strategies and understand the underlying mechanisms of H19 regulation. H19 may be a biomarker for targeted treatment of colon cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02342-8.
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Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China
| | - Xiaoxian Pan
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zhihua Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Suyong Lin
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China.
| | - Shaoqin Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China.
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207
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Anti-Cancer Role and Therapeutic Potential of Extracellular Vesicles. Cancers (Basel) 2021; 13:cancers13246303. [PMID: 34944923 PMCID: PMC8699603 DOI: 10.3390/cancers13246303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 02/07/2023] Open
Abstract
Cell-cell communication is an important mechanism in biological processes. Extracellular vesicles (EVs), also referred to as exosomes, microvesicles, and prostasomes, are microvesicles secreted by a variety of cells. EVs are nanometer-scale vesicles composed of a lipid bilayer and contain biological functional molecules, such as microRNAs (miRNAs), mRNAs, and proteins. In this review, "EVs" is used as a comprehensive term for vesicles that are secreted from cells. EV research has been developing over the last four decades. Many studies have suggested that EVs play a crucial role in cell-cell communication. Importantly, EVs contribute to cancer malignancy mechanisms such as carcinogenesis, proliferation, angiogenesis, metastasis, and escape from the immune system. EVs derived from cancer cells and their microenvironments are diverse, change in nature depending on the condition. As EVs are thought to be secreted into body fluids, they have the potential to serve as diagnostic markers for liquid biopsy. In addition, cells can encapsulate functional molecules in EVs. Hence, the characteristics of EVs make them suitable for use in drug delivery systems and novel cancer treatments. In this review, the potential of EVs as anti-cancer therapeutics is discussed.
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208
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Khashkhashi Moghadam S, Bakhshinejad B, Khalafizadeh A, Mahmud Hussen B, Babashah S. Non-coding RNA-associated competitive endogenous RNA regulatory networks: Novel diagnostic and therapeutic opportunities for hepatocellular carcinoma. J Cell Mol Med 2021; 26:287-305. [PMID: 34907642 PMCID: PMC8743668 DOI: 10.1111/jcmm.17126] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC), as the most prevalent liver malignancy, is annually diagnosed in more than half a million people worldwide. HCC is strongly associated with hepatitis B and C viral infections as well as alcohol abuse. Obesity and nonalcoholic fatty liver disease (NAFLD) also significantly enhance the risk of liver cancer. Despite recent improvements in therapeutic approaches, patients diagnosed in advanced stages show poor prognosis. Accumulating evidence provides support for the regulatory role of non-coding RNAs (ncRNAs) in cancer. There are a variety of reports indicating the regulatory role of microRNAs (miRNAs) in different stages of HCC. Long non-coding RNAs (LncRNAs) exert their effects by sponging miRNAs and controlling the expression of miRNA-targeted genes. Circular RNAs (circRNAs) perform their biological functions by acting as transcriptional regulators, miRNA sponges and protein templates. Diverse studies have illustrated that dysregulation of competing endogenous RNA networks (ceRNETs) is remarkably correlated with HCC-causing diseases such as chronic viral infections, nonalcoholic steatohepatitis and liver fibrosis/cirrhosis. The aim of the current article was to provide an overview of the role and molecular mechanisms underlying the function of ceRNETs that modulate the characteristics of HCC such as uncontrolled cell proliferation, resistance to cell death, metabolic reprogramming, immune escape, angiogenesis and metastasis. The current knowledge highlights the potential of these regulatory RNA molecules as novel diagnostic biomarkers and therapeutic targets in HCC.
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Affiliation(s)
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Sadegh Babashah
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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209
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Liu D, Sun W, Zhang D, Yu Z, Qin W, Liu Y, Zhang K, Yin J. Long noncoding RNA GSEC promotes neutrophil inflammatory activation by supporting PFKFB3-involved glycolytic metabolism in sepsis. Cell Death Dis 2021; 12:1157. [PMID: 34907156 PMCID: PMC8671582 DOI: 10.1038/s41419-021-04428-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/03/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
Metabolic reprogramming is a hallmark of neutrophil activation in sepsis. LncRNAs play important roles in manipulating cell metabolism; however, their specific involvement in neutrophil activation in sepsis remains unclear. Here we found that 11 lncRNAs and 105 mRNAs were differentially expressed in three transcriptome datasets (GSE13904, GSE28750, and GSE64457) of gene expression in blood leukocytes and neutrophils of septic patients and healthy volunteers. After Gene Ontology biological process analysis and lncRNA-mRNA pathway network construction, we noticed that GSEC lncRNA and PFKFB3 were co-expressed and associated with enhanced glycolytic metabolism. Our clinical observations confirmed the expression patterns of GSEC lncRNA and PFKFB3 genes in neutrophils in septic patients. Performing in vitro experiments, we found that the expression of GSEC lncRNA and PFKFB3 was increased when neutrophils were treated with inflammatory stimuli. Knockdown and overexpression experiments showed that GSEC lncRNA was essential for mediating PFKFB3 mRNA expression and stability in neutrophil-like dHL-60 cells. In addition, we found that GSEC lncRNA-induced PFKFB3 expression was essential for mediating dHL-60 cell inflammatory cytokine expression. Performing mechanistic experiments, we found that glycolytic metabolism with PFKFB3 involvement supported inflammatory cytokine expression. In summary, our study uncovers a mechanism by which GSEC lncRNA promotes neutrophil inflammatory activation in sepsis by supporting glycolytic metabolism with PFKFB3.
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Affiliation(s)
- Dadong Liu
- Department of Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wen Sun
- Department of Critical Care Medicine, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, China
| | - Danying Zhang
- Department of Laboratory Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Zongying Yu
- Department of Electrocardiograph, The No. 4 Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Weiting Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yishu Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Kai Zhang
- Department of Otorhinolaryngology and Head and Neck Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Jiangtao Yin
- Department of Critical Care Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
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210
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Ma F, Li CC, Zhang CY. Nucleic acid amplification-integrated single-molecule fluorescence imaging for in vitro and in vivo biosensing. Chem Commun (Camb) 2021; 57:13415-13428. [PMID: 34796887 DOI: 10.1039/d1cc04799j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule fluorescence imaging is among the most advanced analytical technologies and has been widely adopted for biosensing due to its distinct advantages of simplicity, rapidity, high sensitivity, low sample consumption, and visualization capability. Recently, a variety of nucleic acid amplification approaches have been developed to provide a straightforward and highly efficient way for amplifying low abundance target signals. The integration of single-molecule fluorescence imaging with nucleic acid amplification has greatly facilitated the construction of various fluorescent biosensors for in vitro and in vivo detection of DNAs, RNAs, enzymes, and live cells with high sensitivity and good selectivity. Herein, we review the advances in the development of fluorescent biosensors by integrating single-molecule fluorescence imaging with nucleic acid amplification based on enzyme (e.g., DNA polymerase, RNA polymerase, exonuclease, and endonuclease)-assisted and enzyme-free (e.g., catalytic hairpin assembly, entropy-driven DNA amplification, ligation chain reaction, and hybridization chain reaction) strategies, and summarize the principles, features, and in vitro and in vivo applications of the emerging biosensors. Moreover, we discuss the remaining challenges and future directions in this area. This review may inspire the development of new signal-amplified single-molecule biosensors and promote their practical applications in fundamental and clinical research.
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Affiliation(s)
- Fei Ma
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China. .,School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chen-Chen Li
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China. .,Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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211
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Zheng Y, Bian Y, Wu R, Chen W, Fu L, Li P, Wang Y, Yang X, Zhao S, Shi Y. High-Throughput Sequencing Profiles About lncRNAs and mRNAs of Ovarian Granulosa Cells in Polycystic Ovary Syndrome. Front Med (Lausanne) 2021; 8:741803. [PMID: 34881258 PMCID: PMC8645594 DOI: 10.3389/fmed.2021.741803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/26/2021] [Indexed: 02/01/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders in women of reproductive age, which is characterized by ovulatory dysfunction, clinical and/or biochemical androgen excess, polycystic ovaries on ultrasound and genetic heterogeneity. It was well-accepted that many lncRNAs and mRNAs were associated with PCOS, however, remain unclear. Therefore, the purpose of our study was to examine different expression profiles of lncRNAs and mRNAs in ovarian granulosa cells (GCs) in PCOS and Controls, and identify the correlation between lncRNAs, mRNAs and clinical parameters. Sixty five PCOS patients and 65 Controls were enrolled in this study and adopted standard long agonist protocols or GnRH antagonist protocols. Then 6 GCs samples in each group were subjected to high-thoughput sequencing and the remaining samples were used for the further verification by quantitative real-time PCR (qRT-PCR). Gene Oncology (GO), Kyoto Encyclopedia Genes and Genomes (KEGG) enrichment analysis were performed. We predicted the relationship between lncRNAs and mRNAs by Cytoscape software. According to the expression level of lncRNAs, mRNAs and the clinical parameters, we also explored their relationship and evaluate their predictive values for embryos quality and PCOS. We identified 1,049 differential expressed lncRNAs and 3,246 mRNAs (fold-change ≥2, p-value < 0.05). Seven lncRNAs (NONHSAT101926.2, NONHSAT136825.2, NONHSAT227177.1, NONHSAT010538.2, NONHSAT191377.1, NONHSAT230904.1, ENST00000607307) and 3 mRNAs (EREG, ENTPD6, YAP1) were validated consistent with sequence profile. Seven lncRNAs were related to hormone level and follicle counts, 3 mRNAs had connections with lipid metabolism. The area under curve (AUC) of 7 lncRNAs were valuable in distinguishing patients with PCOS from Controls. The AUC of NONHSAT230904.1 and NONHSAT227177.1 were 0.6807 and 0.6410, respectively, for distinguishing whether the rate of high-quality embryos exceeds 50%. Our study showed that the GCs lncRNAs and mRNAs were involved in the occurrence and development of PCOS, which contribute to clarify the pathogenesis mechanism of PCOS.
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Affiliation(s)
- Yanjun Zheng
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Yuehong Bian
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Richao Wu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Wei Chen
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Linlin Fu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Ping Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Ying Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Xiao Yang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Shigang Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Yuhua Shi
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
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ETV5-mediated upregulation of lncRNA CTBP1-DT as a ceRNA facilitates HGSOC progression by regulating miR-188-5p/MAP3K3 axis. Cell Death Dis 2021; 12:1146. [PMID: 34887384 PMCID: PMC8660778 DOI: 10.1038/s41419-021-04256-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is a common and lethal cancer of the female reproductive system. Long non-coding RNAs (lncRNAs) are aberrantly expressed in various cancers and play crucial roles in tumour progression. However, their function and molecular mechanism in HGSOC remain largely unknown. Based on public databases and bioinformatics analyses, the overexpression of lncRNA CTBP1-DT in HGSOC tissues was detected and validated in a cohort of HGSOC tissues. High expression of lncRNA CTBP1-DT was associated with poor prognosis and was an independent risk factor for survival. Overexpression of lncRNA CTBP1-DT promoted malignant biological behaviour of HGSOC cells, whereas its depletion induced growth arrest of HGSOC cells by vitro and in vivo assays. Mechanistically, lncRNA CTBP1-DT could competitively bind to miR-188-5p to protect MAP3K3 from degradation. Moreover, our results revealed that ETV5 could specifically interact with the promoter of lncRNA CTBP1-DT and activate its transcription. Collectively, these results reveal a novel ETV5/lncRNA CTBP1-DT/miR-188-5p/MAP3K3 pathway for HGSOC progression and suggest that lncRNA CTBP1-DT might be a potential biomarker and therapeutic target for HGSOC. ![]()
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Hamdy SM, Sayed ON, Ibrahim HA, Ayoub SE. Evaluation of serum long non-coding RNA (Gas5) level and keratinocyte transglutaminase 1 (TGM1) activity as novel biomarkers in psoriasis patients. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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214
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Selem NA, Youness RA, Gad MZ. What is beyond LncRNAs in breast cancer: A special focus on colon cancer-associated Transcript-1 (CCAT-1). Noncoding RNA Res 2021; 6:174-186. [PMID: 34938928 PMCID: PMC8666458 DOI: 10.1016/j.ncrna.2021.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) play a vital role in the process of malignant transformation. In breast cancer (BC), lncRNAs field is currently under intensive investigations. Yet, the role of lncRNAs as promising diagnostic and/or prognostic biomarkers and as therapeutic target/tool among BC patients still needs a special focus from the biomedical scientists. In BC, triple negative breast cancer patients (TNBC) are the unlucky group as they are always represented with the worst prognosis and the highest mortality rates. For that reason, a special focus on TNBC and associated lncRNAs was addressed in this review. Colon cancer-associated transcript 1 (CCAT-1) is a newly discovered oncogenic lncRNA that has been emerged as a vital biomarker for diagnosis, prognosis and therapeutic interventions in multiple malignancies and showed differential expression among TNBC patients. In this review, the authors shed the light onto the general role of lncRNAs in BC and the specific functional activities, molecular mechanisms, competing endogenous ncRNA role of CCAT-1 in TNBC.
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Affiliation(s)
- Noha A. Selem
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Rana A. Youness
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, New Administrative Capital, 11586, Cairo, Egypt
| | - Mohamed Z. Gad
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
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215
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Li Y, Yu X, Zhang Y, Wang X, Zhao L, Liu D, Zhao G, Gao X, Fu J, Zang A, Jia Y. Identification of a novel prognosis-associated ceRNA network in lung adenocarcinoma via bioinformatics analysis. Biomed Eng Online 2021; 20:117. [PMID: 34819106 PMCID: PMC8611860 DOI: 10.1186/s12938-021-00952-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of nonsmall-cell lung cancer (NSCLC) and has a high incidence rate and mortality. The survival of LUAD patients has increased with the development of targeted therapeutics, but the prognosis of these patients is still poor. Long noncoding RNAs (lncRNAs) play an important role in the occurrence and development of LUAD. The purpose of this study was to identify novel abnormally regulated lncRNA–microRNA (miRNA)–messenger RNA (mRNA) competing endogenous RNA (ceRNA) networks that may suggest new therapeutic targets for LUAD or relate to LUAD prognosis. Methods We used the SBC human ceRNA array V1.0 to screen for differentially expressed (DE) lncRNAs and mRNAs in four paired LUAD samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the DE lncRNAs and mRNAs. R bioinformatics packages, The Cancer Genome Atlas (TCGA) LUAD database, and Kaplan–Meier (KM) survival analysis tools were used to validate the microarray data and construct the lncRNA–miRNA–mRNA ceRNA regulatory network. Then, quantitative real-time PCR (qRT-PCR) was used to validate the DE lncRNAs in 7 LUAD cell lines. Results A total of 2819 DE lncRNAs and 2396 DE mRNAs (P < 0.05 and fold change ≥ 2 or ≤ 0.5) were identified in four paired LUAD tissue samples. In total, 255 of the DE lncRNAs were also identified in TCGA. The GO and KEGG analysis results suggested that the DE genes were most enriched in angiogenesis and cell proliferation, and were closely related to human cancers. Moreover, the differential expression of ENST00000609697, ENST00000602992, and NR_024321 was consistent with the microarray data, as determined by qRT-PCR validation in 7 LUAD cell lines; however, only ENST00000609697 was associated with the overall survival of LUAD patients (log-rank P = 0.029). Finally, through analysis of ENST00000609697 target genes, we identified the ENST00000609697–hsa-miR-6791-5p–RASL12 ceRNA network, which may play a tumor-suppressive role in LUAD. Conclusion ENST00000609697 was abnormally expressed in LUAD. Furthermore, downregulation of ENST00000609697 and its target gene RASL12 was associated with poor prognosis in LUAD. The ENST00000609697–hsa-miR-6791-5p–RASL12 axis may play a tumor-suppressive role. These results suggest new potential prognostic and therapeutic biomarkers for LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00952-x.
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Affiliation(s)
- Yumiao Li
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, 071000, Hebei, People's Republic of China
| | - Xiaoxue Yu
- College of Clinical Medicine, Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, 071000, Hebei, People's Republic of China
| | - Yuhao Zhang
- College of Clinical Medicine, Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, 071000, Hebei, People's Republic of China
| | - Xiaofang Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, 071000, Hebei, People's Republic of China
| | - Linshan Zhao
- College of Clinical Medicine, Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, 071000, Hebei, People's Republic of China
| | - Dan Liu
- College of Clinical Medicine, Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, 071000, Hebei, People's Republic of China
| | - Guofa Zhao
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, 071000, Hebei, People's Republic of China
| | - Xiangpeng Gao
- College of Clinical Medicine, Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Baoding, 071000, Hebei, People's Republic of China
| | - Jiejun Fu
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Guangxi Medical University, Nanning, 530021, Guangxi, People's Republic of China
| | - Aimin Zang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, 071000, Hebei, People's Republic of China
| | - Youchao Jia
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, 071000, Hebei, People's Republic of China.
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Zhou X, Zeng B, Li Y, Wang H, Zhang X. LINC02532 Contributes to Radiosensitivity in Clear Cell Renal Cell Carcinoma through the miR-654-5p/YY1 Axis. Molecules 2021; 26:molecules26227040. [PMID: 34834139 PMCID: PMC8625588 DOI: 10.3390/molecules26227040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Studies have shown that long non-coding RNAs (lncRNAs) play essential roles in tumor progression and can affect the response to radiotherapy, including in clear cell renal cell carcinoma (ccRCC). LINC02532 has been found to be upregulated in ccRCC. However, not much is known about this lncRNA. Hence, this study aimed to investigate the role of LINC02532 in ccRCC, especially in terms of radioresistance. Methods: Quantitative real-time PCR was used to detect the expression of LINC02532, miR-654-5p, and YY1 in ccRCC cells. Protein levels of YY1, cleaved PARP, and cleaved-Caspase-3 were detected by Western blotting. Cell survival fractions, viability, and apoptosis were determined by clonogenic survival assays, CCK-8 assays, and flow cytometry, respectively. The interplay among LINC02532, miR-654-5p, and YY1 was detected by chromatin immunoprecipitation and dual-luciferase reporter assays. In addition, in vivo xenograft models were established to investigate the effect of LINC02532 on ccRCC radioresistance in 10 nude mice. Results: LINC02532 was highly expressed in ccRCC cells and was upregulated in the cells after irradiation. Moreover, LINC02532 knockdown enhanced cell radiosensitivity both in vitro and in vivo. Furthermore, YY1 activated LINC02532 in ccRCC cells, and LINC02532 acted as a competing endogenous RNA that sponged miR-654-5p to regulate YY1 expression. Rescue experiments indicated that miR-654-5p overexpression or YY1 inhibition recovered ccRCC cell functions that had been previously impaired by LINC02532 overexpression. Conclusions: Our results revealed a positive feedback loop of LINC02532/miR-654-5p/YY1 in regulating the radiosensitivity of ccRCC, suggesting that LINC02532 might be a potential target for ccRCC radiotherapy. This study could serve as a foundation for further research on the role of LINC02532 in ccRCC and other cancers.
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Affiliation(s)
- Xiaoguang Zhou
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China; (X.Z.); (B.Z.); (Y.L.); (H.W.)
| | - Bowen Zeng
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China; (X.Z.); (B.Z.); (Y.L.); (H.W.)
- Department of Urology, Affiliated Hospital of Sergeant School of Army Medical University, Shijiazhuang 050044, China
| | - Yansheng Li
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China; (X.Z.); (B.Z.); (Y.L.); (H.W.)
| | - Haozhou Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China; (X.Z.); (B.Z.); (Y.L.); (H.W.)
| | - Xiaodong Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China; (X.Z.); (B.Z.); (Y.L.); (H.W.)
- Correspondence: ; Tel.: +86-010-85231247
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217
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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218
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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219
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Li Q, Sun H, Luo D, Gan L, Mo S, Dai W, Liang L, Yang Y, Xu M, Li J, Zheng P, Li X, Li Y, Wang Z. Lnc-RP11-536 K7.3/SOX2/HIF-1α signaling axis regulates oxaliplatin resistance in patient-derived colorectal cancer organoids. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:348. [PMID: 34740372 PMCID: PMC8570024 DOI: 10.1186/s13046-021-02143-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/14/2021] [Indexed: 02/08/2023]
Abstract
Background Resistance to oxaliplatin is a major obstacle for the management of locally advanced and metastatic colon cancer (CC). Although long noncoding RNAs (lncRNAs) play key roles in CC, the relationships between lncRNAs and resistance to oxaliplatin have been poorly understood yet. Methods Chemo-sensitive and chemo-resistant organoids were established from colon cancer tissues of the oxaliplatin-sensitive or -resistant patients. Analysis of the patient cohort indicated that lnc-RP11-536 K7.3 had a potential oncogenic role in CC. Further, a series of functional in vitro and in vivo experiments were conducted to assess the effects of lnc-RP11-536 K7.3 on CC proliferation, glycolysis, and angiogenesis. RNA pull-down assay, luciferase reporter and fluorescent in situ hybridization assays were used to confirm the interactions between lnc-RP11-536 K7.3, SOX2 and their downstream target HIF-1α. Results In this study, we identified a novel lncRNA, lnc-RP11-536 K7.3, was associated with resistance to oxaliplatin and predicted a poor survival. Knockout of lnc-RP11-536 K7.3 inhibited the proliferation, glycolysis, and angiogenesis, whereas enhanced chemosensitivity in chemo-resistant organoids and CC cells both in vitro and in vivo. Furthermore, we found that lnc-RP11-536 K7.3 recruited SOX2 to transcriptionally activate USP7 mRNA expression. The accumulative USP7 resulted in deubiquitylation and stabilization of HIF-1α, thereby facilitating resistance to oxaliplatin. Conclusion In conclusion, our findings indicated that lnc-RP11-536 K7.3 could promote proliferation, glycolysis, angiogenesis, and chemo-resistance in CC by SOX2/USP7/HIF-1α signaling axis. This revealed a new insight into how lncRNA could regulate chemosensitivity and provide a potential therapeutic target for reversing resistance to oxaliplatin in the management of CC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02143-x.
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Affiliation(s)
- Qingguo Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Huizhen Sun
- Clinical Medicine Transformation Center and Office of Academic Research, Shanghai Hospital of Traditional Chinese Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.,Department of Obstetrics and Gynecology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - Dakui Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lu Gan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
| | - Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lei Liang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yufei Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Midie Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Pathology and Biobank, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jing Li
- Department of CyberKnife Center, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Peiyong Zheng
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, 518055, China.
| | - Ziliang Wang
- Clinical Medicine Transformation Center and Office of Academic Research, Shanghai Hospital of Traditional Chinese Medicine Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China.
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Feng X, Gong J, Li Q, Xing C, Pan J, Zou R, Zheng L, Chen F. Identification and functional annotation of differentially expressed long noncoding RNAs in retinoblastoma. Exp Ther Med 2021; 22:1447. [PMID: 34721689 DOI: 10.3892/etm.2021.10882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma (RB), the most common intraocular malignancy, typically occurs in pediatric patients under the age of 6 years. The present study aimed to explore the long noncoding RNA (lncRNA) expression profile in RB and identify novel lncRNA biomarkers to facilitate the investigation of molecular mechanisms of RB and improve clinical therapy. Raw microarray data for the comparison of gene expression between three RB and three adjacent normal tissue samples were downloaded from Gene Expression Omnibus (dataset no. GSE111168). After identification of differentially expressed lncRNAs (DELs) and differentially expressed mRNAs (DEMs) in RB, functional enrichment analyses and a DEL-DEM weighted correlation network analysis were performed. A total of 3,915 DELs (1,774 upregulated and 2,141 downregulated) and 3,715 DEMs (1,492 upregulated and 2,223 downregulated) were identified in RB. The DEL-targeted DEMs were highly enriched by genes involved in hexose transport, muscle tissue morphogenesis, the stereocilium membrane, endothelin B receptor binding and γ-filamin/ABP-L, α-actinin and telethonin binding protein of the Z-disc binding. Furthermore, associations of the DELs and DEMs with several pathways were determined, including PI3K/AKT, Hippo and cancer signaling, as well as extracellular matrix-receptor interaction pathways. Coexpression network analysis revealed that the top three DELs, lnc-DAZ1-161, lnc-HDAC7-21 and lnc-OR52A1-55, formed coexpression modules with 181, 156 and 210 DEMs, respectively. In addition, the top three DEMs, namely EIF1AY, GSTM1 and NLRP11, formed coexpression modules with 33, 50 and 41 DELs, respectively. Validation using reverse transcription-quantitative PCR indicated that the expression of representative lncRNAs (lnc-DAZ1-161 and lnc-HDAC7-21) in RB cells in vitro was consistent with that in RB tissues in the database, while the expression of lnc-OR52A1-55 was not consistent with the database. These results suggested that the aberrant lncRNA expression profile in RB is related to the differential regulation of numerous physiological and pathological processes. The lncRNA and mRNA profiles in RB identified may provide novel targets for the investigation of its molecular mechanisms and thus lead to improvements in clinical therapy for RB.
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Affiliation(s)
- Xiaofen Feng
- Pediatric Fundus Department, School of Optometry & Ophthalmology, Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Jian Gong
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Qian Li
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Chao Xing
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Jiandong Pan
- Pediatric Fundus Department, School of Optometry & Ophthalmology, Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ruitao Zou
- Pediatric Fundus Department, School of Optometry & Ophthalmology, Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Liya Zheng
- Pediatric Fundus Department, School of Optometry & Ophthalmology, Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Feng Chen
- Pediatric Fundus Department, School of Optometry & Ophthalmology, Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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Jiang Y, Peng J, Song J, He J, Jiang M, Wang J, Ma L, Wang Y, Lin M, Wu H, Zhang Z, Gao D, Zhao Y. Loss of Hilnc prevents diet-induced hepatic steatosis through binding of IGF2BP2. Nat Metab 2021; 3:1569-1584. [PMID: 34750570 PMCID: PMC9235319 DOI: 10.1038/s42255-021-00488-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022]
Abstract
The Hedgehog (Hh) signalling pathway plays a critical role in regulating liver lipid metabolism and related diseases. However, the underlying mechanisms are poorly understood. Here, we show that the Hh signalling pathway induces a previously undefined long non-coding RNA (Hilnc, Hedgehog signalling-induced long non-coding RNA), which controls hepatic lipid metabolism. Mutation of the Gli-binding sites in the Hilnc promoter region (HilncBM/BM) decreases the expression of Hilnc in vitro and in vivo. HilncBM/BM and Hilnc-knockout mice are resistant to diet-induced obesity and hepatic steatosis through attenuation of the peroxisome proliferator-activated receptor signalling pathway, as Hilnc directly interacts with IGF2BP2 to enhance Pparγ mRNA stability. Furthermore, we identify a potential functional human homologue of Hilnc, h-Hilnc, which has a similar function in regulating cellular lipid metabolism. These findings uncover a critical role of the Hh-Hilnc-IGF2BP2 signalling axis in lipid metabolism and suggest a potential therapeutic target for the treatment of diet-induced hepatic steatosis.
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Affiliation(s)
- Yiao Jiang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiayin Peng
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiawen Song
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan He
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Man Jiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jia Wang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liya Ma
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuang Wang
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Moubin Lin
- Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Hailong Wu
- Shanghai Key Laboratory for Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine and Health Science, Shanghai, P. R. China
| | - Zhao Zhang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dong Gao
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shangha, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- The State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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Wang PS, Wang Z, Yang C. Dysregulations of long non-coding RNAs - The emerging "lnc" in environmental carcinogenesis. Semin Cancer Biol 2021; 76:163-172. [PMID: 33823237 PMCID: PMC8487435 DOI: 10.1016/j.semcancer.2021.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 02/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are more than 200 nucleotides in length and usually lack protein-coding capacity. LncRNAs play important roles in regulating gene expression as well as many aspects of normal physiological processes. Dysregulations of lncRNA expressions and functions are considered to be critically involved in the development and progression of many diseases especially cancer. The lncRNA research in the field of cancer biology over the past decade reveals that a large number of lncRNAs are dysregulated in various types of cancer and that dysregulated lncRNAs may play important roles in cancer initiation, metastasis and therapeutic responses. Metal carcinogens and other common environmental carcinogens such as polycyclic aromatic hydrocarbons, fine particular matters, cigarette smoke, ultraviolet and ionizing radiation are important cancer etiology factors. However, the mechanisms of how metal carcinogens and other common environmental carcinogen exposures initiate cancer and promote cancer progression remain largely unknown. Accumulating evidence show that exposure to metal carcinogens and other common environmental carcinogens dysregulate lncRNA expression in various model systems, which may offer novel mechanistic insights for environmental carcinogenesis. This review will first provide a brief introduction about lncRNA biology and the mechanisms of lncRNA functions, followed by summarizing and discussing recent studies about lncRNA dysregulation by metal carcinogen and other common environment carcinogen exposures and the potential roles of dysregulated lncRNAs in environmental carcinogenesis. A perspective for future studies in this emerging and important field is also presented.
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Affiliation(s)
- Po-Shun Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA
| | - Zhishan Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA
| | - Chengfeng Yang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA.
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Cai W, Yin L, Jiang H, Weizmann Y, Wang X. Intelligent Bio-Responsive Fluorescent Au-shRNA Complexes for Regulated Autophagy and Effective Cancer Bioimaging and Therapeutics. BIOSENSORS 2021; 11:bios11110425. [PMID: 34821640 PMCID: PMC8615530 DOI: 10.3390/bios11110425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 05/05/2023]
Abstract
The long non-coding RNA (lncRNA) MALAT1 acts as an oncogene. RNA interference (RNAi) is an effective method to control the expression of specific genes and can be used for the treatment of tumors, but an effective and safe carrier system is a significant obstacle to gene therapy. Herein, we explored the possibility of constructing an in situ bio-responsive self-assembled fluorescent gold-short hairpin RNA nanocomplex (Au-shRNA NCs) delivery system by co-incubating gold and MALAT1-shRNA for precise hepatocellular carcinoma (HCC) imaging and treatment. Due to the characteristics of the cancer microenvironment, Au-shRNA NCs self-assembled in HCC cells (HepG2) but did not occur in control cells (L02) under the same conditions. The in situ bio-responsive self-assembled Au-shRNA NCs delivery system can realize cancer cell bioimaging and promote cell uptake and endosomal escape mechanism, thereby realizing effective transfection. They effectively silenced target gene MALAT1, and with the downregulation of MALAT1, we found that several molecules involved in autophagic flux were also regulated. In vitro and tumor-bearing mouse model experiments demonstrated that the as-prepared fluorescent Au-shRNA NCs can readily realize tumor bioimaging and effectively silence the target gene MALAT1, and those autophagy-related pathway molecules were significantly downregulated, thereby exerting a tumor suppressor efficiency. This raises the possibility of realizing accurate multi-scale bio-imaging from the molecular-level with targeted gene-recognition to cancer cell imaging as well as in vivo tumor tissue imaging for the simultaneous precise cancer therapy.
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Affiliation(s)
- Weijuan Cai
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (W.C.); (H.J.)
| | - Liang Yin
- Department of Endocrinology and Metabolism, Shunde Hospital of Southern Medical University, Shunde 528300, China;
| | - Hui Jiang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (W.C.); (H.J.)
| | - Yossi Weizmann
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (Y.W.); (X.W.)
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (W.C.); (H.J.)
- Correspondence: (Y.W.); (X.W.)
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Ren Y, Zhao C, He Y, Min X, Xu H, Hu X. RPARP-AS1/miR125a-5p Axis Promotes Cell Proliferation, Migration and Invasion in Colon Cancer. Onco Targets Ther 2021; 14:5035-5043. [PMID: 34675548 PMCID: PMC8520480 DOI: 10.2147/ott.s304494] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022] Open
Abstract
Background It was reported that long-noncoding RNAs (lncRNAs) had been identified as a novel class of regulators related to various cancers. RPARP-AS1, a differentially-expressed gene, was found in analysis of the gene expression profile of CRC from GEO database. However, its function has not been clear. Methods RPARP-AS1 expression was determined by qPCR and Startbase3 analysis. Knockdown of RPARP-AS1 in CRC cell lines was performed by RNAi technology, named si-RPARP-AS1 HCT116 and si-RPARP-AS1 LoVo. Cell proliferation was examined by CCK8 and colony formation assay. RNA pull-down and Luciferase reporter assay were performed to confirm the interaction between RPARP-AS1 and miR-125a-5p. Results In the study, we found that the expression of RPARP-AS1 was significantly up-regulated in CRC tissues and multiple CRC cell lines, which was closely related to poor prognosis of CRC patients. Loss-of-function studies indicated that knockdown of RPARP-AS1 inhibited CRC cell proliferation, migration and invasion in HCT116 and LoVo cell lines. Results of research on the mechanisms showed that RPARP-AS1 functioned as a competitive endogenous RNA (ceRNA) to sponge miR-125a-5p, therefore promoting CRC procession. Conclusion In summary, these results indicated that RPARP-AS1/miR-125a-5p axis played a positive role in promoting cell proliferation, migration and invasion in CC. It may be as a biomarker used to evaluate CRC prognosis.
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Affiliation(s)
- Yongjun Ren
- Department of Interventional Radiology, Sichuan Key Laboratory of Medical Imaging, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People's Republic of China
| | - Caixia Zhao
- Department of Oncology, Nanchong Central Hospital, Nanchong, Sichuan, 637000, People's Republic of China
| | - Yi He
- Department of Gastrointestinal Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People's Republic of China
| | - Xuli Min
- Department of Interventional Radiology, Sichuan Key Laboratory of Medical Imaging, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People's Republic of China
| | - Hao Xu
- Department of Interventional Radiology, Sichuan Key Laboratory of Medical Imaging, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People's Republic of China
| | - Xiao Hu
- Department of Interventional Radiology, Sichuan Key Laboratory of Medical Imaging, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637000, People's Republic of China
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Zhang H, Zhao Y, Liu X, Liu Y, Wang X, Fu Y, Fu S, Zhang J. A novel upregulated LncRNA-AC026150.8 promotes chemo-resistance and predicts poor prognosis in acute myeloid leukemia. Cancer Med 2021; 10:8614-8629. [PMID: 34664783 PMCID: PMC8633226 DOI: 10.1002/cam4.4349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AML is a common hematological malignancy with poor prognosis, the pathogenesis is still unclear. lncRNA takes part in occurrence and development of AML. This research aims to explore new differentially expressed lncRNAs and their effects on AML. METHODS Database-based bioinformatics analysis was performed to screen differentially expressed lncRNA in AML, real-time PCR was used to analyze gene expression. Kaplan-Meier survival analysis was performed to determine prognostic effect of AC026150.8 in AML. The cell drug resistance experiment was performed to test effect of AC026150.8 on chemo-resistance of AML cells. Catrapid online software and RNA pull-down, mass spectrometry, western-blot were used to predict and verify the combination of AC026150.8 and RNA splicing factors. RESULTS AC026150.8 was upregulated in AML patients and related to poor prognosis. High leukocyte counts, FAB classification, MLL-AF9 expression and NPM1 mutations were associated with high AC026150.8 expression. Upregulated of AC026150.8 increased the drug resistance of AML cells. AC026150.8 could be combined with splicing factor PCBP1. CONCLUSIONS For the first time, our study found that the upregulated AC026150.8 in AML is related to poor prognosis, overexpression of AC026150.8 could increase drug resistance of AML cells, and confirmed its scaffolding effect in combination with splicing factors. It is necessary to further study AC026150.8 and its downstream target genes to clarify the mechanism of AC026150.8 in AML.
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Affiliation(s)
- Henan Zhang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Zhao
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuan Liu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yusi Liu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaohui Wang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu Fu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Fu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jihong Zhang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
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226
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Peng PH, Hsu KW, Chieh-Yu Lai J, Wu KJ. The role of hypoxia-induced long noncoding RNAs (lncRNAs) in tumorigenesis and metastasis. Biomed J 2021; 44:521-533. [PMID: 34654684 PMCID: PMC8640553 DOI: 10.1016/j.bj.2021.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are noncoding RNAs with length greater than 200 nt. The biological roles and mechanisms mediated by lncRNAs have been extensively investigated. Hypoxia is a proven microenvironmental factor that promotes solid tumor metastasis. Epithelial-mesenchymal transition (EMT) is one of the major mechanisms induced by hypoxia to contribute to metastasis. Many lncRNAs have been shown to be induced by hypoxia and their roles have been delineated. In this review, we focus on the hypoxia-inducible lncRNAs that interact with protein/protein complex and chromatin/epigenetic factors, and the mechanisms that contribute to metastasis. The role of a recently discovered lncRNA RP11-390F4.3 in hypoxia-induced EMT is discussed. Whole genome approaches to delineating the association between lncRNAs and histone modifications are discussed. Other topics related to hypoxia-induced tumor progression but require further investigation are also mentioned. The clinical significance and treatment strategy targeted against lncRNAs are discussed. The review aims to identify suitable lncRNA targets that may provide feasible therapeutic venues for hypoxia-involved cancers.
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Affiliation(s)
- Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kai-Wen Hsu
- Research Center for Cancer Biology, Institute of New Drug Development, China Medical University, Taichung, Taiwan
| | | | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.
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Liu Y, Liang L, Ji L, Zhang F, Chen D, Duan S, Shen H, Liang Y, Chen Y. Potentiated lung adenocarcinoma (LUAD) cell growth, migration and invasion by lncRNA DARS-AS1 via miR-188-5p/ KLF12 axis. Aging (Albany NY) 2021; 13:23376-23392. [PMID: 34644678 PMCID: PMC8544313 DOI: 10.18632/aging.203632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/18/2021] [Indexed: 12/12/2022]
Abstract
Lung adenocarcinoma (LUAD) is the most common histological type of non-small cell lung cancer (NSCLC). Due to the nonspecific early symptoms, the majority of the diagnosed LUAD patients are in the middle and late stages, with multiple metastases, and have missed the optimal period for treatment. Current studies have reported lncRNA DARS-AS1 as a cancer-promoting gene that expedites tumorigenesis. This is the first study demonstrating that DARS-AS1 is involved in the mediating process of LUAD. Cell functional experiments revealed that lncRNA DARS-AS1 participated in enhancing LUAD proliferation, invasion, and migration by inhibiting miR-188-5p. The investigation on DARS-AS1/miR-188-5p led to the discovery of KLF12 as a downstream target of miR-188-5p, and the regulatory pathway was established as DARS-AS1/miR-188-5p/KLF12. According to western blot results, DARS-AS1 promoted LUAD cell growth, migration, and invasion via stimulation of the PI3K/AKT pathway, activating the EMT process, and up-regulating the CyclinD1 and Bcl-2 proteins. This was the first report on the DARS-AS1/miR-188-5p/KLF12 axis and offered a novel strategy for early diagnosis, a new therapeutic method, and an improved prognosis for LUAD.
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Affiliation(s)
- Yangyang Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of General Surgery, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Lu Liang
- Department of General Surgery, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Liang Ji
- Department of General Surgery, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Fuquan Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Donglai Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Shanzhou Duan
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Shen
- Department of General Surgery, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Yao Liang
- Department of General Surgery, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Yongbing Chen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Chang YS, Lee YT, Yen JC, Chang YC, Lin LL, Chan WL, Chang WC, Lin SY, Chang JG. Long Noncoding RNA NTT Context-Dependently Regulates MYB by Interacting With Activated Complex in Hepatocellular Carcinoma Cells. Front Oncol 2021; 11:592045. [PMID: 34616668 PMCID: PMC8488295 DOI: 10.3389/fonc.2021.592045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/09/2021] [Indexed: 01/10/2023] Open
Abstract
Background Long noncoding RNA (lncRNA) mediates the pathogenesis of various diseases, including cancer and cardiovascular, infectious, and metabolic diseases. This study examined the role of lncRNA NTT in the development and progression of cancer. Methods The expression of NTT was determined using tissues containing complementary DNA (cDNA) from patients with liver, lung, kidney, oral, and colon cancers. The expression of cis-acting genes adjacent to the NTT locus (CTGF, STX7, MYB, BCLAF1, IFNGR1, TNFAIP3, and HIVEP2) was also assessed. We used knockdown and chromatin immunoprecipitation (ChIP) assays to identify the cis-acting genes that interact with NTT. Results NTT was most significantly downregulated in hepatocellular carcinoma (HCC), while a higher NTT level correlated with a shorter survival time of patients with HCC. Multivariate analysis indicated NTT was not an independent predictor for overall survival. MYB was significantly upregulated, and its increased expression was associated with dismal survival in HCC patients, similar to the results for NTT. NTT knockdown significantly decreased cellular migration. ChIP of HCC cell lines revealed that NTT is regulated by the transcription factor ATF3 and binds to the MYB promoter via the activated complex. Additionally, when NTT was knocked down, the expression of MYB target genes such as Bcl-xL, cyclinD1, and VEGF was also downregulated. NTT could play a positive or negative regulator for MYB with a context-dependent manner in both HCC tissues and animal model. Conclusion Our study suggests that NTT plays a key role in HCC progression via MYB-regulated target genes and may serve as a novel therapeutic target.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
| | - Ya-Ting Lee
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Ju-Chen Yen
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Yuli C Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Li-Li Lin
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wen-Ling Chan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Shyr-Yi Lin
- Division of Gastroenterology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
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Sun HT, Li JP, Qian WQ, Yin MF, Yin H, Huang GC. Quercetin suppresses inflammatory cytokine production in rheumatoid arthritis fibroblast-like synoviocytes. Exp Ther Med 2021; 22:1260. [PMID: 34603528 PMCID: PMC8453329 DOI: 10.3892/etm.2021.10695] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/11/2021] [Indexed: 01/19/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, progressive and systemic autoimmune disease mainly characterized by symmetric multijoint synovitis. Quercetin has anti-inflammatory, anti-oxidation and immune regulation activities, and therefore shows high medicinal value. The present study aimed to observe the effect of quercetin on fibroblast-like synoviocytes (FLSs) in RA. Rheumatoid arthritis fibroblast-like synoviocytes (RAFLSs) were pretreated with 50 nmol/l quercetin for 2 h and were then stimulated using TNF-α for 24 h for subsequent experiments. RAFLSs were transfected with short interfering (si)-X-inactive specific transcript (XIST), microRNA (miR)-485 mimic, miR-485 inhibitor or si-PSMB8 or combination. ELISA, PCR and western blotting was used to evaluate the effect of quercetin on RAFLSs treated with TNF-α. It was revealed that quercetin inhibited the production of inflammatory cytokines and the expression of XIST in RAFLSs induced by TNF-α. Bioinformatics analysis indicated that XIST acted as a sponge for miR-485 and that proteasome subunit β type-8 (PSMB8) was a direct target of miR-485. Moreover, PSMB8 functioned as a suppressor in inflammatory cytokine production of RAFLSs induced by TNF-α. Overall, quercetin was observed to inhibit the production of inflammatory cytokines and the expression of XIST in RAFLSs induced by TNF-α. Moreover, XIST-silencing could suppress the inflammatory reaction by sponging miR-485 in cells treated with TNF-α. Altogether, quercetin could suppress the development of RA in vitro.
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Affiliation(s)
- Hai-Tao Sun
- Laboratory of New Techniques of Restoration and Reconstruction of Orthopedics and Traumatology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China.,Department of Emergency Trauma Center, Wuxi Huishan District People's Hospital, Wuxi, Jiangsu 214187, P.R. China
| | - Jian-Peng Li
- Department of Orthopedics, Tianjin Medical University, Tianjin 300070, P.R. China.,Department of Orthopedics, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Wei-Qing Qian
- Department of Orthopedics, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210001, P.R. China
| | - Meng-Fan Yin
- Department of Orthopedics, Tianjin Fifth Central Hospital, Tianjin 300450, P.R. China
| | - Hong Yin
- Department of Orthopedics, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210001, P.R. China
| | - Gui-Cheng Huang
- Laboratory of New Techniques of Restoration and Reconstruction of Orthopedics and Traumatology, The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
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Identification of a Four-lncRNA Prognostic Signature for Colon Cancer Based on Genome Instability. JOURNAL OF ONCOLOGY 2021; 2021:7408893. [PMID: 34594379 PMCID: PMC8478558 DOI: 10.1155/2021/7408893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/23/2022]
Abstract
LncRNAs (long noncoding RNAs) are closely associated with genome instability. However, the identification of lncRNAs related to the genome instability and their relationship with the prognosis and clinical signature of cancer remains to be explored. In this paper, we analyzed differential lncRNA expression based on the somatic mutation profiles of colon cancer patients from TCGA database and finally identified 153 lncRNAs that are associated with genome instability in colon cancer. Taking four lncRNAs from these 153, we established a genome-instability-related prognostic signature (GIRlncPSig). By applying the GIRlncPSig, we calculated a risk score for each patient, and using their risk scores, we divided them into low- and high-risk groups. We found that the prognosis between the two risk groups was significantly different, and the results were further verified in different independent patient cohorts. Moreover, we observed that the GIRlncPSig was related to somatic mutation rates in colon cancer, indicating that it may be a potential means of measuring genome instability levels in colon cancer. We also revealed that the GIRlncPSig was correlated with BRAF and DPYD mutation rates and that it may be a potential mutation marker for the BRAF and DPYD gene. In summary, we constructed a genome-instability-related lncRNA prognostic signature (GIRlncPSig), which has a significant effect on prognosis prediction and may allow for the discovery of new colon cancer biomarkers.
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231
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Zhao M, Yang F, Sang C, Yan C, Wang Z. BGL3 inhibits papillary thyroid carcinoma progression via regulating PTEN stability. J Endocrinol Invest 2021; 44:2165-2174. [PMID: 33543443 DOI: 10.1007/s40618-021-01519-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE BGL3, a novel long non-coding RNA (lncRNA) that plays a crucial role in several human malignancies. However, the clinical significance and biological function of BGL3 in papillary thyroid carcinoma (PTC) have not been explored. Herein, we aimed to investigate the role of BGL3 in human PTC. METHODS A total of 85 pairs of PTC and normal tissues were collected for clinicopathological analysis. Expression of BGL3 was determined by quantitative real-time polymerase chain reaction (qRT-PCR). The effects of BGL3 on PTC cells ware determined by CCK-8, colony formation, EdU and wound healing assays. The molecular mechanism underlying BGL3 was tested by ChIP, Co-IP, RNA pull-down and luciferase reporter assays. In vivo experiments were conducted using xenografts in nude mice. RESULTS BGL3 was significantly decreased in PTC tissues compared to adjacent normal thyroid tissues, and it was transcriptionally repressed by oncogene Myc. Low BGL3 is positively related to larger tumor size, lymph node metastasis, later TNM stage and poor prognosis. Overexpression of BGL3 inhibited PTC cell proliferation and migration in vitro, and reduced tumor size and lung metastasis nodules in vivo. BGL3 was mainly located in the cytoplasm, in which interacted with PTEN and recruited OTUD3, enhancing the de-ubiquitination effect of OTUD3 on PTEN, resulting in increasing PTEN protein stability and inactivating carcinogenic PI3K/AKT signaling. CONCLUSIONS Our data underscore the critical tumor-inhibiting role of BGL3 in PTC via post-translational regulation of PTEN protein stability, which may serve as a novel therapeutic target and prognostic biomarker in human PTC.
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Affiliation(s)
- M Zhao
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - F Yang
- Department of Orthopedics, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - C Sang
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - C Yan
- Department of General Surgery, Yanqing District Hospital, Beijing and Yanqing Hospital, Peking University Third Hospital, Beijing, People's Republic of China
| | - Z Wang
- Department of General Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People's Republic of China.
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232
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Lu H, Guo R, Zhang Y, Su S, Zhao Q, Yu Y, Shi H, Sun H, Zhang Y, Li S, Shi D, Chu X, Sun C. Inhibition of lncRNA TCONS_00077866 Ameliorates the High Stearic Acid Diet-Induced Mouse Pancreatic β-Cell Inflammatory Response by Increasing miR-297b-5p to Downregulate SAA3 Expression. Diabetes 2021; 70:2275-2288. [PMID: 34261739 DOI: 10.2337/db20-1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/06/2021] [Indexed: 11/13/2022]
Abstract
Long-term consumption of a high-fat diet increases the circulating concentration of stearic acid (SA), which has a potent toxic effect on β-cells, but the underlying molecular mechanisms of this action have not been fully elucidated. Here, we evaluated the role of long noncoding (lnc)RNA TCONS_00077866 (lnc866) in SA-induced β-cell inflammation. lnc866 was selected for study because lncRNA high-throughput sequencing analysis demonstrated it to have the largest fold-difference in expression of five lncRNAs that were affected by SA treatment. Knockdown of lnc866 by virus-mediated shRNA expression in mice or by Smart Silencer in mouse pancreatic β-TC6 cells significantly inhibited the SA-induced reduction in insulin secretion and β-cell inflammation. According to lncRNA-miRNAs-mRNA coexpression network analysis and luciferase reporter assays, lnc866 directly bound to miR-297b-5p, thereby preventing it from reducing the expression of its target serum amyloid A3 (SAA3). Furthermore, overexpression of miR-297b-5p or inhibition of SAA3 also had marked protective effects against the deleterious effects of SA in β-TC6 cells and mouse islets. In conclusion, lnc866 silencing ameliorates SA-induced β-cell inflammation by targeting the miR-297b-5p/SAA3 axis. lnc866 inhibition may represent a new strategy to protect β-cells against the effects of SA during the development of type 2 diabetes.
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MESH Headings
- Animals
- Cells, Cultured
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diabetes Mellitus, Type 2/prevention & control
- Diet, High-Fat/adverse effects
- Down-Regulation/drug effects
- Gene Expression Regulation/drug effects
- HEK293 Cells
- Humans
- Inflammation/etiology
- Inflammation/genetics
- Inflammation/pathology
- Inflammation/prevention & control
- Insulin Secretion/drug effects
- Insulin-Secreting Cells/drug effects
- Insulin-Secreting Cells/metabolism
- Insulin-Secreting Cells/pathology
- Male
- Mice
- Mice, Inbred C57BL
- MicroRNAs/genetics
- Palmitic Acid/adverse effects
- Palmitic Acid/pharmacology
- Pancreatitis/etiology
- Pancreatitis/genetics
- Pancreatitis/pathology
- Pancreatitis/prevention & control
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Small Interfering/pharmacology
- Serum Amyloid A Protein/genetics
- Stearic Acids/adverse effects
- Stearic Acids/pharmacology
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Affiliation(s)
- Huimin Lu
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Rui Guo
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Yunjin Zhang
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Shenghan Su
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Qingrui Zhao
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Yue Yu
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoran Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongjian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shenglong Li
- Department of General Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dan Shi
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Xia Chu
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
| | - Changhao Sun
- Department of Nutrition and Food Hygiene (National Key Discipline), Public Health College, Harbin Medical University, Harbin, China
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233
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Yadav G, Kulshreshtha R. Metastasis associated long noncoding RNAs in glioblastoma: Biomarkers and therapeutic targets. J Cell Physiol 2021; 237:401-420. [PMID: 34533835 DOI: 10.1002/jcp.30577] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023]
Abstract
Glioblastoma (GBM) is the most aggressive, malignant, and therapeutically challenging Grade IV tumor of the brain. Although the possibility of distant metastasis is extremely rare, GBM is known to cause intracranial metastasis forming aggressive secondary lesions resulting in a dismal prognosis. Metastasis also plays an important role in tumor dissemination and recurrence making GBM largely incurable. Recent studies have indicated the importance of long noncoding RNAs (lncRNAs) in GBM metastasis. lncRNAs are a class of regulatory noncoding RNAs (>200 nt) that interact with DNA, RNA, and proteins to regulate various biological processes. This is the first comprehensive review summarizing the lncRNAs associated with GBM metastasis and the underlying molecular mechanism involved in migration/invasion. We also highlight the complex network of lncRNA/miRNA/protein that collaborate/compete to regulate metastasis-associated genes. Many of these lncRNAs also show attractive potential as diagnostic/prognostic biomarkers. Finally, we discuss various therapeutic strategies and potential applications of lncRNAs as therapeutic targets for the treatment of GBM.
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Affiliation(s)
- Garima Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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234
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Wickhorst PJ, Druzhinin SI, Ihmels H, Müller M, Sutera Sardo M, Schönherr H, Viola G. A Dimethylaminophenyl‐Substituted Naphtho[1,2‐
b
]quinolizinium as a Multicolor NIR Probe for the Fluorimetric Detection of Intracellular Nucleic Acids and Proteins. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Sergey I. Druzhinin
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Mareike Müller
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | | | - Holger Schönherr
- Department of Chemistry – Biology University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ) Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Giampietro Viola
- Department of Women's and Child's health Oncohematology laboratory University of Padova Via Giustiniani 2 I-35128 Padova Italy
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235
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Zheng L, Guan Z, Xue M. A crucial role for the long non-coding RNA CASC11 in the pathogenesis of human cancers. Am J Transl Res 2021; 13:10922-10932. [PMID: 34650773 PMCID: PMC8507062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs more than 200 nucleotides in length. Although they do not encode proteins, lncRNAs can regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging data show that lncRNAs are important for tumorigenesis and cancer progression. Cancer susceptibility candidate 11 (CASC11) is a prominent lncRNA that is upregulated in various types of cancers. Moreover, its overexpression correlates with larger tumor size, more advanced cancer stages, cancer metastasis, and poor overall survival for most types of cancer. Functionally, the knockdown of CASC11 can inhibit cell proliferation, invasion, and migration, while enhancing apoptosis through its regulation of gene expression and signaling pathways and its interactions with functional proteins. Here, we discuss the identification, expression, and function of CASC11. Additionally, we discuss the potential roles of CASC11 as a diagnostic biomarker, prognostic biomarker, and therapeutic target in various cancers.
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Affiliation(s)
- Lian Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Zhenjie Guan
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Miaomiao Xue
- Department of General Dentistry, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
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236
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Dong A, Cheung TH. Deciphering the chromatin organization and dynamics for muscle stem cell function. Curr Opin Cell Biol 2021; 73:124-132. [PMID: 34534837 DOI: 10.1016/j.ceb.2021.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 12/28/2022]
Abstract
The chromatin landscape represents a critical regulatory layer for precise transcriptional control. Chromosome architecture restrains the physical access to the DNA elements and is one of the determinants that specifies cell identity. Adult stem cells possess the unique ability to differentiate into a specific lineage. One of the underexplored areas in skeletal muscle biology is the molecular mechanism guiding the chromatin organization changes in muscle stem cell specification, myogenic determination, and differentiation. In this review, we focus on the regulatory network guiding the progression of muscle stem cells to differentiated progeny. We summarize recent findings regarding the mechanisms directing myogenic cell fate decision and differentiation, with a particular focus on three-dimensional chromosome architecture and long noncoding RNA-associated chromatin accessibility changes.
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Affiliation(s)
- Anqi Dong
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tom H Cheung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China.
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237
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Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, Detmar M. The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. BMC Genom Data 2021; 22:33. [PMID: 34521352 PMCID: PMC8439024 DOI: 10.1186/s12863-021-00992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. Results To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. Conclusion In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00992-1.
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Affiliation(s)
- Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Eliane Sibler
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.,Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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238
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Mirzaei S, Paskeh MDA, Hashemi F, Zabolian A, Hashemi M, Entezari M, Tabari T, Ashrafizadeh M, Raee P, Aghamiri S, Aref AR, Leong HC, Kumar AP, Samarghandian S, Zarrabi A, Hushmandi K. Long non-coding RNAs as new players in bladder cancer: Lessons from pre-clinical and clinical studies. Life Sci 2021; 288:119948. [PMID: 34520771 DOI: 10.1016/j.lfs.2021.119948] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022]
Abstract
The clinical management of bladder cancer (BC) has become an increasing challenge due to high incidence rate of BC, malignant behavior of cancer cells and drug resistance. The non-coding RNAs are considered as key factors involved in BC progression. The long non-coding RNAs (lncRNAs) are RNA molecules and do not encode proteins. They have more than 200 nucleotides in length and affect gene expression at epigenetic, transcriptional and post-transcriptional phases. The lncRNAs demonstrate abnormal expression in BC cells and tissues. The present aims to identifying lncRNAs with tumor-suppressor and tumor-promoting roles, and evaluating their roles as regulatory of growth and migration. Apoptosis, glycolysis and EMT are tightly regulated by lncRNAs in BC. Response of BC cells to cisplatin, doxorubicin and gemcitabine chemotherapy is modulated by lncRNAs. LncRNAs regulate immune cell infiltration in tumor microenvironment and affect response of BC cells to immunotherapy. Besides, lncRNAs are able to regulate microRNAs, STAT3, Wnt, PTEN and PI3K/Akt pathways in affecting both proliferation and migration of BC cells. Noteworthy, anti-tumor compounds and genetic tools such as siRNA, shRNA and CRISPR/Cas systems can regulate lncRNA expression in BC. Finally, lncRNAs and exosomal lncRNAs can be considered as potential diagnostic and prognostic tools in BC.
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Affiliation(s)
- Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Mahshid Deldar Abad Paskeh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Farid Hashemi
- Department of Comparative Biosciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Teimour Tabari
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey; Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey.
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Xsphera Biosciences Inc., 6 Tide Street, Boston, MA 02210, USA
| | - Hin Chong Leong
- Cancer Science Institute of Singapore, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
| | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey.
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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239
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Gurer DC, Erdogan İ, Ahmadov U, Basol M, Sweef O, Cakan-Akdogan G, Akgül B. Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells. Front Cell Dev Biol 2021; 9:688855. [PMID: 34497804 PMCID: PMC8419520 DOI: 10.3389/fcell.2021.688855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Cisplatin is a well-known cancer chemotherapeutic agent but how extensively long non-coding RNA (lncRNA) expression is modulated by cisplatin is unknown. It is imperative to employ a comprehensive approach to obtain a better account of cisplatin-mediated changes in the expression of lncRNAs. In this study, we used a transcriptomics approach to profile lncRNAs in cisplatin-treated HeLa cells, which resulted in identification of 10,214 differentially expressed lncRNAs, of which 2,500 were antisense lncRNAs. For functional analyses, we knocked down one of the cisplatin inducible lncRNAs, death receptor 5 antisense (DR5-AS) lncRNA, which resulted in a morphological change in HeLa cell shape without inducing any cell death. A second round of transcriptomics-based profiling revealed differential expression of genes associated with immune system, motility and cell cycle in DR5-AS knockdown HeLa cells. Cellular analyses showed that DR5-AS reduced cell proliferation and caused a cell cycle arrest at S and G2/M phases. Moreover, DR5-AS knockdown reduced the invasive capacity of HeLa cells in zebrafish xenograft model. These results suggest that cisplatin-mediated pleiotropic effects, such as reduction in cell proliferation, metastasis and cell cycle arrest, may be mediated by lncRNAs.
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Affiliation(s)
- Dilek Cansu Gurer
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Ízmir, Institute of Technology, Izmir, Turkey
| | - İpek Erdogan
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Ízmir, Institute of Technology, Izmir, Turkey
| | - Ulvi Ahmadov
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Ízmir, Institute of Technology, Izmir, Turkey
| | - Merve Basol
- Izmir Biomedicine and Genome Center, Ízmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Ízmir, Turkey
| | - Osama Sweef
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Ízmir, Institute of Technology, Izmir, Turkey
| | | | - Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Ízmir, Institute of Technology, Izmir, Turkey
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240
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Shen T, Xia W, Min S, Yang Z, Cheng L, Wang W, Zhan Q, Shao F, Zhang X, Wang Z, Zhang Y, Shen G, Zhang H, Wu LL, Yu GY, Kong QP, Wang X. A pair of long intergenic non-coding RNA LINC00887 variants act antagonistically to control Carbonic Anhydrase IX transcription upon hypoxia in tongue squamous carcinoma progression. BMC Biol 2021; 19:192. [PMID: 34493285 PMCID: PMC8422755 DOI: 10.1186/s12915-021-01112-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are important regulators in tumor progression. However, their biological functions and underlying mechanisms in hypoxia adaptation remain largely unclear. Results Here, we established a correlation between a Chr3q29-derived lncRNA gene and tongue squamous carcinoma (TSCC) by genome-wide analyses. Using RACE, we determined that two novel variants of this lncRNA gene are generated in TSCC, namely LINC00887_TSCC_short (887S) and LINC00887_TSCC_long (887L). RNA-sequencing in 887S or 887L loss-of-function cells identified their common downstream target as Carbonic Anhydrase IX (CA9), a gene known to be upregulated by hypoxia during tumor progression. Mechanistically, our results showed that the hypoxia-augmented 887S and constitutively expressed 887L functioned in opposite directions on tumor progression through the common target CA9. Upon normoxia, 887S and 887L interacted. Upon hypoxia, the two variants were separated. Each RNA recognized and bound to their responsive DNA cis-acting elements on CA9 promoter: 887L activated CA9’s transcription through recruiting HIF1α, while 887S suppressed CA9 through DNMT1-mediated DNA methylation. Conclusions We provided hypoxia-permitted functions of two antagonistic lncRNA variants to fine control the hypoxia adaptation through CA9. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01112-2.
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Affiliation(s)
- Tao Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Wangxiao Xia
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China
| | - Sainan Min
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Zixuan Yang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Lehua Cheng
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China
| | - Wei Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Qianxi Zhan
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Fanghong Shao
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Xuehan Zhang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Zhiyu Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University, Baoding, 071000, China
| | - Yan Zhang
- School of Health Services Management, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Guodong Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China
| | - Huafeng Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, 100191, China
| | - Guang-Yan Yu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. .,Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei, China. .,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
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Liu M, Sun X, Zhu L, Zhu M, Deng K, Nie X, Mo H, Du T, Huang B, Hu L, Liang L, Wang D, Luo Y, Yi J, Zhang J, Zhong X, Cao C, Chen H. Long Noncoding RNA RP11-115N4.1 Promotes Inflammatory Responses by Interacting With HNRNPH3 and Enhancing the Transcription of HSP70 in Unexplained Recurrent Spontaneous Abortion. Front Immunol 2021; 12:717785. [PMID: 34484222 PMCID: PMC8414257 DOI: 10.3389/fimmu.2021.717785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Background Unexplained recurrent spontaneous abortion (URSA) is a common pregnancy complication and the etiology is unknown. URSA-associated lncRNAs are expected to be potential biomarkers for diagnosis, and might be related to the disease pathogenesis. Objective To investigate differential lncRNAs in peripheral blood of non-pregnant URSA patients and matched healthy control women and to explore the possible mechanism of differential lncRNAs leading to URSA. Methods We profiled lncRNAs expression in peripheral blood from 5 non-pregnant URSA patients and 5 matched healthy control women by lncRNA microarray analysis. Functions of URSA-associated lncRNAs were further investigated in vitro. Results RP11-115N4.1 was identified as the most differentially expressed lncRNA which was highly upregulated in peripheral blood of non-pregnant URSA patients (P = 3.63E-07, Fold change = 2.96), and this dysregulation was further validated in approximately 26.67% additional patients (4/15). RP11-115N4.1 expression was detected in both lymphocytes and monocytes of human peripheral blood, and in vitro overexpression of RP11-115N4.1 decreased cell proliferation in K562 cells significantly. Furthermore, heat-shock HSP70 genes (HSPA1A and HSPA1B) were found to be significantly upregulated upon RP11-115N4.1 overexpression by transcriptome analysis (HSPA1A (P = 4.39E-08, Fold change = 4.17), HSPA1B (P = 2.26E-06, Fold change = 2.99)). RNA pull down and RNA immunoprecipitation assay (RIP) analysis demonstrated that RP11-115N4.1 bound to HNRNPH3 protein directly, which in turn activate heat-shock proteins (HSP70) analyzed by protein-protein interaction and HNRNPH3 knockdown assays. Most importantly, the high expression of HSP70 was also verified in the serum of URSA patients and the supernatant of K562 cells with RP11-115N4.1 activation, and HSP70 in supernatant can exacerbate inflammatory responses in monocytes by inducing IL-6, IL-1β, and TNF-α and inhibit the migration of trophoblast cells, which might associate with URSA. Conclusion Our results demonstrated that the activation of RP11-115N4.1 can significantly increase the protein level of HSP70 via binding to HNRNPH3, which may modulate the immune responses and related to URSA. Moreover, RP11-115N4.1 may be a novel etiological biomarker and a new therapeutic target for URSA.
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Affiliation(s)
- Meilan Liu
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoyue Sun
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Liqiong Zhu
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Menglan Zhu
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Kewen Deng
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaolu Nie
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hanjie Mo
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tao Du
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bingqian Huang
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Lihao Hu
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Liuhong Liang
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dongyan Wang
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yinger Luo
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jinling Yi
- Department of Gynecology, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jianping Zhang
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xingming Zhong
- Key Laboratory of Male Reproduction and Genetics of National Health Council, Family Planning Research Institute of Guangdong Province, Guangzhou, China.,Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Chunwei Cao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Hui Chen
- Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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242
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He T, Yuan C, Zhao C. Long intragenic non-coding RNA p53-induced transcript (LINC-PINT) as a novel prognosis indicator and therapeutic target in cancer. Biomed Pharmacother 2021; 143:112127. [PMID: 34474342 DOI: 10.1016/j.biopha.2021.112127] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/15/2021] [Accepted: 08/24/2021] [Indexed: 12/18/2022] Open
Abstract
Cancer involves complex etiology factors, multiple stages, and intricate gene mutations. Long non-coding RNAs (lncRNAs) are implicated as molecular mechanisms underlying human genomic activity in various physiologic and pathophysiologic conditions. However, the sophisticated modifications and regulatory processes linking lncRNAs to cancer initiation and progression have not yet been fully explored. Long intragenic non-coding RNA p53-induced transcript (LINC-PINT) is an lncRNA that functions as a tumor suppressor gene involved in various tumors and malignant activities. LINC-PINT is downregulated in nasopharyngeal cancer, renal carcinoma, non-small cell lung cancer, glioblastoma, thyroid cancer, retinoblastoma, ovarian cancer, breast cancer, esophageal squamous cell carcinoma, osteosarcoma, melanoma, and gastric cancer. Furthermore, decreased LINC-PINT expression predicts poor prognosis and advanced clinical tumor stages. Together, these studies indicate that LINC-PINT could serve as a diagnostic and prognostic indicator in cancer. The specific lncRNA regulatory mechanism of LINC-PINT may also be a novel target for cancer therapies.
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Affiliation(s)
- Tiefei He
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
| | - Chendong Yuan
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
| | - Cansong Zhao
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
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243
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Wu R, Hu W, Chen H, Wang Y, Li Q, Xiao C, Fan L, Zhong Z, Chen X, Lv K, Zhong S, Shi Y, Chen J, Zhu W, Zhang J, Hu X, Wang J. A Novel Human Long Noncoding RNA SCDAL Promotes Angiogenesis through SNF5-Mediated GDF6 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004629. [PMID: 34319658 PMCID: PMC8456203 DOI: 10.1002/advs.202004629] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Indexed: 06/08/2023]
Abstract
Angiogenesis is essential for vascular development. The roles of regulatory long noncoding RNAs (lncRNAs) in mediating angiogenesis remain under-explored. Human embryonic stem cell-derived mesenchymal stem cells (hES-MSCs) are shown to exert more potent cardioprotective effects against cardiac ischemia than human bone marrow-derived MSCs (hBM-MSCs), associated with enhanced neovascularization. The purpose of this study is to search for angiogenic lncRNAs enriched in hES-MSCs, and investigate their roles and mechanisms. AC103746.1 is one of the most highly expressed intergenic lncRNAs detected in hES-MSCs versus hBM-MSCs, and named as SCDAL (stem cell-derived angiogenic lncRNA). SCDAL knockdown significantly reduce the angiogenic potential and reparative effects of hES-MSCs in the infarcted hearts, while overexpression of SCDAL in either hES-MSCs or hBM-MSCs exhibits augmented angiogenesis and cardiac function recovery. Mechanistically, SCDAL induces growth differentiation factor 6 (GDF6) expression via direct interaction with SNF5 at GDF6 promoter. Secreted GDF6 promotes endothelial angiogenesis via non-canonical vascular endothelial growth factor receptor 2 activation. Furthermore, SCDAL-GDF6 is expressed in human endothelial cells, and directly enhances endothelial angiogenesis in vitro and in vivo. Thus, these findings uncover a previously unknown lncRNA-dependent regulatory circuit for angiogenesis. Targeted intervention of the SCDAL-GDF6 pathway has potential as a therapy for ischemic heart diseases.
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Affiliation(s)
- Rongrong Wu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Wangxing Hu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Huan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang ProvinceHangzhou310012P. R. China
| | - Yingchao Wang
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Qingju Li
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Changchen Xiao
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Lin Fan
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Zhiwei Zhong
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Xiaoying Chen
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Kaiqi Lv
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Shuhan Zhong
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Yanna Shi
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jinghai Chen
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Wei Zhu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jianyi Zhang
- Department of Biomedical EngineeringUniversity of Alabama at BirminghamSchool of Medicine and School of EngineeringBirminghamAL35294USA
| | - Xinyang Hu
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
| | - Jian'an Wang
- Department of CardiologySecond Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310009P. R. China
- Cardiovascular Key Laboratory of Zhejiang ProvinceHangzhou310009P. R. China
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244
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Hu Y, Ye C, Cheng S, Chen J. Propofol Downregulates lncRNA MALAT1 to Alleviate Cerebral Ischemia-Reperfusion Injury. Inflammation 2021; 44:2580-2591. [PMID: 34427851 DOI: 10.1007/s10753-021-01525-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
Propofol (PPF) is reported to play a protective role in ischemia/reperfusion (I/R) injury, including cerebral ischemia-reperfusion injury (CIRI). This study aims to investigate the mechanism by which PPF ameliorates CIRI. Kunming mice were used to establish the middle cerebral artery occlusion (MCAO)/reperfusion mouse model in vivo. PPF pre-treatment was performed before CIRI. Lactate dehydrogenase (LDH) and creatine phosphokinase (CPK) levels were detected to evaluate the tissue injury. PC12 cells were exposed to hypoxia/reoxygenation (H/R) to construct the in vitro CIRI model, and PC12 cells were pre-treated with PPF before H/R. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to detect the expression of lncRNA MALAT1 and miR-182-5p. Flow cytometry was used to detect the apoptosis of PC12 cells. Bioinformatics analysis, qRT-PCR, dual-luciferase reporter gene experiments, and RNA immunoprecipitation (RIP) experiments were performed to predict and validate the targeting relationship between MALAT1 and miR-182-5p. Western blot was used to detect Toll-like receptor 4 (TLR4) expression at protein level. PPF pre-treatment remarkably inhibited LDH and CPK levels in the serum of the mice with CIRI, and reduced the apoptosis of PC12 cells exposed to H/R. Besides, PPF pre-treatment markedly suppressed MALAT1 expression in both in vivo and in vitro models and upregulated miR-182-5p expression. MiR-182-5p was validated to be a downstream target gene of MALAT1, and MALAT1 could increase the expression of TLR4 by suppressing miR-182-5p. The effects of PPF on the injury of the mice brain and PC12 cells were partly counteracted by the restoration of MALAT1. PPF protects the brain against I/R-induced injury by regulating MALAT1/miR-182-5p/TLR4 axis.
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Affiliation(s)
- Yubo Hu
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Erdao District, 126 Sendai Street, Changchun, Jilin Province, 130033, China
| | - Cong Ye
- Department of Obstetrics and Gynecology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130033, China
| | - Shuang Cheng
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Erdao District, 126 Sendai Street, Changchun, Jilin Province, 130033, China
| | - Junyang Chen
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Erdao District, 126 Sendai Street, Changchun, Jilin Province, 130033, China. .,Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Erdao District, 126 Sendai Street, Changchun, Jilin Province, 130033, China.
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245
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Rusek M, Krasowska D. Non-Coding RNA in Systemic Sclerosis: A Valuable Tool for Translational and Personalized Medicine. Genes (Basel) 2021; 12:1296. [PMID: 34573278 PMCID: PMC8471866 DOI: 10.3390/genes12091296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors are heritable and ultimately play a role in modulating gene expression and, thus, in regulating cell functions. Non-coding RNAs have growing recognition as novel biomarkers and crucial regulators of pathological conditions in humans. Their characteristic feature is being transcribed in a tissue-specific pattern. Now, there is emerging evidence that lncRNAs have been identified to be involved in the differentiation of human skin, wound healing, fibrosis, inflammation, and immunological response. Systemic sclerosis (SSc) is a heterogeneous autoimmune disease characterized by fibrosis, vascular abnormalities, and immune system activation. The pathogenesis remains elusive, but clinical manifestations reveal autoimmunity with the presence of specific autoantibodies, activation of innate and adaptive immunity, vascular changes, and active deposition of extracellular matrix components leading to fibrosis. The use of multi-omics studies, including NGS, RNA-seq, or GWAS, has proposed that the non-coding genome may be a significant player in its pathogenesis. Moreover, it may unravel new therapeutic targets in the future. The aim of this review is to show the pathogenic role of long non-coding RNAs in systemic sclerosis. Investigation of these transcripts' functions has the potential to elucidate the molecular pathology of SSc and provide new opportunities for drug-targeted therapy for this disorder.
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Affiliation(s)
- Marta Rusek
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
- Department of Pathophysiology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
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246
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Genetic Editing of Long Noncoding RNA Using CRISPR/Cas9 Technology. Methods Mol Biol 2021. [PMID: 34417751 DOI: 10.1007/978-1-0716-1697-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNA transcripts greater than 200 nucleotides in length and makeup a considerable part of the human genome. LncRNAs are well established as crucial players in a myriad of physiological and pathological processes; however, despite their abundance and versatility, the functional characteristics of lncRNAs remain largely unknown predominantly due to the lack of suitable genetic editing strategies. The complexity of their genetic structure and regulation combined with their unique functionality poses several limitations in the application of classic genetic manipulation methods in lncRNA functional studies. Several reports have demonstrated the successful implementation of CRISPR/Cas9 technology in screening and identifying the function of specific lncRNAs. Here, we describe a detailed protocol utilizing CRISPR/Cas9 genetic editing technology for knocking down lncRNAs in vitro.
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247
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Guo Q, Zhang X, Shen T, Wang X. Identification of Autophagy- and Ferroptosis-Related lncRNAs Functioned through Immune-Related Pathways in Head and Neck Squamous Carcinoma. Life (Basel) 2021; 11:life11080835. [PMID: 34440579 PMCID: PMC8399325 DOI: 10.3390/life11080835] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The interplay between autophagy and ferroptosis has been highlighted as an important event to decide cancer cell fate. However, the underlying mechanisms remain largely unclear. In this study, we systematically explored the expression, prognostic value and functional roles of lncRNA in autophagy and ferroptosis. By a set of bioinformatics analyses, we identified 363 autophagy- and ferroptosis-related lncRNAs (AF-lncRNAs) and found 17 of them are dramatically related to the prognosis of head and neck squamous cell carcinoma (HNSC) patients, named as prognosis-related AF-lncRNAs (PAF-lncRNAs). Based on six key PAF-lncRNAs, a risk score model was developed and used to categorize the TCGA-retrieved HNSC patients into two groups (high-risk vs. low-risk). Functional analysis showed the differentially expressed genes (DEGs) between the two groups were mainly enriched in immune-related pathways and regulated by a PAF-lncRNA-directed ceRNA (competitive endogenous RNA) network. Combined with a variety of immune infiltration analyses, we also found a decreased landscape of immune cell infiltration in high-risk groups. Together, by revealing PAF-lncRNAs with tumor prognostic features functioned through immune-related pathways, our work would contribute to show the pathogenesis of a lncRNA-directed interplay among autophagy, ferroptosis and tumor immunity in HNSC and to develop potential prognostic biomarkers and targets for tumor immunotherapy.
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Affiliation(s)
- Qi Guo
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xuehan Zhang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Tao Shen
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Correspondence: (T.S.); (X.W.); Tel./Fax: +86-551-63600080 (T.S. & X.W.)
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Q.G.); (X.Z.)
- Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230026, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Correspondence: (T.S.); (X.W.); Tel./Fax: +86-551-63600080 (T.S. & X.W.)
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. Int J Mol Sci 2021; 22:8719. [PMID: 34445436 PMCID: PMC8395733 DOI: 10.3390/ijms22168719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Apart from protein-coding Ribonucleic acids (RNAs), there exists a variety of non-coding RNAs (ncRNAs) which regulate complex cellular and molecular processes. High-throughput sequencing technologies and bioinformatics approaches have largely promoted the exploration of ncRNAs which revealed their crucial roles in gene regulation, miRNA binding, protein interactions, and splicing. Furthermore, ncRNAs are involved in the development of complicated diseases like cancer. Categorization of ncRNAs is essential to understand the mechanisms of diseases and to develop effective treatments. Sub-cellular localization information of ncRNAs demystifies diverse functionalities of ncRNAs. To date, several computational methodologies have been proposed to precisely identify the class as well as sub-cellular localization patterns of RNAs). This paper discusses different types of ncRNAs, reviews computational approaches proposed in the last 10 years to distinguish coding-RNA from ncRNA, to identify sub-types of ncRNAs such as piwi-associated RNA, micro RNA, long ncRNA, and circular RNA, and to determine sub-cellular localization of distinct ncRNAs and RNAs. Furthermore, it summarizes diverse ncRNA classification and sub-cellular localization determination datasets along with benchmark performance to aid the development and evaluation of novel computational methodologies. It identifies research gaps, heterogeneity, and challenges in the development of computational approaches for RNA sequence analysis. We consider that our expert analysis will assist Artificial Intelligence researchers with knowing state-of-the-art performance, model selection for various tasks on one platform, dominantly used sequence descriptors, neural architectures, and interpreting inter-species and intra-species performance deviation.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- National Center for Artificial Intelligence (NCAI), National University of Sciences and Technology, Islamabad 44000, Pakistan;
- School of Electrical Engineering & Computer Science, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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249
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Jing H, Wang C, Zhao L, Cheng J, Qin P, Lin H. Propofol protects cardiomyocytes from hypoxia/reoxygenation injury via regulating MALAT1/miR-206/ATG3 axis. J Biochem Mol Toxicol 2021; 35:e22880. [PMID: 34383354 DOI: 10.1002/jbt.22880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/06/2021] [Accepted: 07/29/2021] [Indexed: 01/24/2023]
Abstract
Previous studies have shown that propofol (PPF) plays a protective role in ischemia-reperfusion (I/R) in multiple organs and tissues. This study was aimed to explore the mechanism of PPF in ameliorating myocardial ischemia-reperfusion injury (MIRI). MIRI model was established with Sprague-Dawley rats, and PPF pretreatment was performed before reperfusion. Creatine kinase isoform (CK-MB), lactate dehydrogenase (LDH), and hematoxylin and eosin stain were used to evaluate the severity of MIRI. H9c2 cells were treated with hypoxia/reoxygenation (H/R) to simulate I/R injury in vitro. Real-time quantitative polymerase chain reaction (qPCR) was employed to assess MALAT1 and microRNA (miR)-206 expressions. Autophagy-related 3 (ATG3), LC3BⅡ/LC3BⅠ, and Beclin-1 expression were examined by western blot. Apoptosis was monitored using flow cytometry. Interaction between MALAT1 and miR-206 was determined by bioinformatics analysis, dual-luciferase reporter gene assay, RIP assay, and RNA pull-down assay. PPF pretreatment remarkably reduced CK-MB level, LDH level, myocardial infarct size, and LC3BⅡ/LC3BⅠ ratio and Beclin-1 expression in the rats with MIRI, and repressed the apoptosis of H9c2 cells exposed to H/R. PPF pretreatment markedly suppressed MALAT1 expression and enhanced miR-206 expression in both in vivo and in vitro models. MiR-206 was identified as a target of MALAT1 in cardiomyocytes, and MALAT1 could increase the expression of ATG3. Additionally, the upregulation of MALAT1 partially reversed the protective effect of PPF on cardiomyocytes in vitro. PPF modulated MALAT1/miR-206/ATG3 axis to protect cardiomyocytes against I/R injury.
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Affiliation(s)
- Haijuan Jing
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China.,Department of Anesthesiology, Central China Fuwai Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Chuan Wang
- Department of Anesthesiology, Hebei North University, Zhangjiakou, Hebei, China
| | - Liang Zhao
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Jing Cheng
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Pengyu Qin
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
| | - Hongqi Lin
- Department of Anesthesiology, Henan Provincial People's Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China.,Department of Anesthesiology, Central China Fuwai Hospital (Central China Fuwai Hospital of Zhengzhou University), Zhengzhou, Henan, China
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An integrative approach identifies dysregulated long non-coding RNAs as microRNA decoys during nevus to melanoma transformation. Melanoma Res 2021; 30:594-598. [PMID: 32976222 DOI: 10.1097/cmr.0000000000000695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mounting evidence supports a role for dysregulated long non-coding RNAs (lncRNA) in the development of many cancers. A recently discovered function of lncRNAs is to act as microRNA (miR) decoys or competing endogenous RNAs, which sequester specific miRs and relieve negative regulation of mRNA expression by miRs. Although a large number of non-coding RNAs are thought to function as competing endogenous RNAs, miR-sequestering lncRNAs involved in nevus to melanoma transformation remain largely unknown. In this study, we applied a bioinformatics approach to a unique dataset of benign melanocytic nevi and primary melanomas of the skin in order to fill this research gap. We modified a previously published miR target prediction algorithm, RNAhybrid, and improved its search efficiency. We reported the presence of many lncRNAs and miRs deregulated when transitioning from a senescence-like state of nevi to melanoma. We provided evidence of a relatively new and understudied mechanism of gene regulation during this process and identified for the first time lncRNAs (n = 122) that may potentially function as miR decoys as well as their target miRs during nevus to melanoma transformation. The knowledge presented here can be employed for developing biomarkers for diagnostic and risk stratification purposes.
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