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Bonilauri B, Ribeiro AL, Spangenberg L, Dallagiovanna B. Unveiling Polysomal Long Non-Coding RNA Expression on the First Day of Adipogenesis and Osteogenesis in Human Adipose-Derived Stem Cells. Int J Mol Sci 2024; 25:2013. [PMID: 38396700 PMCID: PMC10888724 DOI: 10.3390/ijms25042013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/25/2024] Open
Abstract
Understanding the intricate molecular mechanisms governing the fate of human adipose-derived stem cells (hASCs) is essential for elucidating the delicate balance between adipogenic and osteogenic differentiation in both healthy and pathological conditions. Long non-coding RNAs (lncRNAs) have emerged as key regulators involved in lineage commitment and differentiation of stem cells, operating at various levels of gene regulation, including transcriptional, post-transcriptional, and post-translational processes. To gain deeper insights into the role of lncRNAs' in hASCs' differentiation, we conducted a comprehensive analysis of the lncRNA transcriptome (RNA-seq) and translatome (polysomal-RNA-seq) during a 24 h period of adipogenesis and osteogenesis. Our findings revealed distinct expression patterns between the transcriptome and translatome during both differentiation processes, highlighting 90 lncRNAs that are exclusively regulated in the polysomal fraction. These findings underscore the significance of investigating lncRNAs associated with ribosomes, considering their unique expression patterns and potential mechanisms of action, such as translational regulation and potential coding capacity for microproteins. Additionally, we identified specific lncRNA gene expression programs associated with adipogenesis and osteogenesis during the early stages of cell differentiation. By shedding light on the expression and potential functions of these polysome-associated lncRNAs, we aim to deepen our understanding of their involvement in the regulation of adipogenic and osteogenic differentiation, ultimately paving the way for novel therapeutic strategies and insights into regenerative medicine.
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Affiliation(s)
- Bernardo Bonilauri
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Annanda Lyra Ribeiro
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
| | - Lucía Spangenberg
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay;
| | - Bruno Dallagiovanna
- Stem Cell Basic Biology Laboratory (LABCET), Carlos Chagas Institute—Fiocruz/PR, Curitiba 81350-010, PR, Brazil;
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Liu Y, Xing K, Ao H, Zhang F, Zhao X, Liu H, Shi Y, Yu Y, Wang C. Competing endogenous RNA network construction based on long non-coding RNAs, microRNAs, and mRNAs related to fat deposition in Songliao black swine. Anim Genet 2023; 54:132-143. [PMID: 36596449 DOI: 10.1111/age.13283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023]
Abstract
China has a long history of pig breeding and a number of local breeds. The Songliao Black pig, bred in China in 2009, shows high variation in backfat thickness and therefore is well-suited to fat deposition research. Fat deposition is a complex trait, and the underlying regulatory factors are not fully characterized. In this study, the molecular basis of fat deposition traits was evaluated by comparisons between three individuals with extremely high-backfat thickness and three with extremely low-backfat thickness selected from 53 gilts. Subcutaneous adipose tissues of the back were collected for strand-specific library RNA sequencing (RNA-seq) and small RNA-seq. We identified 13 184 mRNAs, 2046 long non-coding (lnc)RNAs, and 494 micro (mi)RNAs by high-throughput sequencing. Furthermore, we detected 150 differentially expressed mRNAs, 66 differentially expressed lncRNAs, and eight differentially expressed miRNAs. A functional enrichment analysis indicated that these genes are involved in multiple fat metabolism-related pathways, including positive regulation of fat cell differentiation, and fat digestion and absorption. We used various algorithms (miRanda, TargetScan, and RNAhybrid) to predict targeting relationships and constructed a competing endogenous RNA network containing seven lncRNAs, three miRNAs, and six mRNAs. All these genes were differentially expressed between the extremely high and low backfat thickness groups or enriched in pathways related to fat metabolism. Our results provide insight into the regulatory mechanisms by which non-coding RNAs and their target genes influence backfat deposition in pigs. Furthermore, our newly constructed competing endogenous RNA (lncRNA-miRNA-mRNA) network provides a basis for further exploration of fat deposition traits and non-coding RNA functions.
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Affiliation(s)
- Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hong Ao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xitong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huatao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Chang W, Wang M, Zhang Y, Yu F, Hu B, Goljanek-Whysall K, Li P. Roles of long noncoding RNAs and small extracellular vesicle-long noncoding RNAs in type 2 diabetes. Traffic 2022; 23:526-537. [PMID: 36109347 PMCID: PMC9828071 DOI: 10.1111/tra.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/17/2022] [Accepted: 09/14/2022] [Indexed: 01/20/2023]
Abstract
The prevalence of a high-energy diet and a sedentary lifestyle has increased the incidence of type 2 diabetes (T2D). T2D is a chronic disease characterized by high blood glucose levels and insulin resistance in peripheral tissues. The pathological mechanism of this disease is not fully clear. Accumulated evidence has shown that noncoding RNAs have an essential regulatory role in the progression of diabetes and its complications. The roles of small noncoding RNAs, such as miRNAs, in T2D, have been extensively investigated, while the function of long noncoding RNAs (lncRNAs) in T2D has been unstudied. It has been reported that lncRNAs in T2D play roles in the regulation of pancreatic function, peripheral glucose homeostasis and vascular inflammation. In addition, lncRNAs carried by small extracellular vesicles (sEV) were shown to mediate communication between organs and participate in diabetes progression. Some sEV lncRNAs derived from stem cells are being developed as potential therapeutic agents for diabetic complications. In this review, we summarize the current knowledge relating to lncRNA biogenesis, the mechanisms of lncRNA sorting into sEV and the regulatory roles of lncRNAs and sEV lncRNAs in diabetes. Knowledge of lncRNAs and sEV lncRNAs in diabetes will aid in the development of new therapeutic drugs for T2D in the future.
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Affiliation(s)
- Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Man Wang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
| | - Bin Hu
- The Institute of Medical Sciences (IMS), School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Katarzyna Goljanek-Whysall
- Department of Physiology, Nursing and Health Sciences, College of Medicine, National University of Ireland, Galway, Ireland
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital, College of Medicine, Qingdao University, Qingdao, China
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Lu Y, Ying D, Tian Y, Ruan Y, Cheng G, Lv K, Zhou X, Han S. LncRNA LINC01857 drives pancreatic adenocarcinoma progression via modulating miR-19a-3p/SMOC2. Clinics (Sao Paulo) 2022; 77:100047. [PMID: 35662010 PMCID: PMC9168480 DOI: 10.1016/j.clinsp.2022.100047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Emerging evidence has demonstrated that LINC01857 exerts a pivotal function in many cancers. However, its function in Pancreatic Ductal Adenocarcinoma (PDAC) still remains unclear. This study was designed to investigate the regulatory character of LINC01857 in PDAC. METHODS Bioinformatic tools and databases were used to seek potential miRNAs and mRNAs. Gene expression was evaluated by Reverse Transcription quantitative real-time Polymerase Chain Reaction (RT-qPCR), and western blot was used for protein level detection. A subcellular fraction assay was done to ascertain the location of LINC01857 in PANC-1 and BxPC-3 human pancreatic cancer cells. CCK-8, EdU, wound healing and Transwell assays were performed to inquire into the influence of LINC01857, and SPARC -related Modular Calcium-binding protein-2 (SMOC2) on cell viability, proliferation, migration, and invasion, respectively. The interaction between LINC01857 and its downstream genes was explored by RNA immunoprecipitation and luciferase reporter assays. RESULTS LINC01857 levels were significantly elevated in PDAC. Knockdown of LINC01857 significantly restrained the proliferation, migration, invasion, and Epithelial-Mesenchymal Transition (EMT) process of PDAC cells. MiR-19a-3p was a downstream target of LINC01857, and miR-19a-3p levels were significantly decreased in PDAC cells. In addition, SMOC2 expression had a negative correlation with that of miR-19a-3p, and SMOC2 was a downstream target of miR-19a-3p. Furthermore, SMOC2 upregulation partially abolished the inhibitive influence of LINC01857 downregulation on cell proliferation, migration, invasion, and the EMT process. CONCLUSION LINC01857 promotes malignant phenotypes of PDAC cells via upregulation of SMOC2 by interacting with miR-19a-3p.
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Affiliation(s)
- Yeting Lu
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Dongjian Ying
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Yuan Tian
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Yi Ruan
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Gong Cheng
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Kaiji Lv
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Xinhua Zhou
- Department of General Surgery, The Affiliated Lihuili Hospital, Ningbo University(Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China
| | - Shuo Han
- Department of Healthcare Security and Price Management, The Affiliated Lihuili Hospital, Ningbo University (Ningbo Medical Center Lihuili Hospital), Ningbo 315100, Zhejiang, China.
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Liu X, Bai Y, Cui R, He S, Zhao X, Wu K, Fang M. Sus_circPAPPA2 Regulates Fat Deposition in Castrated Pigs through the miR-2366/GK Pathway. Biomolecules 2022; 12:biom12060753. [PMID: 35740877 PMCID: PMC9220968 DOI: 10.3390/biom12060753] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023] Open
Abstract
CircRNAs play an important role in fat deposition, and testosterone-deficient boars exhibit significantly increased fat deposition; however, the mechanism by which testosterone regulates fat deposition through circRNAs remains unclear. In this study, circRNA-seq of backfat and abdominal fat from castrated and intact full-sib Yorkshire pigs was performed. The GO and KEGG enrichment analyses revealed that the host genes of the dorsal DE circRNAs were mainly involved in fatty acid transport, while in abdominal tissues, these genes were mainly involved in adipogenesis and inflammation. The interaction among sus_circPAPPA2, ssc-miR-2366 and GK was verified by dual fluorescence experiments and in porcine preadipocytes. The overexpression of sus_circPAPPA2 significantly inhibited the differentiation of preadipocytes. The expression of sus_circPAPPA2 was increased after adding 100 nM of testosterone, and preadipocyte differentiation was significantly inhibited. Testosterone can affect preadipocyte differentiation by upregulating the expression of sus_circPAPPA2, sponging miR-2366 and regulating the expression of genes, such as GK. These results indicate that testosterone can regulate the expression of adipocyte differentiation- and lipid metabolism-related genes by regulating the expression of circRNA, and ceRNA networks are different in the testosterone regulation of adipose deposition in different parts. This study provides basic data enhancing the understanding of the interaction between the hormone environment and mir-2366/GK to regulate trait performance in pigs.
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Affiliation(s)
- Ximing Liu
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China;
| | - Ran Cui
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
| | - Shuaihan He
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
| | - Keliang Wu
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
| | - Meiying Fang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (R.C.); (S.H.); (X.Z.); (K.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
- Correspondence: ; Tel./Fax: +86-10-62734943
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6
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He C, Wang Y, Zhu J, Li Y, Chen J, Lin Y. Integrative Analysis of lncRNA-miRNA-mRNA Regulatory Network Reveals the Key lncRNAs Implicated Potentially in the Differentiation of Adipocyte in Goats. Front Physiol 2022; 13:900179. [PMID: 35600305 PMCID: PMC9117728 DOI: 10.3389/fphys.2022.900179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
Goats are popular in China because of their superior meat quality, delicate flesh, and unique flavor. Long noncoding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation of gene expression. However, the effects of lncRNAs on adipocyte differentiation in goat has not been fully elucidated yet. In this investigation, we performed RNA-Seq analysis of intramuscular and subcutaneous adipocytes from Jianzhou Daer goat before and after differentiation, including both intramuscular preadipocytes (IMPA) vs. intramuscular adipocytes (IMA) and subcutaneous preadipocytes (SPA) vs. subcutaneous adipocytes (SA). A total of 289.49 G clean reads and 12,519 lncRNAs were obtained from 20 samples. In total, 3,733 differentially expressed RNAs (182 lncRNAs and 3,551 mRNAs) were identified by pairwise comparison. There were 135 differentially expressed lncRNAs (DELs) specific to intramuscular adipocytes, 39 DELs specific to subcutaneous adipocytes, and 8 DELs common to both adipocytes in these 182 DELs. Some well-known and novel pathways associated with preadipocyte differentiation were identified: fat acid metabolism, TGF-beta signaling pathway and PI3K-Akt signaling pathway. By integrating miRNA-seq data from another study, we also identified hub miRNAs in both types of fat cells. Our analysis revealed the unique and common lncRNA-miRNA-mRNA networks of two kinds of adipocytes. Several lncRNAs that regulate potentially goat preadipocyte differentiation were identified, such as XR_001918 647.1, XR_001917728.1, XR_001297263.2 and LNC_004191. Furthermore, our findings from the present study may contribute to a better understanding of the molecular mechanisms underlying in goat meat quality and provide a theoretical basis for further goat molecular breeding.
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Affiliation(s)
- Changsheng He
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yanyan Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Juan Chen
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- College of Food Science and Technology, Southwest Minzu University, Chengdu, China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu, China
- *Correspondence: Yaqiu Lin,
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MicroRNA Expression Analysis of Mice Retinas with Oxygen-Induced Retinopathy by RNA Sequencing. J Ophthalmol 2022; 2022:9738068. [PMID: 35282140 PMCID: PMC8913133 DOI: 10.1155/2022/9738068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/31/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose. To characterize the microRNA (miRNA) expression profiles in the retinas of mice with oxygen-induced retinopathy by RNA sequencing and to ascertain miRNAs associated with retinal neovascularization. Methods. Retina samples were obtained from 3 groups (6 retinas/group) of OIR mice and normal mice at P17. RNA was isolated from 24 retina samples and then detected on an Illumina HiSeq. Twelve retina samples were used for quantitative polymerase chain reaction to validate the RNA sequencing. Bioinformatics analyses were performed. Result. The RNA sequence showed that 565 miRNAs were detected in the retina of OIR mice and 583 miRNAs in the retina of normal control mice. A total of 553 miRNAs were expressed in both groups. Thirty-eight miRNAs showed altered expression in both groups (
). Compared with the control group, 2 miRNAs were significantly upregulated in the OIR group, while 36 miRNAs were significantly downregulated. Meanwhile, 2 candidate miRNAs (miR-181a-5p and miR-21a-5p) with significant differences in miRNA expression (
) were selected for validation. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to confirm the relative expression of the two miRNAs. Bioinformatics analyses showed that pathways involved in ischemic retinopathy (such as TGF-β, Ras, Hippo, PI3K-Akt, VEGF, and HIF-1 signaling pathways) were enriched. Conclusions. Our study provided an overall view of miRNA profiling in the OIR retina. These miRNA profiles provide a valuable framework for the potential therapy of retinal angiogenesis.
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De la Fuente-Hernandez MA, Sarabia-Sanchez MA, Melendez-Zajgla J, Maldonado-Lagunas V. Role of lncRNAs into Mesenchymal Stromal Cell Differentiation. Am J Physiol Cell Physiol 2022; 322:C421-C460. [PMID: 35080923 DOI: 10.1152/ajpcell.00364.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Currently, findings support that 75% of the human genome is actively transcribed, but only 2% is translated into a protein, according to databases such as ENCODE (Encyclopedia of DNA Elements) [1]. The development of high-throughput sequencing technologies, computational methods for genome assembly and biological models have led to the realization of the importance of the previously unconsidered non-coding fraction of the genome. Along with this, noncoding RNAs have been shown to be epigenetic, transcriptional and post-transcriptional regulators in a large number of cellular processes [2]. Within the group of non-coding RNAs, lncRNAs represent a fascinating field of study, given the functional versatility in their mode of action on their molecular targets. In recent years, there has been an interest in learning about lncRNAs in MSC differentiation. The aim of this review is to address the signaling mechanisms where lncRNAs are involved, emphasizing their role in either stimulating or inhibiting the transition to differentiated cell. Specifically, the main types of MSC differentiation are discussed: myogenesis, osteogenesis, adipogenesis and chondrogenesis. The description of increasingly new lncRNAs reinforces their role as players in the well-studied field of MSC differentiation, allowing a step towards a better understanding of their biology and their potential application in the clinic.
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Affiliation(s)
- Marcela Angelica De la Fuente-Hernandez
- Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio de Epigenética, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Miguel Angel Sarabia-Sanchez
- Facultad de Medicina, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Wu Q, Yang H, Tai R, Li C, Xia T, Liu Y, Sun C. Lnc-hipk1 inhibits mouse adipocyte apoptosis as a sponge of miR-497. Biofactors 2022; 48:135-147. [PMID: 34856026 DOI: 10.1002/biof.1807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/02/2021] [Indexed: 11/06/2022]
Abstract
Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long noncoding RNAs (lncRNA), and circular RNAs are closely related to the biological processes related to obesity. As a miRNA that widely present in different cell types, miR497 is proved to be involved in cell development. However, research on the role of miR-497 as a key factor in regulating the development of adipocytes is still in gap. The role of miR-497 in the apoptosis and proliferation of mouse-derived adipocytes was detected by RNA-seq analysis, RT-qPCR, Western blot, immunofluorescence, and dual-luciferase reporter assay. Using miR-497 mimics to treat 3T3-L1 cells, we found that miR-497 targeted Bcl-2 to promote adipocyte apoptosis through the mitochondrial pathway, and this effect was consistent in the apoptosis model composed of palmitic acid (PA) and hydrogen peroxide (H2 O2 ). LncRNA homeodomain-interacting protein kinase 1 (lnc-hipk1) sponged miR-148b to weaken its silencing of Bcl-2, forming the competitive endogenous RNAs (CeRNAs) regulatory network. Furthermore, overexpression of lnc-hipk1 inhibited the apoptosis of adipocytes by targeting miR-497/Bcl-2. Co-treatment of miR-497 and lnc-hipk1 showed that lnc-hipk1 reversed the apoptosis of adipocytes caused by miR-497 overexpression. And in vivo experiments further confirmed that this effect was also achieved by the CeRNA system of lnc-hipk1/miR-497/Bcl-2. In summary, lnc-hipk1 targets miR-497/Bcl-2 to regulate adipocyte apoptosis through the mitochondrial pathway. This research enriches the research content of ncRNAs and CeRNA in adipocyte development, and provides new targets for the treatment of obesity and other metabolic syndromes.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Department of Pathophysiology, Medical College, Qinghai University, Xining, China
| | - Hong Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruiqing Tai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chaowei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tianyu Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongnian Liu
- Department of Pathophysiology, Medical College, Qinghai University, Xining, China
| | - Chao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Alipoor B, Nikouei S, Rezaeinejad F, Malakooti-Dehkordi SN, Sabati Z, Ghasemi H. Long non-coding RNAs in metabolic disorders: pathogenetic relevance and potential biomarkers and therapeutic targets. J Endocrinol Invest 2021; 44:2015-2041. [PMID: 33792864 DOI: 10.1007/s40618-021-01559-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND It has been suggested that dysregulation of long non-coding RNAs (lncRNAs) could be associated with the incidence and development of metabolic disorders. AIM Accordingly, this narrative review described the molecular mechanisms of lncRNAs in the development of metabolic diseases including insulin resistance, diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), cirrhosis, and coronary artery diseases (CAD). Furthermore, we investigated the up-to-date findings on the association of deregulated lncRNAs in the metabolic disorders, and potential use of lncRNAs as biomarkers and therapeutic targets. CONCLUSION LncRNAs/miRNA/regulatory proteins axis plays a crucial role in progression of metabolic disorders and may be used in development of therapeutic and diagnostic approaches.
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Affiliation(s)
- B Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - S Nikouei
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | - F Rezaeinejad
- Department of Biochemistry, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Z Sabati
- MSc student of Hematology, Student Research Committee, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - H Ghasemi
- Abadan Faculty of Medical Sciences, Abadan, Iran.
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11
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Yi X, He Z, Tian T, Kou Z, Pang W. LncIMF2 promotes adipogenesis in porcine intramuscular preadipocyte through sponging MiR-217. Anim Biotechnol 2021; 34:268-279. [PMID: 34346296 DOI: 10.1080/10495398.2021.1956509] [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] [Indexed: 01/22/2023]
Abstract
Intramuscular fat is positively related to meat quality including tenderness, flavor, and juiciness. Long noncoding RNA (LncRNA) plays a vital role in regulating adipogenesis. However, it is largely unknown about lncRNAs associated with porcine intramuscular adipocyte adipogenesis. In the present study, we focus on a novel LncRNA, which is named lncIMF2, associated with adipogenesis by our previous RNA-sequence analysis and bioinformatics analysis. We demonstrated LncIMF2 knockdown inhibited the proliferation of porcine intramuscular adipocytes while expression of cell cycle-related genes was decreased. Besides, we found LncIMF2 knockdown inhibited expression of adipogenic differentiation marker genes including PPARγ (Peroxisome proliferator-activated reporter gamma) and ATGL (Adipose triglyceride lipase). Similarly, overexpression of LncIMF2 promotes proliferation and differentiation of porcine intramuscular preadipocytes. Moreover, we proved that IncIMF2 acts as a molecular sponge for MicroRNA-217 (miR-217), which has been found associated with adipogenesis, thereby affecting the expression of the miR-217 target gene. Collectively, our findings will contribute to a deeper understanding of the role of LncRNA in pig IMF deposition for the improvement of meat quality.
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Affiliation(s)
- XuDong Yi
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - ZhaoZhao He
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - TingTing Tian
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - ZhongYun Kou
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - WeiJun Pang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
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12
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Zhang B, Xu S, Liu J, Xie Y, Xiaobo S. Long Noncoding RNAs: Novel Important Players in Adipocyte Lipid Metabolism and Derivative Diseases. Front Physiol 2021; 12:691824. [PMID: 34168572 PMCID: PMC8217837 DOI: 10.3389/fphys.2021.691824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 01/08/2023] Open
Abstract
Obesity, a global public health issue, is characterized by excessive adiposity and is strongly related to some chronic diseases including cardiovascular diseases and diabetes. Extra energy intake-induced adipogenesis involves various transcription factors and long noncoding RNAs (lncRNAs) that control lipogenic mRNA expression. Currently, lncRNAs draw much attention for their contribution to adipogenesis and adipose tissue function. Increasing evidence also manifests the pivotal role of lncRNAs in modulating white, brown, and beige adipose tissue development and affecting the progression of the diseases induced by adipose dysfunction. The aim of this review is to summarize the roles of lncRNAs in adipose tissue development and obesity-caused diseases to provide novel drug targets for the treatment of obesity and metabolic diseases.
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Affiliation(s)
- Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Saijun Xu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jinyan Liu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Xie
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sun Xiaobo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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13
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Zhao J, Song Y, Zeng Y, Chen L, Yan F, Chen A, Wu B, Wang Y. Improvement of hyperlipidemia by aerobic exercise in mice through a regulatory effect of miR-21a-5p on its target genes. Sci Rep 2021; 11:11966. [PMID: 34099844 PMCID: PMC8184843 DOI: 10.1038/s41598-021-91583-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/25/2021] [Indexed: 11/09/2022] Open
Abstract
Hyperlipidemia is a risk factor for cardiovascular disease, and miR-21a-5p plays an important role in the occurrence and progression of hyperlipidemia. Here, we aimed to investigate the mechanism of aerobic exercise improved hyperlipidemia through enhancing miR-21a-5p expression. In this study, high-fat/high-cholesterol diet mice received 8 weeks of aerobic exercise intervention, then we collected plasma and liver samples, we found that there had a notable improvement in weight gain, blood lipid level, and liver steatosis in hyperlipidemia mice after 8 weeks of aerobic exercise intervention. Besides, aerobic exercise significantly up-regulated the expression of miR-21a-5p and provoked favorable changes in the expression of target genes. Knockdown of miR-21a-5p resulted in dysregulation of lipid metabolism and increased expression of FABP7, HMGCR, ACAT1, and OLR1. While aerobic exercise could alleviate miR-21a-5p knock-down induced lipid metabolism disorder. Taken together, these results demonstrated that aerobic exercise improved hyperlipidemia through miR-21a-5p-induced inhibition of target genes FABP7, HMGCR, ACAT1, and OLR1.
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Affiliation(s)
- Jinfeng Zhao
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Yicun Song
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Yu Zeng
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Longchang Chen
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Feng Yan
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Anping Chen
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China
| | - Baoai Wu
- School of Physical Education, Shanxi University, Taiyuan, Shanxi, China.
| | - Yaxin Wang
- Department of Exercise Physiology, Beijing Sports University, Beijing, China.
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14
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Du G, Zhang Y, Hu S, Zhou X, Li Y. Non-coding RNAs in exosomes and adipocytes cause fat loss during cancer cachexia. Noncoding RNA Res 2021; 6:80-85. [PMID: 33997537 PMCID: PMC8081875 DOI: 10.1016/j.ncrna.2021.04.001] [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: 02/19/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer Cachexia (CC) is a disease that changes various metabolisms in human body. Fat metabolism is significantly affected in CC, leading to fat loss. Non-coding RNAs (ncRNAs) in adipocytes and exosomes secreted by tumor play an important role in fat loss. However, there is no related reviews summarizing how ncRNAs contribute to fat loss during CC. This review screens recent articles to summarize how ncRNAs are packaged, transported in exosomes, and play the role in fat loss. Not only does this review summarize the mechanisms, we also point out the research orientations in the future.
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Affiliation(s)
| | | | - Shoushan Hu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Xueer Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yi Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
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15
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Lai S, Du K, Shi Y, Li C, Wang G, Hu S, Jia X, Wang J, Chen S. Long Non-Coding RNAs in Brown Adipose Tissue. Diabetes Metab Syndr Obes 2020; 13:3193-3204. [PMID: 32982350 PMCID: PMC7507876 DOI: 10.2147/dmso.s264830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022] Open
Abstract
Obesity has become a widespread disease that is harmful to human health. Fat homeostasis is essentially maintained by fat accumulation and energy expenditure. Studies on brown adipose tissue (BAT) represent a promising opportunity to identify a pharmaceutical intervention against obesity through increased energy expenditure. Long non-coding RNAs (lncRNAs) were thought to be critical regulators in a variety of biological processes. Recent studies have revealed that lncRNAs, including ones that are BAT-specific, conserved, and located at key protein-coding genes, function in brown adipogenesis, white adipose browning (ie, beige adipogenesis), and brown thermogenesis. In this review, we describe lncRNA properties and highlight functional lncRNAs in these biological processes, with the goal of establishing links between lncRNAs and BAT. Based on the advances of lncRNAs in the regulation of BAT, we discussed the advantages of potential lncRNA-based obesity drugs. Further BAT lncRNA-based drug development may provide new exciting approaches to defend obesity by regulation of fat homeostasis.
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Affiliation(s)
- Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Cao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Guoze Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang550025, People’s Republic of China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu611130, People’s Republic of China
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16
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Chen L, Ren P, Zhang Y, Gong B, Yu D, Sun X. Long non‑coding RNA GAS5 increases the radiosensitivity of A549 cells through interaction with the miR‑21/PTEN/Akt axis. Oncol Rep 2020; 43:897-907. [PMID: 32020207 PMCID: PMC7041238 DOI: 10.3892/or.2020.7467] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/19/2019] [Indexed: 12/27/2022] Open
Abstract
Radioresistance hinders the therapeutic outcomes of radiotherapy in non-small cell lung cancer (NSCLC). Although long non-coding RNAs (lncRNAs) have been demonstrated to participate in the regulation of multiple cell behaviors, whether they can modulate the radiosensitivity of NSCLC and the underlying molecular mechanisms have not been well investigated. In the present study, it was revealed that NSCLC NCI-H460 cells were more sensitive to ionizing radiation (IR) than A549 cells. Using the RNA-Seq method, four highly differentially expressed lncRNAs were identified, including the growth arrest-specific transcript 5 (GAS5), syntaxin binding protein 5 antisense RNA 1 (STXBP5-AS1), metastasis associated lung adenocarcinoma transcript 1 (MALAT1) and X-inactive specific transcript (XIST), which were predicted to play roles in the acquisition of radiosensitivity. Using real-time quantitative PCR (qPCR), it was demonstrated that lncRNA GAS5 was significantly upregulated in NCI-H460 cells but not in A549 cells during IR. Mechanistically, it was demonstrated that overexpression of lncRNA GAS5 decreased the level of microRNA-21 (miR-21). Overexpression of lncRNA GAS5 or suppression of miR-21 markedly increased the IR-induced cell apoptosis of A549 cells. It was also demonstrated that overexpression of lncRNA GAS5 increased PTEN expression and suppressed Akt phosphorylation through the modulation of miR-21. Notably, it was revealed that IR enhanced the interaction between lncRNA GAS5 and the miR-21/PTEN/Akt axis. In summary, the present findings revealed that lncRNA GAS5 has a radiosensitization effect on NSCLC, indicating the potential application of lncRNA GAS5 in NSCLC radiotherapy.
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Affiliation(s)
- Li Chen
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Department of Oral Radiology, School and Hospital of Stomatology, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ping Ren
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yandong Zhang
- Department of Rheumatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Baijuan Gong
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Department of Orthodontics, School and Hospital of Stomatology, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Dehai Yu
- The Laboratory of Cancer Precision Medicine of The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Xiguang Sun
- Hand Surgery Department, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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17
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Zhang TN, Wang W, Yang N, Huang XM, Liu CF. Regulation of Glucose and Lipid Metabolism by Long Non-coding RNAs: Facts and Research Progress. Front Endocrinol (Lausanne) 2020; 11:457. [PMID: 32765426 PMCID: PMC7381111 DOI: 10.3389/fendo.2020.00457] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/10/2020] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a type of non-coding RNA with a length that exceeds 200 nucleotides. Previous studies have shown that lncRNAs play an important role in the pathogenesis of various diseases. Research in both animal models and humans has begun to unravel the profound complexity of lncRNAs and demonstrated that lncRNAs exert direct effects on glucose and lipid metabolism both in vivo and in vitro. Such research has elucidated the regulatory role of lncRNAs in glucose and lipid metabolism in human disease. lncRNAs mediate glucose and lipid metabolism under physiological and pathological conditions and contribute to various metabolism disorders. This review provides an update on our understanding of the regulatory role of lncRNAs in glucose and lipid metabolism in various diseases. As our understanding of the function of lncRNAs improves, the future is promising for the development of new diagnostic biomarkers that utilize lncRNAs and treatments that target lncRNAs to improve clinical outcomes.
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Affiliation(s)
- Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Tie-Ning Zhang
| | - Wei Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin-Mei Huang
- Department of Endocrinology, the Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
- Department of Obstetrics and Gynecology, Yale University School of Medicine, New Haven, CT, United States
- Xin-Mei Huang
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Chun-Feng Liu
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18
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Chang H, Cai Z, Roberts TM. The Mechanisms Underlying PTEN Loss in Human Tumors Suggest Potential Therapeutic Opportunities. Biomolecules 2019; 9:biom9110713. [PMID: 31703360 PMCID: PMC6921025 DOI: 10.3390/biom9110713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/13/2022] Open
Abstract
In this review, we will first briefly describe the diverse molecular mechanisms associated with PTEN loss of function in cancer. We will then proceed to discuss the molecular mechanisms linking PTEN loss to PI3K activation and demonstrate how these mechanisms suggest possible therapeutic approaches for patients with PTEN-null tumors.
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Affiliation(s)
- Hyeyoun Chang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (H.C.); (Z.C.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
- KIST-DFCI On-Site Lab, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhenying Cai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (H.C.); (Z.C.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Thomas M. Roberts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (H.C.); (Z.C.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
- Correspondence: ; Tel.: +1-617-632-3049
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19
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Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes. Genes (Basel) 2019; 10:genes10100795. [PMID: 31614854 PMCID: PMC6826404 DOI: 10.3390/genes10100795] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence indicates that long noncoding RNAs (lncRNAs) play important roles in the regulation of cell differentiation by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA and the lncRNA-associated ceRNA network involved in adipogenic differentiation of chicken preadipocytes remain elusive. Here, we first constructed the chicken preadipocyte in vitro induction model. Then, we identified differentially expressed lncRNAs (DELs), miRNAs (DEMis), and mRNAs (DEMs) between differentiated and undifferentiated preadipocytes. Furthermore, we constructed the lncRNA associated ceRNA network by gene expression correlation analysis and target prediction of DELs, DEMis, and DEMs. Finally, we determined twelve candidate lncRNA-miRNA-mRNA interactions from the lncRNA associated ceRNA network. Eight out of the twelve interactions were validated by RT-qPCR, indicating their potential role in the regulation of chicken preadipocytes differentiation. Among the eight interactions, TCONS_00026544-gga-miR-128-1-5p-RASD1, TCONS_00055280-gga-miR-135a-5p-JAM3, TCONS_00055280-gga-miR-135a-5p-GPR133, TCONS_00055280-gga-miR-135a-5p-CLDN1, and TCONS_00055280-gga-miR-135a-5p-TMEM123 may promote adipogenic differentiation of chicken preadipocytes while TCONS_00057272-gga-miR-146a-3p-FOXO6, TCONS_00057242-gga-miR-6615-3p-FOXO6, and TCONS_00057242-gga-miR-6615-3p-ENSGALT00000043224 have the opposite effects. Our results not only provide novel insights into ceRNA roles of lncRNAs in chicken preadipocytes differentiation and but also contribute to a better understanding of chicken fat deposition.
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20
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Goustin AS, Thepsuwan P, Kosir MA, Lipovich L. The Growth-Arrest-Specific ( GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers. Noncoding RNA 2019; 5:ncrna5030046. [PMID: 31533355 PMCID: PMC6789762 DOI: 10.3390/ncrna5030046] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading frames (smORFs) that may encode short proteins. Any given lncRNA may have more than one of these functions. This review focuses on one fascinating case—the growth-arrest-specific (GAS)-5 gene, encoding a complicated repertoire of alternatively-spliced lncRNA isoforms. GAS5 is also a host gene of numerous small nucleolar (sno) RNAs, which are processed from its introns. Publications about this lncRNA date back over three decades, covering its role in cell proliferation, cell differentiation, and cancer. The GAS5 story has drawn in contributions from prominent molecular geneticists who attempted to define its tumor suppressor function in mechanistic terms. The evidence suggests that rodent Gas5 and human GAS5 functions may be different, despite the conserved multi-exonic architecture featuring intronic snoRNAs, and positional conservation on syntenic chromosomal regions indicating that the rodent Gas5 gene is the true ortholog of the GAS5 gene in man and other apes. There is no single answer to the molecular mechanism of GAS5 action. Our goal here is to summarize competing, not mutually exclusive, mechanistic explanations of GAS5 function that have compelling experimental support.
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Affiliation(s)
- Anton Scott Goustin
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | | | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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21
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Ghasemi A, Hashemy SI, Azimi-Nezhad M, Dehghani A, Saeidi J, Mohtashami M. The cross-talk between adipokines and miRNAs in health and obesity-mediated diseases. Clin Chim Acta 2019; 499:41-53. [PMID: 31476303 DOI: 10.1016/j.cca.2019.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Multiple studies have revealed a direct correlation between obesity and the development of multiple comorbidities, including metabolic diseases, cardiovascular disorders, chronic inflammatory disease, and cancers. However, the molecular mechanism underlying the link between obesity and the progression of these diseases is not completely understood. Adipokines are factors that are secreted by adipocytes and play a key role in whole body homeostasis. Collaboratively, miRNAs are suggested to have key functions in the development of obesity and obesity-related disorders. Based on recently emerging evidence, obesity leads to the dysregulation of both adipokines and obesity-related miRNAs. In the present study, we described the correlations between obesity and its related diseases that are mediated by the mutual regulatory effects of adipokines and miRNAs. METHODS We reviewed current knowledge of the modulatory effects of adipokines on miRNAs activity and their relevant functions in pathological conditions and vice versa. RESULTS Our research reveals the ability of adipokines and miRNAs to control the expression and activity of the other class of molecules, and their effects on obesity-related diseases. CONCLUSIONS This study may help researchers develop a roadmap for future investigations and provide opportunities to develop new therapeutic and diagnostic methods for treating obesity-related diseases.
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Affiliation(s)
- Ahmad Ghasemi
- Non-communicable Disease Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran.
| | - Seyed Isaac Hashemy
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohsen Azimi-Nezhad
- Non-communicable Disease Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran; UMR INSERM U 1122, IGE-PCV, Interactions Gène-Environment en Physiopathologie Cardiovascular Université de Lorraine, France
| | - Alireza Dehghani
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Jafar Saeidi
- Department of Physiology, School of Basic Science, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Mahnaz Mohtashami
- Department of Biology, School of Basic Science, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
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22
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Li P, Chen X, Chang X, Tang T, Qi K. A preliminary study on the differential expression of long noncoding RNAs and messenger RNAs in obese and control mice. J Cell Biochem 2019; 121:1126-1143. [PMID: 31464023 DOI: 10.1002/jcb.29348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/13/2019] [Indexed: 12/21/2022]
Abstract
Obesity has become one of the public health problems that threatens children's health, but its specific etiology and pathogenesis are still unclear. Recently, many long noncoding RNAs (lncRNAs) have been shown to be involved in the occurrence of obesity. However, their roles are still poorly understood. Thus, the aim of this study was to discover the profiles of the lncRNAs and messenger RNAs (mRNAs) altered in obesity. Epididymal fat samples were collected from mice fed with control and high-fat diets (HFD) for 16 weeks to investigate the differentially expressed lncRNAs and mRNAs by lncRNA microarray, after which seven lncRNAs and nine mRNAs were validated using reverse-transcription polymerase chain reaction (RT-PCR). Bioinformatics analysis and predictions were used to determine the potential biofunctions of these differentially expressed lncRNAs. Then a coexpression network was constructed to determine the transcriptional regulatory relationship of the differentially expressed lncRNAs and mRNAs between the control and HFD groups. The body weight of the HFD group was much higher than that of the control group, as a result of the increased energy intake. In total, 8421 differentially expressed lncRNAs and 6840 mRNAs were profiled using the lncRNAs microarray. Bioinformatics predictions and the coexpression network all indicated that the occurrence of obesity was attributed to those differentially expressed lncRNAs and mRNAs associated with energy metabolism, cell differentiation, and oxidative phosphorylation. The expression levels of Cyp2e1, Atp5b, Hibch, Cnbp, Frmd6, Ptchd3, ENSMUST00000155948, AK140152, ENSMUST00000135194, and ENSMUST00000180861 were significantly different between the control and HFD groups. All these Results suggested that obesity was partially attributed to those lncRNAs associated with energy metabolism, cell differentiation, and oxidative phosphorylation.
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Affiliation(s)
- Ping Li
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaoyu Chen
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xuelian Chang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tiantian Tang
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kemin Qi
- Laboratory of Nutrition and Development, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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23
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Wei S, Li A, Zhang L, Du M. GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12. J Anim Sci 2019; 97:2644-2657. [PMID: 30959518 DOI: 10.1093/jas/skz114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/05/2019] [Indexed: 12/22/2022] Open
Abstract
Sequencing technology, especially next-generation RNA sequencing, has greatly facilitated the identification and annotation of long noncoding RNAs (lncRNAs). In mammals, a large number of lncRNAs have been identified, which regulate various biological processes. An increasing number of lncRNAs have been identified which could function as key regulators of adipogenesis (adipocyte formation), a key step of the development of adipose tissue. Because proper adipose tissue development is a key factor affecting animal growth efficiency, lean/fat ratio, and meat quality, summarizing the roles and recent advances of lncRNAs in adipogenesis is needed in order to develop strategies to effectively manage fat deposition. In this review, we updated lncRNAs contributed to the regulation of adipogenesis, focusing on their roles in fat development of farm animals.
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Affiliation(s)
- Shengjuan Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Anning Li
- Department of Animal Sciences, Washington State University, Pullman, WA
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA
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24
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Sun L, Lin JD. Function and Mechanism of Long Noncoding RNAs in Adipocyte Biology. Diabetes 2019; 68:887-896. [PMID: 31010880 PMCID: PMC6477904 DOI: 10.2337/dbi18-0009] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Abstract
The last two decades have witnessed an explosion of interest in adipocyte biology, coinciding with the upsurge of obesity and metabolic syndrome. Now we have new perspectives on the distinct developmental origins of white, brown, and beige adipocytes and their role in metabolic physiology and disease. Beyond fuel metabolism, adipocytes communicate with the immune system and other tissues by releasing diverse paracrine and endocrine factors to orchestrate adipose tissue remodeling and maintain systemic homeostasis. Significant progress has been made in delineating the regulatory networks that govern different aspects of adipocyte biology. Here we provide an overview on the emerging role of long noncoding RNAs (lncRNAs) in the regulation of adipocyte development and metabolism and discuss the implications of the RNA-protein regulatory interface in metabolic control.
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Affiliation(s)
- Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI
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25
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An T, Zhang J, Lv B, Liu Y, Huang J, Lian J, Wu Y, Gao S, Jiang G. Salvianolic acid B plays an anti-obesity role in high fat diet-induced obese mice by regulating the expression of mRNA, circRNA, and lncRNA. PeerJ 2019; 7:e6506. [PMID: 30842902 PMCID: PMC6397762 DOI: 10.7717/peerj.6506] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Background Adipose tissue plays a central role in obesity-related metabolic diseases such as type 2 diabetes. Salvianolic acid B (Sal B), a water-soluble ingredient derived from Salvia miltiorrhiza, has been shown to reduce obesity and obesity-related metabolic diseases by suppressing adipogenesis. However, the role of Sal B in white adipose tissue (WAT) is not yet clear. Methods Illumina Hiseq 4000 was used to study the effects of Sal B on the expression of long non-coding RNA (lncRNA) and circular RNA (circRNA) in epididymal white adipose tissue induced by a high fat diet in obese mice. Results RNA-Seq data showed that 234 lncRNAs, 19 circRNAs, and 132 mRNAs were differentially expressed in WAT under Sal B treatment. The up-regulated protein-coding genes in WAT of the Sal B-treated group were involved in the insulin resistance pathway, while the down-regulated genes mainly participated in the IL-17 signaling pathway. Other pathways may play an important role in the formation and differentiation of adipose tissue, such as B cell receptor signaling. Analysis of the lncRNA–mRNA network provides potential targets for lncRNAs in energy metabolism. We speculate that Sal B may serve as a potential therapeutic approach for obesity.
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Affiliation(s)
- Tian An
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Zhang
- Department of Endocrinology, Tangshan Workers Hospital, Tangshan, China
| | - Bohan Lv
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yufei Liu
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | | | - Juan Lian
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yanxiang Wu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Sihua Gao
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Guangjian Jiang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
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26
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Zhou B, Guo H, Tang J. Long Non-Coding RNA TFAP2A-AS1 Inhibits Cell Proliferation and Invasion in Breast Cancer via miR-933/SMAD2. Med Sci Monit 2019; 25:1242-1253. [PMID: 30768589 PMCID: PMC6383438 DOI: 10.12659/msm.912421] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/14/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND It is well documented that long non-coding RNAs (lncRNAs) are involved in the progression of multiple human tumors by sponging microRNAs (miRNAs). However, whether lncRNA TFAP2A-AS1 plays a role in the tumorigenesis of breast cancer (BC) remains undetermined. MATERIAL AND METHODS Real-time PCR (qRT-PCR) assay was performed to detect the relative mRNA expression of TFAP2A-AS1 and miR-933. Flow cytometry analysis, CCK-8 assay, and Transwell assay were applied to detect the effects of TFAP2A-AS1 overexpression on cell cycle, apoptosis, viability, and invasion of BC cells. In vivo proliferation assay was performed to evaluate the effects of TFAP2A-AS1 overexpression on tumor growth. Bioinformatics methods, dual-luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays were used to predict and validate the interaction between TFAP2A-AS1 and miR-933, as well as SMAD2 and miR-933. Western blot assay was performed to examine the protein expression of SMAD2 in treated BC cells. RESULTS TFAP2A-AS1 expression was significantly lower in BC tissues and cell lines, and patients with high TFAP2A-AS1 expression exhibited a better prognosis than those with low TFAP2A-AS1 expression. Overexpression of TFAP2A-AS1 in BC cells caused cell cycle arrest, promoted cell apoptosis, suppressed cell ability, and attenuated cell invasion in vitro, and inhibited tumor growth in vivo. TFAP2A-AS1 was revealed to act as a miRNA sponge for miR-933 and then regulated the expression of Smad2. CONCLUSIONS Results from the present study suggest that TFAP2A-AS1 acts as a tumor suppressor in BC via the miR-933/SMAD2 axis.
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Affiliation(s)
- Bin Zhou
- Department of General Surgery, Jiangsu Cancer Hospital (Affiliated Cancer Hospital of Nanjing Medical University), Nanjing, Jiangsu, P.R. China
| | - Haiyan Guo
- Department of Infectious Diseases, Jiangsu Province Hospital of Traditional Chinese medicine (TCM), Affiliated Hospital of Nanjing University of TCM, Nanjing, Jiangsu, P.R.China
| | - Jinhai Tang
- Department of General Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
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27
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Goudarzi M, Berg K, Pieper LM, Schier AF. Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility. eLife 2019; 8:40815. [PMID: 30620332 PMCID: PMC6347452 DOI: 10.7554/elife.40815] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/08/2019] [Indexed: 12/28/2022] Open
Abstract
Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs have no overt roles in embryogenesis, viability and fertility.
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Affiliation(s)
- Mehdi Goudarzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Kathryn Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Lindsey M Pieper
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Center for Brain Science, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, United States.,Biozentrum, University of Basel, Basel, Switzerland
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28
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Ji E, Kim C, Kim W, Lee EK. Role of long non-coding RNAs in metabolic control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1863:194348. [PMID: 30594638 DOI: 10.1016/j.bbagrm.2018.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression by influencing various biological processes including proliferation, apoptosis, differentiation, and senescence. Accumulating evidence implicates lncRNAs in the maintenance of metabolic homeostasis; dysregulation of certain lncRNAs promotes the progression of metabolic disorders such as diabetes, obesity, and cardiovascular diseases. In this review, we discuss our understanding of lncRNAs implicated in metabolic control, focusing on in particular diseases arising from chronic inflammation, insulin resistance, and lipid homeostasis. We have analyzed lncRNAs and their molecular targets involved in the pathogenesis of chronic liver disease, diabetes, and obesity, and have discussed the rising interest in lncRNAs as diagnostic and therapeutic targets improving metabolic homeostasis. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Eunbyul Ji
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea
| | - Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea.
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