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Shi L, Li B, Zhang Y, Chen Y, Tan J, Chen Y, Li J, Xiang M, Xing HR, Wang J. Exosomal lncRNA Mir100hg derived from cancer stem cells enhance glycolysis and promote metastasis of lung adenocarcinoma through mircroRNA-15a-5p/31-5p. Cell Commun Signal 2023; 21:248. [PMID: 37735657 PMCID: PMC10512609 DOI: 10.1186/s12964-023-01281-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Exosomes are a new class of molecular entities in the metastatic microenvironment, which can mediate bidirectional communication between cells. While exosomes-mediated interactions between tumor cells and other cell populations in the tumor microenvironment have attracted most attention, little is known about the significance of exosomes in mediating the interaction between non-stemness cancer cells and cancer stem cells during cancer progression. METHODS The structure, sequence and downstream target miRNAs of lncRNA Mir100hg were predicted by online web resources. The bioinformatics prediction results were validated with experimental verification: exosome tracing, electron microscopy, Luciferase assay, metabolomics sequencing and mouse tail vein model of pulmonary metastasis. A complex regulatory network of "cancer stem cells-exosomal lncRNA-non-stem cancer cells" was constructed. RESULTS This study demonstrates firstly that lncRNA Mir100hg is upregulated in lung cancer stem cell LLC-SD (Lung cancer stem cells) and can be delivered to non-stemness cancer cells LLC (Lewis lung cancer cells) via exosomes. In LLC, Mir100hg targets miR-15a-5p and miR-31-5p which leads to the increase of the global glycolytic activity of lung cancer cells and consequently, the enhancement of their metastatic capability. CONCLUSION We delineated a complex regulatory network that utilized by cancer stem cells to transfer their high metastatic activity to the low-metastatic non-stemness cancer cells through exosomal Mir100hg, thereby providing new mechanistic insights into the communication between two heterogeneous tumor cells. Video Abstract.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Bowen Li
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Yuhan Zhang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Yuting Chen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Jiyu Tan
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Yan Chen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Jie Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Meng Xiang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - H Rosie Xing
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China.
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China.
| | - Jianyu Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
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Wu Y, Wang Z, Yu S, Liu D, Sun L. LncmiRHG-MIR100HG: A new budding star in cancer. Front Oncol 2022; 12:997532. [PMID: 36212400 PMCID: PMC9544809 DOI: 10.3389/fonc.2022.997532] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/12/2022] [Indexed: 11/24/2022] Open
Abstract
MIR100HG, also known as lncRNA mir-100-let-7a-2-mir-125b-1 cluster host gene, is a new and critical regulator in cancers in recent years. MIR100HG is dysregulated in various cancers and plays an oncogenic or tumor-suppressive role, which participates in many tumor cell biology processes and cancer-related pathways. The errant expression of MIR100HG has inspired people to investigate the function of MIR100HG and its diagnostic and therapeutic potential in cancers. Many studies have indicated that dysregulated expression of MIR100HG is markedly correlated with poor prognosis and clinicopathological features. In this review, we will highlight the characteristics and introduce the role of MIR100HG in different cancers, and summarize the molecular mechanism, pathways, chemoresistance, and current research progress of MIR100HG in cancers. Furthermore, some open questions in this rapidly advancing field are proposed. These updates clarify our understanding of MIR100HG in cancers, which may pave the way for the application of MIR100HG-targeting approaches in future cancer diagnosis, prognosis, and therapy.
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Affiliation(s)
- Yingnan Wu
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Zhenzhen Wang
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Shan Yu
- Department of Pathology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dongzhe Liu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen, China
- *Correspondence: Litao Sun, ; Dongzhe Liu,
| | - Litao Sun
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou, China
- *Correspondence: Litao Sun, ; Dongzhe Liu,
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Yousefi F, Najafi H, Behmanesh M, Soltani BM. OCC-1D regulates Wnt signaling pathway: potential role of long noncoding RNA in colorectal cancer. Mol Biol Rep 2022; 49:3377-3387. [DOI: 10.1007/s11033-021-07110-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/17/2021] [Indexed: 10/18/2022]
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Zhang Z, Li Y, Yuan W, Wang Z, Wan C. Proteomic-driven identification of short open reading frame-encoded peptides. Proteomics 2022; 22:e2100312. [PMID: 35384297 DOI: 10.1002/pmic.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
Accumulating evidence has shown that a large number of short open reading frames (sORFs) also have the ability to encode proteins. The discovery of sORFs opens up a new research area, leading to the identification and functional study of sORF encoded peptides (SEPs) at the omics level. Besides bioinformatics prediction and ribosomal profiling, mass spectrometry (MS) has become a significant tool as it directly detects the sequence of SEPs. Though MS-based proteomics methods have proved to be effective for qualitative and quantitative analysis of SEPs, the detection of SEPs is still a great challenge due to their low abundance and short sequence. To illustrate the progress in method development, we described and discussed the main steps of large-scale proteomics identification of SEPs, including SEP extraction and enrichment, MS detection, data processing and quality control, quantification, and function prediction and validation methods. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zheng Zhang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Yujie Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Wenqian Yuan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Zhiwei Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, People's Republic of China
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Yuanyuan J, Xinqiang Y. Micropeptides Identified from Human Genomes. J Proteome Res 2022; 21:865-873. [DOI: 10.1021/acs.jproteome.1c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Yuanyuan
- School of Public Health, North Sichuan Medical College, Nanchong 637000, China
| | - Yin Xinqiang
- School of Basic Medicine and Forensics, North Sichuan Medical College, Nanchong 637000, China
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MicroRNA-100 Reduced Fetal Bovine Muscle Satellite Cell Myogenesis and Augmented Intramuscular Lipid Deposition by Modulating IGF1R. Cells 2022; 11:cells11030451. [PMID: 35159261 PMCID: PMC8833961 DOI: 10.3390/cells11030451] [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: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Previously, microRNA-100 (miR-100) and its putative mRNA target, insulin-like growth factor receptor-1 (IGF1R) were identified as differentially and inversely expressed in bovine longissimus dorsi (LD) muscles with divergent intramuscular fat (IMF) content by our group. While IGF1R signaling is implicated in myogenesis and muscle lipid metabolism, the underlying regulatory mechanisms are poorly understood. In the present study, we aimed to investigate the regulation of IGF1R by miR-100 during bovine muscle satellite cell (BMSC) myogenesis and lipid deposition. MiR-100 was confirmed to target the IGF1R 3′-untranslated region (3′-UTR) by luciferase reporter assay. Furthermore, expression of miR-100 and IGF1R was reciprocal during BMSC differentiation, suggesting a crosstalk between the two. Correspondingly, miR-100 mimic (agomiR) suppressed the levels of IGF1R, PI3K/AKT pathway signaling, myogenic gene MYOG, muscle structural components MYH7 and MYH8, whereas the inhibitor (antagomiR) had no clear stimulating effects. The IGF1R inhibitor (BMS-754807) curtailed receptor levels and triggered atrophy in muscle myotubes but did not influence miR-100 expression. AgomiR increased oleic acid-induced lipid deposition in BMSC myotubes supporting its involvement in intramuscular fat deposition, while antagomiR had no effect. Moreover, mitochondrial beta-oxidation and long-chain fatty acid synthesis-related genes were modulated by agomiR addition. Our results demonstrate modulatory roles of miR-100 in BMSC development, lipid deposition, and metabolism and suggest a role of miR-100 in marbling characteristics of meat animals and fat oxidation in muscle.
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Zhao S, Meng J, Luan Y. LncRNA-Encoded Short Peptides Identification Using Feature Subset Recombination and Ensemble Learning. Interdiscip Sci 2021; 14:101-112. [PMID: 34304369 DOI: 10.1007/s12539-021-00464-1] [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: 03/24/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
Abstract
Long non-coding RNA (lncRNA), which is a type of non-coding RNA, was reported to contain short open reading frames (sORFs). SORFs-encoded short peptides (SEPs) have been demonstrated to play a crucial role in regulating the biological processes such as growth, development, and resistance response. The identification of SEPs is vital to further understanding their function. However, there is still a lack of methods for identifying SEPs effectively and rapidly. In this study, a novel method for lncRNA-encoded short peptides identification based on feature subset recombination and ensemble learning, lncPepid, is developed. lncPepid transforms the data of Zea mays and Arabidopsis thaliana into hybrid features from two aspects including sequence composition and physicochemical properties separately. It optimizes hybrid features by proposing a novel weighted iteration-based feature selection method to recombine a stable subset that characterizes SEPs effectively. Different classification models with different optimized features are constructed and tested separately. The outputs of the optimal models are integrated for ensemble classification to improve efficiency. Experimental results manifest that the geometric mean of sensitivity and specificity of lncPepid is about 70% on the identification of functional SEPs derived from multiple species. It is an effective and rapid method for the identification of lncRNA-encoded short peptides. This study can be extended to the research on SEPs from other species and have crucial implications for further findings and studies of functional genomics.
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Affiliation(s)
- Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, Liaoning, China.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, Liaoning, China
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Zhou J, Liu J, Xing H, Shen Y, Xie M, Chai J, Yang M. Implications of protein ubiquitination modulated by lncRNAs in gastrointestinal cancers. Biochem Pharmacol 2021; 188:114558. [PMID: 33844983 DOI: 10.1016/j.bcp.2021.114558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA transcripts longer than 200 nucleotides and mostly cannot be translated into proteins. Next-generation transcriptome sequencing of various cell types has enabled the annotation of tens of thousands of lncRNAs in human genome. Varying levels of evidence supports the implications of lncRNAs in the onset and progression of cancers. Ubiquitin is an evolutionarily conserved protein and could post-translationally mark a number of proteins. The most important proteolytic role of ubiquitination is degradation of substrate proteins by the 26S proteasome. Compiling evidences demonstrated that lncRNAs are involved in the accurate execution of protein stability programs via the ubiquitin-proteasome system. In the current review, we systematically summarize the detailed mechanisms how lncRNAs modulate ubiquitination of target proteins, regulate cancerous signaling pathways and control tumorigenesis of gastrointestinal cancers. Although there are still considerable studies on unraveling the complicated interactions between lncRNAs and proteins, we believe that lncRNAs are promising but challenging molecules which may strongly facilitate precision cancer therapeutics in the future.
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Affiliation(s)
- Jianyuan Zhou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jie Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Huaixin Xing
- Department of Anesthesiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Yue Shen
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mengyu Xie
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jie Chai
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
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Cai G, Jin G, Liang J, Li G, Chen X, Liang H, Ding Z. Pan-cancer analysis of the prognostic value of C12orf75 based on data mining. Aging (Albany NY) 2021; 13:15214-15239. [PMID: 34074799 PMCID: PMC8221310 DOI: 10.18632/aging.203081] [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: 12/08/2020] [Accepted: 05/11/2021] [Indexed: 01/14/2023]
Abstract
The differential expression of chromosome 12 open reading frame 75 (C12orf75) is closely related with cancer progression. Here, we studied the expression levels of C12orf75 and investigated its prognostic value in various cancers across distinct datasets including ONCOMINE, PrognoScan, GEPIA, and TCGA. The correlation between genetic alteration of C12orf75 and immune infiltration was investigated using the cBioPortal and TIMER databases. RNA interference was used to verify the influence of C12orf75 knockdown on the biological phenotype of hepatocellular carcinoma cells. C12orf75 showed increased expression in most tested human cancers. The increased expression of C12orf75 was related with a poor prognosis in urothelial bladder carcinoma and hepatocellular liver carcinoma, but it was surprisingly converse in renal papillary cell carcinoma. In urothelial bladder carcinoma and hepatocellular liver carcinoma, we observed positive correlations between the expression of C12orf75 and the infiltration of immune cells, including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. The knockdown of C12orf75 in hepatocellular carcinoma cells suppressed the proliferation, migration, and invasion and arrested the cell cycle. This is the first report C12orf75 has potential as a prognostic biomarker and therapeutic target for molecularly targeted drugs in urothelial bladder carcinoma, hepatocellular liver carcinoma, and renal papillary cell carcinoma.
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Affiliation(s)
- Guangzhen Cai
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Guannan Jin
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Ganxun Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
| | - Zeyang Ding
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, PR China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, PR China
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Experimental Study of lncRNA RP11-815M8.1 Promoting Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5512370. [PMID: 33855069 PMCID: PMC8019361 DOI: 10.1155/2021/5512370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 01/01/2023]
Abstract
Objective This study is aimed at investigating the role of long noncoding RNA (lncRNA) RP11-815M8.1 in the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs). Methods RT-PCR was used to detect the expression of lncRNA RP11-815M8.1 before and after osteogenic differentiation of hBMSCs. The lncRNA RP11-815M8.1 in hBMSCs was overexpressed or silenced via lentiviral transfection. The transfection efficiency was detected by RT-PCR, and the proliferation of hBMSCs was determined by CCK-8. After 14 days of osteogenic differentiation of transfected hBMSCs, the expression of osteogenic transcription factors (ALP, OCN, OPN, Runx2, and Osterix) was detected by alizarin red staining and RT-PCR. The mRNAs directly regulated by lncRNA RP11-815M8.1 and targeted miRNAs were analyzed according to the positional relationship between lncRNA and mRNA in the genome and miRanda software. Results The expression of lncRNA RP11-815M8.1 enhanced with increasing osteogenic differentiation time of hBMSCs. Two days after the transfection of hBMSCs, lncRNA RP11-815M8.1 expression was significantly increased in the overexpression group and significantly decreased in the knockdown group, compared to control cells. The CCK-8 assay showed that overexpression and knockdown of lncRNA RP11-815M8.1 did not affect the proliferation of hBMSCs. After 14 days of differentiation of hBMSCs, stronger alizarin red staining was observed in the overexpression groups, and the expression of osteogenic transcription factors was increased in the overexpression group compared to the control. In the knockdown group, alizarin red staining and the expression of osteogenic transcription factors were decreased. Bioinformatics analysis showed that lncRNA RP11-815M8.1 was directly associated with one mRNA, 27 interacting miRNAs, and 20 miRNA-targeted mRNAs. Conclusion The osteogenic differentiation of hBMSCs can be promoted by lncRNA RP11-815M8.1 in vitro.
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LINC00978 promotes hepatocellular carcinoma carcinogenesis partly via activating the MAPK/ERK pathway. Biosci Rep 2021; 40:222177. [PMID: 32077915 PMCID: PMC7064789 DOI: 10.1042/bsr20192790] [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: 08/09/2019] [Revised: 11/20/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Objective: To study the role of long non-coding RNA (lncRNA) LINC00978 in hepatocellular carcinoma (HCC) carcinogenesis. Materials and methods: LINC00978 expression level was measured by reverse transcription quantitative real-time PCR (RT-qPCR) in HCC tissues and adjacent healthy liver tissues from 49 HCC patients. MTT assay, colony forming assay, and flow cytometry were performed to evaluate the effects of shRNA-mediated LINC00978 knockdown on HCC cell proliferation, cell cycle progression, and apoptosis in vitro. Xenograft tumor model was performed to determine the effects of LINC00978 knockdown on HCC tumor growth in vivo. Western blot was used to assess the activation of signaling molecules in the apoptosis and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway. Results: LINC00978 expression was significantly up-regulated in human HCC tissue relative to adjacent normal tissue, and LINC00978 high expression was correlated with poor HCC overall survival. LINC00978 was up-regulated in HCC cell lines. ShRNA-mediated LINC00978 knockdown significantly decreased HCC cell proliferation, and induced HCC cell cycle arrest and apoptosis in vitro. LINC00978 knockdown led to significant decrease in tumor xenograft size in vivo. Western blots revealed LINC00978 inhibition decreased ERK, p38, and c-Jun N-terminal kinase (JNK) phosphorylation in HCC cells. Conclusions: LINC00978 is highly expressed in human HCC tissue and correlates with poor HCC prognosis. LINC00978 promotes HCC cell proliferation, cell cycle progression, and survival, partially by activating the MAPK/ERK pathway. Our findings partially elucidated the roles of LINC00978 in HCC carcinogenesis, and identified a therapeutic target for HCC.
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Kurasawa H, Ohno T, Arai R, Aizawa Y. A guideline and challenges toward the minimization of bacterial and eukaryotic genomes. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Li J, Zhang X, Liu C. The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. Comput Struct Biotechnol J 2020; 18:3666-3677. [PMID: 33304463 PMCID: PMC7710504 DOI: 10.1016/j.csbj.2020.11.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) make up a large proportion of transcriptome in eukaryotes, and have been revealed with many regulatory functions in various biological processes. When studying lncRNAs, the first step is to accurately and specifically distinguish them from the colossal transcriptome data with complicated composition, which contains mRNAs, lncRNAs, small RNAs and their primary transcripts. In the face of such a huge and progressively expanding transcriptome data, the in-silico approaches provide a practicable scheme for effectively and rapidly filtering out lncRNA targets, using machine learning and probability statistics. In this review, we mainly discussed the characteristics of algorithms and features on currently developed approaches. We also outlined the traits of some state-of-the-art tools for ease of operation. Finally, we pointed out the underlying challenges in lncRNA identification with the advent of new experimental data.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
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Kidwai F, Mui BWH, Arora D, Iqbal K, Hockaday M, de Castro Diaz LF, Cherman N, Martin D, Myneni VD, Ahmad M, Futrega K, Ali S, Merling RK, Kaufman DS, Lee J, Robey PG. Lineage-specific differentiation of osteogenic progenitors from pluripotent stem cells reveals the FGF1-RUNX2 association in neural crest-derived osteoprogenitors. Stem Cells 2020; 38:1107-1123. [PMID: 32442326 PMCID: PMC7484058 DOI: 10.1002/stem.3206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells (hPSCs) can provide a platform to model bone organogenesis and disease. To reflect the developmental process of the human skeleton, hPSC differentiation methods should include osteogenic progenitors (OPs) arising from three distinct embryonic lineages: the paraxial mesoderm, lateral plate mesoderm, and neural crest. Although OP differentiation protocols have been developed, the lineage from which they are derived, as well as characterization of their genetic and molecular differences, has not been well reported. Therefore, to generate lineage-specific OPs from human embryonic stem cells and human induced pluripotent stem cells, we employed stepwise differentiation of paraxial mesoderm-like cells, lateral plate mesoderm-like cells, and neural crest-like cells toward their respective OP subpopulation. Successful differentiation, confirmed through gene expression and in vivo assays, permitted the identification of transcriptomic signatures of all three cell populations. We also report, for the first time, high FGF1 levels in neural crest-derived OPs-a notable finding given the critical role of fibroblast growth factors (FGFs) in osteogenesis and mineral homeostasis. Our results indicate that FGF1 influences RUNX2 levels, with concomitant changes in ERK1/2 signaling. Overall, our study further validates hPSCs' power to model bone development and disease and reveals new, potentially important pathways influencing these processes.
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Affiliation(s)
- Fahad Kidwai
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Byron W. H. Mui
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Deepika Arora
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
- Biosystems and Biomaterials DivisionNational Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Kulsum Iqbal
- Department of Health and Human ServicesDental Consult Services, National Institute of Health Dental ClinicBethesdaMarylandUSA
| | - Madison Hockaday
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Luis Fernandez de Castro Diaz
- Department of Health and Human ServicesSkeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Natasha Cherman
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Daniel Martin
- Department of Health and Human ServicesGenomics and Computational Biology Core, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Vamsee D. Myneni
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch/Adult Stem Cell Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Moaz Ahmad
- Department of Health and Human ServicesMolecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Katarzyna Futrega
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Sania Ali
- Biology of Global Health, Department of BiologyGeorgetown UniversityWashingtonDistrict of ColumbiaUSA
| | - Randall K. Merling
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Dan S. Kaufman
- Department of MedicineUniversity of CaliforniaLa JollaCaliforniaUSA
| | - Janice Lee
- Department of Health and Human ServicesCraniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
| | - Pamela G. Robey
- Department of Health and Human ServicesCraniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMarylandUSA
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15
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Liu J, Wu M, Feng G, Li R, Wang Y, Jiao J. Downregulation of LINC00707 promotes osteogenic differentiation of human bone marrow‑derived mesenchymal stem cells by regulating DKK1 via targeting miR‑103a‑3p. Int J Mol Med 2020; 46:1029-1038. [PMID: 32705245 PMCID: PMC7387089 DOI: 10.3892/ijmm.2020.4672] [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: 12/26/2019] [Accepted: 05/21/2020] [Indexed: 12/17/2022] Open
Abstract
Human bone marrow-derived mesenchymal stem cells (HBMSCs) have the potential of multidirectional differentiation and self-renewal, which is important for the formation of human bone. It has been reported that long non-coding RNAs (lncRNAs) serve important roles in HBMSC osteogenic differentiation. The current study aimed to investigate the roles of long intergenic non-protein coding RNA 00707 (LINC00707) and microRNA (miR)-103a-3p in the osteogenic differentiation of HBMSCs. Reverse transcription-quantitative PCR (RT-qPCR) was performed to detect the expression levels of LINC00707, miR-103a-3p and osteogenesis-related genes (Alkaline phosphatase, osteocalcin, osteopontin and RUNX family transcription factor 2) in HBMSCs cultured in proliferation medium (PM) and osteogenic medium (OM). Mineralized matrix deposition was measured using Alizarin Red S staining. The protein expression levels of osteogenesis-related genes were detected by western blotting. The relationships between LINC00707, miR-103a-3p and dickkopf WNT signaling pathway inhibitor 1 (DKK1) were predicted using Starbase and TargetScan7.2, and were further assessed with a dual-luciferase reporter assay. After 21 days of cell culture, the results indicated that expression of LINC00707 was downregulated, and those of miR-103a-3p and osteogenesis-related genes were upregulated in OM-cultured HBMSCs. However, there was no significant difference in the aforementioned gene expression levels in PM-cultured HBMSCs. Small interfering (si)LINC00707 increased the deposition of mineralized matrix and promoted the expression levels of osteogenesis-related proteins. Furthermore, miR-103a-3p was predicted to be a target gene of LINC00707, its expression was significantly upregulated by siLINC00707, while overexpression of miR-103a-3p increased the expression levels of osteogenesis-related proteins. DKK1 was also predicted to be a target gene of miR-103a-3p and could inhibit the expression levels of osteogenesis-related proteins, but such effect of DKK1 could be reversed by the miR-103a-3p mimic. In conclusion, the present results suggested that LINC00707 regulated DKK1 expression by targeting miR-103a-3p to regulate osteogenic differentiation.
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Affiliation(s)
- Jun Liu
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Minfei Wu
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Guang Feng
- The Fourth Medical Center of PLA General Hospital, Beijing 100048, P.R. China
| | - Rui Li
- Department of Hand Surgery, The Second Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Yang Wang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Jianhang Jiao
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
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16
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Decreased ZNF750 promotes angiogenesis in a paracrine manner via activating DANCR/miR-4707-3p/FOXC2 axis in esophageal squamous cell carcinoma. Cell Death Dis 2020; 11:296. [PMID: 32341351 PMCID: PMC7186230 DOI: 10.1038/s41419-020-2492-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 11/24/2022]
Abstract
ZNF750 is one novel significantly mutated gene identified in esophageal squamous cell carcinoma (ESCC) using next-generation sequencing. However, its clinically relevant and potential mechanisms have remained elusive. Using genomic sequencing of 612 ESCC patients, we analyzed the associations of ZNF750 mutations with clinicopathologic features and its prognostic value. We further investigated the function and underlying mechanism of ZNF750 in angiogenesis. The results showed ZNF750 mutations/deletions are significantly associated with malignant progression and poor prognosis of ESCC patients. Decreased ZNF750 in ESCC cells induces enhanced angiogenesis of human umbilical vein endothelial cells (HUVECs) and human arterial endothelial cells (HAECs), and the effect may be indirectly mediated by FOXC2. RNA-seq and ChIP shows lncRNA DANCR is a direct downstream target of ZNF750. Furtherly, knockdown ZNF750 evokes DANCR expression, which prevents miR-4707-3p to interact with FOXC2 as a microRNA sponge in a ceRNA manner, leading to enhanced FOXC2 signaling and angiogenesis. In contrast, ZNF750 expression reverses the effect. Our study reveals a novel mechanism of ZNF750, highlights a significance of ZNF750 as a metastatic and prognostic biomarker, and offers potential therapeutic targets for ESCC patients harboring ZNF750 mutations.
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17
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Jin SJ, Jin MZ, Xia BR, Jin WL. Long Non-coding RNA DANCR as an Emerging Therapeutic Target in Human Cancers. Front Oncol 2019; 9:1225. [PMID: 31799189 PMCID: PMC6874123 DOI: 10.3389/fonc.2019.01225] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators of numerous biological processes, especially in cancer development. Aberrantly expressed and specifically located in tumor cells, they exert distinct functions in different cancers via regulating multiple downstream targets such as chromatins, RNAs, and proteins. Differentiation antagonizing non-protein coding RNA (DANCR) is a cytoplasmic lncRNA that generally works as a tumor promoter. Mechanically, DANCR promotes the functions of vital components in the oncogene network by sponging their corresponding microRNAs or by interacting with various regulating proteins. DANCR's distinct expression in tumor cells and collective involvement in pro-tumor pathways make it a promising therapeutic target for broad cancer treatment. Herein, we summarize the functions and molecular mechanism of DANCR in human cancers. Furthermore, we introduce the use of CRISPR/Cas9, antisense oligonucleotides and small interfering RNAs as well as viral, lipid, or exosomal vectors for onco-lncRNA targeted treatment. Conclusively, DANCR is a considerable promoter of cancers with a bright prospect in targeted therapy.
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Affiliation(s)
- Shi-Jia Jin
- Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, Department of Instrument Science and Engineering, Shanghai Engineering Center for Intelligent Diagnosis and Treatment Instrument, School of Electronic Information and Electronic Engineering, Institute of Nano Biomedicine and Engineering, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Zhu Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bai-Rong Xia
- Department of Gynecology, The Affiliated Tumor Hospital, Harbin Medical University, Harbin, China
| | - Wei-Lin Jin
- Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, Department of Instrument Science and Engineering, Shanghai Engineering Center for Intelligent Diagnosis and Treatment Instrument, School of Electronic Information and Electronic Engineering, Institute of Nano Biomedicine and Engineering, Shanghai Jiao Tong University, Shanghai, China.,National Center for Translational Medicine, Collaborative Innovational Center for System Biology, Shanghai Jiao Tong University, Shanghai, China
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18
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Lan Y, Xiao X, He Z, Luo Y, Wu C, Li L, Song X. Long noncoding RNA OCC-1 suppresses cell growth through destabilizing HuR protein in colorectal cancer. Nucleic Acids Res 2019; 46:5809-5821. [PMID: 29931370 PMCID: PMC6009600 DOI: 10.1093/nar/gky214] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/13/2018] [Indexed: 02/05/2023] Open
Abstract
Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro and in vivo, which is largely due to its ability to inhibit G0 to G1 and G1 to S phase cell cycle transitions. In addition, overexpression of OCC-1 can suppress cell growth in OCC-1 knockdown cells. OCC-1 exerts its function by binding to and destabilizing HuR (ELAVL1), a cancer-associated RNA binding protein (RBP) which can bind to and stabilize thousands of mRNAs. OCC-1 enhances the binding of ubiquitin E3 ligase β-TrCP1 to HuR and renders HuR susceptible to ubiquitination and degradation, thereby reducing the levels of HuR and its target mRNAs, including the mRNAs directly associated with cancer cell growth. These findings reveal that lncRNA OCC-1 can regulate the levels of a large number of mRNAs at post-transcriptional level through modulating RBP HuR stability.
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Affiliation(s)
- Yang Lan
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Xuewei Xiao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Zhengchi He
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Yu Luo
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Chuanfang Wu
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P.R. China.,State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, P.R. China
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19
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Li J, Liu C. Coding or Noncoding, the Converging Concepts of RNAs. Front Genet 2019; 10:496. [PMID: 31178900 PMCID: PMC6538810 DOI: 10.3389/fgene.2019.00496] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of RNA. In this review, we summarize current evidence pointing to dual roles of RNA molecules defined by their coding and non-coding potentials. We also discuss how the emerging roles of RNA transform our understanding of gene expression and evolution.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
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20
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Evangelou P, Groll M, Oppermann H, Gaunitz F, Eisenlöffel C, Müller W, Eschrich K, Schänzer A, Nestler U. Assessment of ApoC1, LuzP6, C12orf75 and OCC-1 in cystic glioblastoma using MALDI-TOF mass spectrometry, immunohistochemistry and qRT-PCR. Med Mol Morphol 2019; 52:217-225. [PMID: 31006040 PMCID: PMC6885021 DOI: 10.1007/s00795-019-00223-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Mass spectrometric analysis of glioblastoma cyst fluids has disclosed a protein peak with m/z 6424–6433. Among the proteins, potentially generating this peak are ApoC1 and LuzP6. To further elucidate protein expression of glioblastoma cells, we analyzed MALDI–TOF results of cyst fluid, performed immunohistochemistry and mRNA analysis. MALDI–TOF protein extraction from 24 glioblastoma cyst fluids was performed with a weak cation exchange. 50 glioblastoma samples were stained with two custom-made antibodies against LuzP6 and commercial antibodies against ApoC1, C12orf75 and OCC-1 and analyzed. For mRNA detection, 16 tissue samples were stored in RNAlater, extracted using the miRNeasy kit and reversely transcribed. For 12 patients, synopsis of results from all three examinations was possible. MALDI–TOF confirmed the peak at 6433 Da in 75% of samples. Immunohistochemically, LuzP6 was detected in 92% (LuzP61–29) and 96% (LuzP630–58) of samples and ApoC1 in 66%. Mean mRNA levels were highest for ApoC1, followed by LuzP6. No correlation between mRNA expression, immunohistochemical staining and intensity of the MALDI–TOF peaks was found. An unequivocal identification of one protein as the source for the 6433 peak is not possible, but our results point to ApoC1 and LuzP6 as the underlying proteins.
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Affiliation(s)
- Petros Evangelou
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Mathias Groll
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Henry Oppermann
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Frank Gaunitz
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Christian Eisenlöffel
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Wolf Müller
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Klaus Eschrich
- Rudolf Schoenheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Ulf Nestler
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany.
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21
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Yuan Y, Cao X, Hu J, Li J, Shen D, You L, Cui X, Wang X, Zhou Y, Gao Y, Zhu L, Xu P, Ji C, Guo X, Wen J. The role and possible mechanism of lncRNA AC092159.2 in modulating adipocyte differentiation. J Mol Endocrinol 2019; 62:137-148. [PMID: 30753134 DOI: 10.1530/jme-18-0215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/11/2019] [Indexed: 01/06/2023]
Abstract
Obesity is a major risk factor for metabolic diseases, while adipocyte differentiation is closely related to obesity occurrence. Long noncoding RNAs (lncRNAs) are a unique class of transcripts in regulation of various biological processes. Using lncRNA microarray, we found lncRNA AC092159.2 was highly expressed in differentiated HPA-v and located ~247 bp upstream of the TMEM18, which was associated with BMI and obesity. We aimed to explore the role of AC092159.2 in adipogenesis and the underlying mechanisms. The effects of AC092159.2 gain- and loss-of-function on HPA-v adipogenesis were determined with lentivirus and siRNA-mediated cell transduction, respectively. Lipid accumulation was evaluated by oil red O staining; the expression of AC092159.2, TMEM18 and several adipogenesis makers in HPA-v were analyzed by qPCR/Western blot. We found that the expression of AC092159.2 gradually increased during HPA-v differentiation, and its expression in omental adipose tissue was positively related with BMI among 48 human subjects. Overexpression of AC092159.2 promoted adipocytes differentiation while knockdown of it led to an adipogenic defect. Moreover, the expression of AC092159.2 and TMEM18 were positively correlated during adipogenic differentiation. AC092159.2 overexpression boosted TMEM18 expression while AC092159.2 knockdown restrained TMEM18 expression. Further rescue experiments showed that TMEM18 knockdown partially restrained adipogenic differentiation in AC092159.2 overexpressed HPA-v and adipogenic defect caused by AC092159.2 knockdown could be rescued by TMEM18 overexpression. Luciferase reporter assays revealed that AC092159.2 had a transcriptional activation effect on TMEM18. We concluded that lncRNA AC092159.2 promoted human adipocytes differentiation possibly by regulating TMEM18.
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Affiliation(s)
- Yingdi Yuan
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
- Department of Pediatrics, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, China
| | - Xinguo Cao
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
- Cancer Care Ontario, Toronto, Canada
| | - Jiaojiao Hu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jingyun Li
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Dan Shen
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lianghui You
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xing Wang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yahui Zhou
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yao Gao
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lijun Zhu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chenbo Ji
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xirong Guo
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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22
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Sun X, Jia B, Qiu XL, Chu HX, Zhang ZQ, Wang ZP, Zhao JJ. Potential functions of long non‑coding RNAs in the osteogenic differentiation of human bone marrow mesenchymal stem cells. Mol Med Rep 2018; 19:103-114. [PMID: 30483739 PMCID: PMC6297760 DOI: 10.3892/mmr.2018.9674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 10/05/2018] [Indexed: 11/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a specific group of RNA molecules that do not encode proteins. They have been shown to serve important regulatory functions in various biological and cell differentiation processes. However, the potential functions and regulatory mechanisms of lncRNAs that are associated with the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) remain to be elucidated. The present study aimed to investigate lncRNAs that are differentially expressed during the osteogenic differentiation of hBMSCs, along with the potential functions of those lncRNAs. To this end, three groups of hBMSCs were stimulated to undergo osteogenic differentiation for 7 days. Known lncRNAs, unknown lncRNAs and mRNAs that demonstrated differential expression prior to and following the osteogenic differentiation of hBMSCs were screened using lncRNA high-throughput sequencing. In addition, 12 lncRNAs were selected for reverse transcription-quantitative polymerase chain reaction (RT-qPCR) validation of the accuracy of the sequencing results. The potential functions and possible targets of the differentially expressed lncRNAs were analyzed using bioinformatics technologies (gene ontology, Kyoto Encyclopedia of Genes and Genomes and gene co-expression network analysis). In total, 64 lncRNAs were differentially expressed by at least two-fold in hBMSCs prior to and following osteogenic differentiation; these included seven known lncRNAs (two upregulated and five downregulated lncRNAs) and 57 unknown lncRNAs (35 upregulated and 22 downregulated lncRNAs). In addition, 409 mRNAs (257 upregulated and 152 downregulated mRNAs) were differentially expressed by at least two-fold. The RT-qPCR results obtained for 12 selected differentially expressed lncRNAs were consistent with the sequencing results. The gene co-expression network analysis of lncRNAs and mRNAs demonstrated that four lncRNAs (ENSG00000238042, lnc_1269, lnc_1369 and lnc_1708) may serve important roles in the osteogenic differentiation of hBMSCs. In conclusion, during the osteogenic differentiation of hBMSCs, the lncRNA expression profile changed significantly; certain of the observed differentially expressed lncRNAs may be derived from protein-coding genes and may serve important roles in osteogenic differentiation.
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Affiliation(s)
- Xiang Sun
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Bo Jia
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Xiao-Ling Qiu
- Department of Endodontics, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Hong-Xing Chu
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Zhao-Qiang Zhang
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Zhi-Ping Wang
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
| | - Jian-Jiang Zhao
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University (Guangdong Provincial Stomatological Hospital), Guangzhou, Guangdong 510280, P.R. China
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23
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Ghalaei A, Kay M, Zarrinfam S, Hoseinpour P, Behmanesh M, Soltani BM. Overexpressed in colorectal carcinoma gene (OCC-1) upregulation and APPL2 gene downregulation in breast cancer specimens. Mol Biol Rep 2018; 45:1889-1895. [PMID: 30218350 DOI: 10.1007/s11033-018-4336-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022]
Abstract
Breast cancer is the most common cancer type and the second cause of cancer death in women. Different mechanisms are contributed to the initiation and progression of the breast cancer. OCC-1 and APPL2 neighboring genes located in 12q.23.3 human chromosome region are related to colorectal cancer. Here, we intended to investigate OCC-1 newly reported transcript variants and APPL2 gene expression alteration in breast cancer specimens and investigate OCC-1 variants overexpression effect on APPL2 and on cell cycle status. Rt-qPCR analysis indicated that the expression level of OCC-1A/B and OCC-1D (not OCC-1C) transcript variants has been increased while, APPL2 gene expression level has been decreased in breast cancer specimen, compared to their normal pairs. Therefore, a negative correlation of expression is evident between APPL2 and OCC-1 genes in breast cancer specimen. Unlike OCC-1A/B which encodes a small protein, OCC-1D noncoding RNA overexpression lead to APPL2 downregulation in MCF7 cells. Consistently, OCC-1D overexpression resulted in increased sub-G1 cell population in MCF7 cells, detected by flow cytometry. Altogether, these results suggest that OCC1-D variant have an inhibitory effect on APPL2 expression and may regulate the cell cycle status.
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Affiliation(s)
| | - Maryam Kay
- Genetics Deptartment, Tarbiat Modares University, Tehran, Iran
| | - Shiva Zarrinfam
- Genetics Deptartment, Tarbiat Modares University, Tehran, Iran
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24
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Yeasmin F, Yada T, Akimitsu N. Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics. Front Genet 2018; 9:144. [PMID: 29922328 PMCID: PMC5996887 DOI: 10.3389/fgene.2018.00144] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species. Recent characterization of a few of these revealed their significant divergent roles in many fundamental biological processes, where some also show important relationships with pathogenesis. Recent works therefore provide new insights for exploring the wealth of information that may lie within sORF-encoded short proteins. Here, we summarize the current progress and view of micropeptides encoded in sORFs of protein-coding genes.
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Affiliation(s)
- Fouzia Yeasmin
- Isotope Science Centre, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
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25
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Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ. lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling. Nat Med 2017; 23:1331-1341. [PMID: 29035371 PMCID: PMC5961502 DOI: 10.1038/nm.4424] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/08/2017] [Indexed: 12/11/2022]
Abstract
De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of known genetic events linked to cetuximab resistance. MIR100HG, miR-100 and miR-125b overexpression was also observed in cetuximab-resistant colorectal cancer and head and neck squamous cell cancer cell lines and in tumors from colorectal cancer patients that progressed on cetuximab. miR-100 and miR-125b coordinately repressed five Wnt/β-catenin negative regulators, resulting in increased Wnt signaling, and Wnt inhibition in cetuximab-resistant cells restored cetuximab responsiveness. Our results describe a double-negative feedback loop between MIR100HG and the transcription factor GATA6, whereby GATA6 represses MIR100HG, but this repression is relieved by miR-125b targeting of GATA6. These findings identify a clinically actionable, epigenetic cause of cetuximab resistance.
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Affiliation(s)
- Yuanyuan Lu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xiaodi Zhao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Ramona Graves-Deal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Zheng Cao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhuminder Singh
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Huaying Hu
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Tianying Wei
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Mingli Yang
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kenyi Saito-Diaz
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Scott Hinger
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Stephan Emmrich
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
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26
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Najafi H, Soltani BM, Dokanehiifard S, Nasiri S, Mowla SJ. Alternative splicing of the OCC-1 gene generates three splice variants and a novel exonic microRNA, which regulate the Wnt signaling pathway. RNA (NEW YORK, N.Y.) 2017; 23:70-85. [PMID: 27986894 PMCID: PMC5159651 DOI: 10.1261/rna.056317.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
The Wnt signaling pathway is hyperactivated in most colorectal cancers (CRC). Finding new regulators of this pathway represents the potential for cancer diagnosis or treatment. OCC-1 was initially reported as an up-regulated gene in colon carcinoma, without knowing its mechanism of action. Here, two novel transcript variants and an exonic microRNA that originated from the OCC-1 gene are reported, showing positive effects on Wnt activity. Up-regulation of the known OCC-1 variant (assigned as OCC-1A/B) was limited to CRC, and its overexpression increased survival of CRC-originated SW480 cells (Wnt+), while resulting in apoptosis of Wnt-suppressed SW480 cells or HeLa cells (Wnt-) detected by PI staining. Immunocytochemistry showed that the OCC-1A/B-encoded peptide was localized to the nucleus, where its overexpression resulted in Wnt signaling up-regulation, detected by TOP/FOPflash assay. The noncoding portion of the OCC-1A/B transcript had a suppressive effect on Wnt activity and had a negative correlation with APPL2 neighboring gene expression. Unlike OCC-1A/B, the novel OCC-1C splice variant had no expression alteration in CRC, and it seemed to encode a smaller peptide with cytoplasmic localization. A 60-nucleotide (nt) fragment containing an AUG start codon is spliced out to produce an OCC-1D noncoding RNA variant. The 60-nt RNA was validated as the precursor of a novel microRNA, which we named miR-ex1 Both OCC-1D and miR-ex1 were coordinately up-regulated in CRC. MiR-ex1 functional analysis revealed that it is targeting the APC2 tumor suppressor gene and is an activator of the Wnt signaling pathway. Overall, the OCC-1 gene is now introduced as a novel Wnt signaling regulator and as a potential therapeutic target.
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Affiliation(s)
- Hadi Najafi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Sadat Dokanehiifard
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Shirzad Nasiri
- Tehran University of Medical Sciences, Shariati Hospital, 1411713135 Tehran, Iran
| | - Seyed Javad Mowla
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
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27
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Huynh NPT, Anderson BA, Guilak F, McAlinden A. Emerging roles for long noncoding RNAs in skeletal biology and disease. Connect Tissue Res 2017; 58:116-141. [PMID: 27254479 PMCID: PMC5301950 DOI: 10.1080/03008207.2016.1194406] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
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Affiliation(s)
- Nguyen P. T. Huynh
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Britta A. Anderson
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA
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28
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Hangelbroek RWJ, Fazelzadeh P, Tieland M, Boekschoten MV, Hooiveld GJEJ, van Duynhoven JPM, Timmons JA, Verdijk LB, de Groot LCPGM, van Loon LJC, Müller M. Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness. J Cachexia Sarcopenia Muscle 2016; 7:604-614. [PMID: 27239416 PMCID: PMC4863830 DOI: 10.1002/jcsm.12099] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/17/2015] [Accepted: 12/04/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The skeletal muscle system plays an important role in the independence of older adults. In this study we examine differences in the skeletal muscle transcriptome between healthy young and older subjects and (pre-)frail older adults. Additionally, we examine the effect of resistance-type exercise training on the muscle transcriptome in healthy older subjects and (pre-)frail older adults. METHODS Baseline transcriptome profiles were measured in muscle biopsies collected from 53 young, 73 healthy older subjects, and 61 frail older subjects. Follow-up samples from these frail older subjects (31 samples) and healthy older subjects (41 samples) were collected after 6 months of progressive resistance-type exercise training. Frail older subjects trained twice per week and the healthy older subjects trained three times per week. RESULTS At baseline genes related to mitochondrial function and energy metabolism were differentially expressed between older and young subjects, as well as between healthy and frail older subjects. Three hundred seven genes were differentially expressed after training in both groups. Training affected expression levels of genes related to extracellular matrix, glucose metabolism ,and vascularization. Expression of genes that were modulated by exercise training was indicative of muscle strength at baseline. Genes that strongly correlated with strength belonged to the protocadherin gamma gene cluster (r = -0.73). CONCLUSIONS Our data suggest significant remaining plasticity of ageing skeletal muscle to adapt to resistance-type exercise training. Some age-related changes in skeletal muscle gene expression appear to be partially reversed by prolonged resistance-type exercise training. The protocadherin gamma gene cluster may be related to muscle denervation and re-innervation in ageing muscle.
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Affiliation(s)
- Roland W J Hangelbroek
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Parastoo Fazelzadeh
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Michael Tieland
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Mark V Boekschoten
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Guido J E J Hooiveld
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - John P M van Duynhoven
- Laboratory of Biophysics Wageningen University Wageningen the Netherlands; Netherlands Metabolomics Centre Leiden the Netherlands
| | | | - Lex B Verdijk
- Top Institute Food and Nutrition Wageningen the Netherlands; Department of Human Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism Maastricht University Maastricht the Netherlands
| | - Lisette C P G M de Groot
- Top Institute Food and Nutrition Wageningenthe Netherlands; Division of Human Nutrition Wageningen University Wageningenthe Netherlands
| | - Luc J C van Loon
- Top Institute Food and Nutrition Wageningen the Netherlands; Department of Human Movement Sciences, NUTRIM School of Nutrition and Translational Research in Metabolism Maastricht University Maastricht the Netherlands
| | - Michael Müller
- Top Institute Food and Nutrition Wageningen the Netherlands; Division of Human Nutrition Wageningen University Wageningen the Netherlands; Norwich Medical School University of East Anglia Norwich UK
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29
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Wang J, Roy B. Single-cell RNA-seq reveals lincRNA expression differences in Hela-S3 cells. Biotechnol Lett 2016; 39:359-366. [DOI: 10.1007/s10529-016-2260-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/15/2016] [Indexed: 12/27/2022]
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30
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Pek SLT, Sum CF, Lin MX, Cheng AKS, Wong MTK, Lim SC, Tavintharan S. Circulating and visceral adipose miR-100 is down-regulated in patients with obesity and Type 2 diabetes. Mol Cell Endocrinol 2016; 427:112-23. [PMID: 26973292 DOI: 10.1016/j.mce.2016.03.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 11/30/2022]
Abstract
Obesity is a major public health problem conferring substantial excess risk for Type 2 diabetes (T2D). The role of microRNAs (miRNAs) in obesity and adipose tissue is not clearly defined. We hypothesize that circulating miRNA expression profiles vary according to differences in body mass index (BMI) and T2D and circulating miRNAs may reflect adipose tissue expression. Compared to healthy, lean individuals, circulating miR-100 was significantly lower in obese normoglycemic subjects and subjects with T2D. In visceral adipose tissue, expression of miR-100 was lower from obese subjects with T2D compared to obese subjects without T2D. miR-100 expression was significantly lower after adipogenic induction in human visceral, subcutaneous adipocytes and 3T3-L1 adipocytes. miR-100 reduced expression of mammalian target of rapamycin (mTOR) and Insulin Growth Factor Receptor (IGFR) directly. Differentiation of 3T3-L1 was accelerated by inhibition of miR-100 and reduced by miR-100 mimic transfection. Our data provide the first evidence of an association of circulating miR-100 with obesity and diabetes. Additionally, our in-vitro findings, and the miR-100 expression patterns in site-specific adipose tissue suggest miR-100 to modulate IGFR, mTOR and mediate adipogenesis.
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Affiliation(s)
| | - Chee Fang Sum
- Diabetes Centre, Khoo Teck Puat Hospital, 768828, Singapore; Division of Endocrinology, Khoo Teck Puat Hospital, 768828, Singapore.
| | | | | | | | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, 768828, Singapore; Diabetes Centre, Khoo Teck Puat Hospital, 768828, Singapore; Division of Endocrinology, Khoo Teck Puat Hospital, 768828, Singapore.
| | - Subramaniam Tavintharan
- Clinical Research Unit, Khoo Teck Puat Hospital, 768828, Singapore; Diabetes Centre, Khoo Teck Puat Hospital, 768828, Singapore; Division of Endocrinology, Khoo Teck Puat Hospital, 768828, Singapore.
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31
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Imamura M, Takahashi A, Yamauchi T, Hara K, Yasuda K, Grarup N, Zhao W, Wang X, Huerta-Chagoya A, Hu C, Moon S, Long J, Kwak SH, Rasheed A, Saxena R, Ma RCW, Okada Y, Iwata M, Hosoe J, Shojima N, Iwasaki M, Fujita H, Suzuki K, Danesh J, Jørgensen T, Jørgensen ME, Witte DR, Brandslund I, Christensen C, Hansen T, Mercader JM, Flannick J, Moreno-Macías H, Burtt NP, Zhang R, Kim YJ, Zheng W, Singh JR, Tam CHT, Hirose H, Maegawa H, Ito C, Kaku K, Watada H, Tanaka Y, Tobe K, Kawamori R, Kubo M, Cho YS, Chan JCN, Sanghera D, Frossard P, Park KS, Shu XO, Kim BJ, Florez JC, Tusié-Luna T, Jia W, Tai ES, Pedersen O, Saleheen D, Maeda S, Kadowaki T. Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes. Nat Commun 2016; 7:10531. [PMID: 26818947 PMCID: PMC4738362 DOI: 10.1038/ncomms10531] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/22/2015] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 80 susceptibility loci for type 2 diabetes (T2D), but most of its heritability still remains to be elucidated. In this study, we conducted a meta-analysis of GWAS for T2D in the Japanese population. Combined data from discovery and subsequent validation analyses (23,399 T2D cases and 31,722 controls) identify 7 new loci with genome-wide significance (P<5 × 10(-8)), rs1116357 near CCDC85A, rs147538848 in FAM60A, rs1575972 near DMRTA1, rs9309245 near ASB3, rs67156297 near ATP8B2, rs7107784 near MIR4686 and rs67839313 near INAFM2. Of these, the association of 4 loci with T2D is replicated in multi-ethnic populations other than Japanese (up to 65,936 T2Ds and 158,030 controls, P<0.007). These results indicate that expansion of single ethnic GWAS is still useful to identify novel susceptibility loci to complex traits not only for ethnicity-specific loci but also for common loci across different ethnicities.
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Affiliation(s)
- Minako Imamura
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory for Omics Informatics, Omics Research Center, National Cerebral And Cardiovascular Center, Suita 565-8565, Japan
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuo Hara
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,Department of Diabetes Endocrinology, Metabolism and Rheumatology, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Kazuki Yasuda
- Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Wei Zhao
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6021, USA
| | - Xu Wang
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 138672, Singapore
| | - Alicia Huerta-Chagoya
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City C.P.14000, Mexico
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Sanghoon Moon
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do 28159, Korea
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203-1738, USA
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Richa Saxena
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Minoru Iwata
- First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan.,Health Administration Center, University of Toyama, Toyama 930-0194, Japan
| | - Jun Hosoe
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Minaka Iwasaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Hayato Fujita
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Ken Suzuki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge CB1 8RN, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1RQ, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup DK-2600, Denmark.,Faculty of Health and Medical Sciences, Department of Public Health, University of Copenhagen, Copenhagen 2200, Denmark.,Faculty of Medicine, University of Aalborg, Aalborg 9220, Denmark
| | | | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus 8000, Denmark.,Danish Diabetes Academy, Odense 5000, Denmark
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle 7100, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense 5230, Denmark
| | | | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Josep M Mercader
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona 08034, Spain.,Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Molecular Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Rong Zhang
- Department of Endocrinology and Metabolism, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Young Jin Kim
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do 28159, Korea
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203-1738, USA
| | - Jai Rup Singh
- Central University of Punjab, Bathinda, Punjab 151001, India
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Hiroshi Maegawa
- Department of Medicine, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Chikako Ito
- Grand Tower Medical Court Life Care Clinic, Hiroshima 730-0012, Japan
| | - Kohei Kaku
- Department of Internal Medicine, Kawasaki Medical School, Kurashiki 701-0192, Japan
| | - Hirotaka Watada
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan.,Sportology Center, Juntendo University Graduate School of Medicine, Tokyo 113-0034, Japan
| | - Yasushi Tanaka
- Division of Metabolism and Endocrinology, Department of Internal Medicine, St Marianna University School of Medicine, Kawasaki 216-8511, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Ryuzo Kawamori
- Sportology Center, Juntendo University Graduate School of Medicine, Tokyo 113-0034, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chunchon, Gangwon-do 24252, Republic of Korea
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Dharambir Sanghera
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.,Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, n
| | | | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37203-1738, USA
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do 28159, Korea
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City C.P.14000, Mexico
| | - Weiping Jia
- Department of Endocrinology and Metabolism, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 138672, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Duke-National University of Singapore Graduate School, Singapore 169857, Singapore
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6021, USA.,Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Shiro Maeda
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara 903-0215, Japan.,Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara 903-0215, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
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Xiao T, Liu L, Li H, Sun Y, Luo H, Li T, Wang S, Dalton S, Zhao RC, Chen R. Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPα. Stem Cell Reports 2015; 5:856-865. [PMID: 26489893 PMCID: PMC4649137 DOI: 10.1016/j.stemcr.2015.09.007] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 01/09/2023] Open
Abstract
C/EBPα is a critical transcriptional regulator of adipogenesis. How C/EBPα transcription is itself regulated is poorly understood, however, and remains a key question that needs to be addressed for a complete understanding of adipogenic development. Here, we identify a lncRNA, ADINR (adipogenic differentiation induced noncoding RNA), transcribed from a position ∼450 bp upstream of the C/EBPα gene, that orchestrates C/EBPα transcription in vivo. Depletion of ADINR leads to a severe adipogenic defect that is rescued by overexpression of C/EBPα. Moreover, we reveal that ADINR RNA specifically binds to PA1 and recruits MLL3/4 histone methyl-transferase complexes so as to increase H3K4me3 and decrease H3K27me3 histone modification in the C/EBPα locus during adipogenesis. These results show that ADINR plays important roles in regulating the differentiation of human mesenchymal stem cells into adipocytes by modulating C/EBPα in cis. The lncRNA ADINR is developmentally regulated during adipogenesis ADINR promotes adipogenesis by activating C/EBPα transcription in cis ADINR activates C/EBPα transcription by an MLL3/4-dependent mechanism MLL3/4 recruitment to the C/EBPα promoter requires binding of PA1 to ADINR
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Affiliation(s)
- Tengfei Xiao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA
| | - Lihui Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Hongling Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yu Sun
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Tangping Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Shihua Wang
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Stephen Dalton
- Paul D. Coverdell Center for Biomedical and Health Sciences, Department of Biochemistry and Molecular Biology, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Robert Chunhua Zhao
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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33
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Lin WC, Shih PH, Wang W, Wu CH, Hsia SM, Wang HJ, Hwang PA, Wang CY, Chen SH, Kuo YT. Inhibitory effects of high stability fucoxanthin on palmitic acid-induced lipid accumulation in human adipose-derived stem cells through modulation of long non-coding RNA. Food Funct 2015; 6:2215-23. [PMID: 26057608 DOI: 10.1039/c5fo00301f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Obesity is a serious worldwide disease, which is growing in epidemic proportions. Adipose-derived stem cells (ADSCs) are characterized as a source of mesenchymal stem cells that have acted as a potential application for regeneration. Recently, seaweeds rich in flavonoids and polysaccharides have been supposed to show the ability to modulate risk factors for obesity and related diseases. In the present study, we investigated the anti-obesity properties of high stability fucoxanthin (HS-Fx) derived from brown seaweeds on the adipogenesis of ADSCs upon treatment with palmitic acid (PA). First, we showed the differentiation capability of ADSCs from morbid obesity patients to transform into different cell types. Second, we found that the co-treatment of ADSCs with HS-Fx and PA showed no significant cytotoxicity against ADSCs, but PA induced the elevation of reactive oxygen species (ROS) and lipid droplet accumulation was abolished. Thirdly, the PA-mediated down-regulation of lipid metabolism genes was reversed by the treatment of HS-Fx. By long non-coding RNAs (lncRNAs) screening, we found that PA-induced increases in the targeted lncRNAs were also decreased upon treatment with HS-Fx. On Silencing, these lncRNAs corresponded to the decrease in the lipid droplet accumulation of ADSCs induced by PA. ADSCs from obese patients would be direct and meaningful model cells to investigate the development of obesity-related diseases and their treatments, rather than cell lines from other species. HS-Fx showed anti-obesity capability through modulating the elevation of ROS, down-regulation of lipid metabolism genes induced by PA, and upstream signaling, which might be critically resulted from the expression of lncRNAs.
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Affiliation(s)
- Wen-Chuan Lin
- Department of Pediatrics Shuang Ho Hospital, Taipei Medical University, 291, Jhongjheng Rd., Jhonghe Dist., New Taipei City 23561, Taiwan.
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34
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López-Díez R, Rastrojo A, Villate O, Aguado B. Complex tissue-specific patterns and distribution of multiple RAGE splice variants in different mammals. Genome Biol Evol 2014; 5:2420-35. [PMID: 24273313 PMCID: PMC3879976 DOI: 10.1093/gbe/evt188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The receptor for advanced glycosylation end products (RAGE) is a multiligand receptor involved in diverse cell signaling pathways. Previous studies show that this gene expresses several splice variants in human, mouse, and dog. Alternative splicing (AS) plays an important role in expanding transcriptomic and proteomic diversity, and it has been related to disease. AS is also one of the main evolutionary mechanisms in mammalian genomes. However, limited information is available regarding the AS of RAGE in a wide context of mammalian tissues. In this study, we examined in detail the different RAGE mRNAs generated by AS from six mammals, including two primates (human and monkey), two artiodactyla (cow and pig), and two rodentia (mouse and rat) in 6–18 different tissues including fetal, adult, and tumor. By nested reverse transcription-polymerase chain reaction (RT-PCR) we identified a high number of splice variants including noncoding transcripts and predicted coding ones with different potential protein modifications affecting mainly the transmembrane and ligand-binding domains that could influence their biological function. However, analysis of RNA-seq data enabled detecting only the most abundant splice variants. More than 80% of the detected RT-PCR variants (87 of 101 transcripts) are novel (different exon/intron structure to the previously described ones), and interestingly, 20–60% of the total transcripts (depending on the species) are noncoding ones that present tissue specificity. Our results suggest that RAGE undergoes extensive AS in mammals, with different expression patterns among adult, fetal, and tumor tissues. Moreover, most splice variants seem to be species specific, especially the noncoding variants, with only two (canonical human Tv1-RAGE, and human N-truncated or Tv10-RAGE) conserved among the six different species. This could indicate a special evolution pattern of this gene at mRNA level.
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Affiliation(s)
- Raquel López-Díez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), Spain
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Fam40b is required for lineage commitment of murine embryonic stem cells. Cell Death Dis 2014; 5:e1320. [PMID: 25010986 PMCID: PMC4123067 DOI: 10.1038/cddis.2014.273] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/25/2014] [Accepted: 05/21/2014] [Indexed: 02/06/2023]
Abstract
FAM40B (STRIP2) is a member of the striatin-interacting phosphatase and kinase (STRIPAK) complex that is involved in the regulation of various processes such as cell proliferation and differentiation. Its role for differentiation processes in embryonic stem cells (ESCs) is till now completely unknown. Short hairpin RNA (shRNA)-mediated silencing of Fam40b expression in ESCs and differentiating embryoid bodies (EBs) led to perturbed differentiation to embryonic germ layers and their derivatives including a complete abrogation of cardiomyogenesis. Pluripotency factors such as Nanog, Oct4 and Sox2 as well as epigenetic factors such as histone acetyltransferase type B (HAT1) and DNA (cytosine-5)-methyltransferase 3-β (Dnmt3b) were highly upregulated in Fam40b knockdown EBs as compared with control and scrambled EBs. To examine the relevance of Fam40b for development in vivo, Fam40b was knocked down in developing zebrafish. Morpholino-mediated knockdown of Fam40b led to severe abnormalities of the cardiovascular system, including an impaired expression of ventricular myosin heavy chain (vmhc) and of cardiac myosin light chain 2 (cmlc2) in the heart. We identified the gene product of Fam40b in ESCs as a perinuclear and nucleolar protein with a molecular weight of 96 kDa. We conclude that the expression of Fam40b is essential for the lineage commitment of murine embryonic stem cells (mESCs) into differentiated somatic cells via mechanisms involving pluripotency and epigenetic networks.
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36
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Kaur P, Liu F, Tan JR, Lim KY, Sepramaniam S, Karolina DS, Armugam A, Jeyaseelan K. Non-Coding RNAs as Potential Neuroprotectants against Ischemic Brain Injury. Brain Sci 2013; 3:360-95. [PMID: 24961318 PMCID: PMC4061830 DOI: 10.3390/brainsci3010360] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/19/2013] [Accepted: 03/06/2013] [Indexed: 01/24/2023] Open
Abstract
Over the past decade, scientific discoveries have highlighted new roles for a unique class of non-coding RNAs. Transcribed from the genome, these non-coding RNAs have been implicated in determining the biological complexity seen in mammals by acting as transcriptional and translational regulators. Non-coding RNAs, which can be sub-classified into long non-coding RNAs, microRNAs, PIWI-interacting RNAs and several others, are widely expressed in the nervous system with roles in neurogenesis, development and maintenance of the neuronal phenotype. Perturbations of these non-coding transcripts have been observed in ischemic preconditioning as well as ischemic brain injury with characterization of the mechanisms by which they confer toxicity. Their dysregulation may also confer pathogenic conditions in neurovascular diseases. A better understanding of their expression patterns and functions has uncovered the potential use of these riboregulators as neuroprotectants to antagonize the detrimental molecular events taking place upon ischemic-reperfusion injury. In this review, we discuss the various roles of non-coding RNAs in brain development and their mechanisms of gene regulation in relation to ischemic brain injury. We will also address the future directions and open questions for identifying promising non-coding RNAs that could eventually serve as potential neuroprotectants against ischemic brain injury.
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Affiliation(s)
- Prameet Kaur
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Fujia Liu
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Jun Rong Tan
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Kai Ying Lim
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Sugunavathi Sepramaniam
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Dwi Setyowati Karolina
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Arunmozhiarasi Armugam
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Kandiah Jeyaseelan
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
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37
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Chai B, Li JY, Fritze D, Zhang W, Xia Z, Mulholland MW. A novel transcript is up-regulated by fasting in the hypothalamus and enhances insulin signalling. J Neuroendocrinol 2013; 25:292-301. [PMID: 22935015 PMCID: PMC4651207 DOI: 10.1111/j.1365-2826.2012.02378.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/16/2012] [Accepted: 08/24/2012] [Indexed: 12/18/2022]
Abstract
A transcript of unknown function, regulated by fasting and feeding, was identified by microarray analysis. The transcript is up-regulated in the fasting state. An 1168-bp cDNA was cloned from rat hypothalamus and sequenced. This sequence is consistent with adipogenesis down-regulating transcript 3 (AGD3) (also known as human OCC-1) mRNA. A protein sequence identical to AGD3 was determined by mass spectrometry. In the rat brain, AGD3 mRNA is distributed in the arcuate nucleus, ventromedial hypothalamus, amygdaloid nuclei, hippocampus, and somatic cortex. Double in situ hybridisation showed that AGD3 mRNA is co-localised with pro-opiomelanocortin and neuropeptide Y in arcuate nucleus neurones. AGD3 binds with insulin receptor substrate 4 and increases insulin-stimulated phospho-Akt and regulates AMP-activated protein kinase and mammalian target of rapamycin downstream target S6 kinase phosphorylation.
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Affiliation(s)
| | | | | | | | | | - Michael W Mulholland
- Corresponding Author: Michael W. Mulholland, M.D., Ph.D., 2101 Taubman Center, 1500 E. Medical Center Dr., Ann Arbor, MI 48109-0346, USA, Tel.: +1 734 936 3236; fax: +1 734 763 5625,
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38
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Mizutani R, Wakamatsu A, Tanaka N, Yoshida H, Tochigi N, Suzuki Y, Oonishi T, Tani H, Tano K, Ijiri K, Isogai T, Akimitsu N. Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells. PLoS One 2012; 7:e34949. [PMID: 22532836 PMCID: PMC3330809 DOI: 10.1371/journal.pone.0034949] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 03/08/2012] [Indexed: 02/02/2023] Open
Abstract
Whole transcriptome analyses have revealed a large number of novel transcripts including long and short noncoding RNAs (ncRNAs). Currently, there is great interest in characterizing the functions of the different classes of ncRNAs and their relevance to cellular processes. In particular, nuclear long ncRNAs may be involved in controlling various aspects of biological regulation, such as stress responses. By a combination of bioinformatic and experimental approaches, we identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Some nuclear long ncRNAs were conserved among vertebrates, whereas others were found only among primates. Expression profiling of the nuclear long ncRNAs in human tissues revealed that most were expressed ubiquitously. A subset of the identified nuclear long ncRNAs was induced by the genotoxic agents mitomycin C or doxorubicin, in HeLa Tet-off cells. There were no commonly altered nuclear long ncRNAs between mitomycin C- and doxorubicin-treated cells. These results suggest that distinct sets of nuclear long ncRNAs play roles in cellular defense mechanisms against specific genotoxic agents, and that particular long ncRNAs have the potential to be surrogate indicators of a specific cell stress.
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Affiliation(s)
- Rena Mizutani
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Ai Wakamatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Hidenori Tani
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Keiko Tano
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Kenichi Ijiri
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Takao Isogai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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Reconstruction of human elastic cartilage by a CD44+ CD90+ stem cell in the ear perichondrium. Proc Natl Acad Sci U S A 2011; 108:14479-84. [PMID: 21836053 DOI: 10.1073/pnas.1109767108] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite the great demands for treating craniofacial injuries or abnormalities, effective treatments are currently lacking. One promising approach involves human elastic cartilage reconstruction using autologous stem/progenitor populations. Nevertheless, definitive evidence of the presence of stem cells in human auricular cartilage remains to be established. Here, we demonstrate that human auricular perichondrium, which can be obtained via a minimally invasive approach, harbors a unique cell population, termed as cartilage stem/progenitor cells (CSPCs). The clonogenic progeny of a single CD44(+) CD90(+) CSPC displays a number of features characteristic of stem cells. Highly chondrogenic CSPCs were shown to reconstruct large (>2 cm) elastic cartilage after extended expansion and differentiation. CSPC-derived cartilage was encapsulated by a perichondrium layer, which contains a CD44(+) CD90(+) self-renewing stem/progenitor population and was maintained without calcification or tumor formation even after 10 mo. This is a unique report demonstrating the presence of stem cells in auricular cartilage. Utilization of CSPCs will provide a promising reconstructive material for treating craniofacial defects with successful long-term tissue restoration.
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40
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Ito T, Tsuruta S, Tomita K, Kikuchi K, Yokoi T, Aizawa Y. Genes that integrate multiple adipogenic signaling pathways in human mesenchymal stem cells. Biochem Biophys Res Commun 2011; 409:786-91. [DOI: 10.1016/j.bbrc.2011.05.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 05/16/2011] [Indexed: 11/24/2022]
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41
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Abstract
New DNA sequencing technologies have provided novel insights into eukaryotic genomes, epigenomes, and the transcriptome, including the identification of new non-coding RNA (ncRNA) classes such as promoter-associated RNAs and long RNAs. Moreover, it is now clear that up to 90% of eukaryotic genomes are transcribed, generating an extraordinary range of RNAs with no coding capacity. Taken together, these new discoveries are modifying the status quo in genomic science by demonstrating that the eukaryotic gene pool is divided into two distinct categories of transcripts: protein-coding and non-coding. The function of the majority of ncRNAs produced by the transcriptome is largely unknown; however, it is probable that many are associated with epigenetic mechanisms. The purpose of this review is to describe the most recent discoveries in the ncRNA field that implicate these molecules as key players in the epigenome.
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Affiliation(s)
- Fabrício F Costa
- Cancer Biology and Epigenomics Program, Children's Memorial Research Center and Northwestern University's Feinberg School of Medicine, 2300 Children's Plaza, Chicago, IL, USA.
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42
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Folkers ME, Delker DA, Maxwell CI, Nelson CA, Schwartz JJ, Nix DA, Hagedorn CH. ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver. PLoS One 2011; 6:e14697. [PMID: 21359205 PMCID: PMC3040182 DOI: 10.1371/journal.pone.0014697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 01/24/2011] [Indexed: 01/02/2023] Open
Abstract
Microarray studies of chronic hepatitis C infection have provided valuable
information regarding the host response to viral infection. However, recent
studies of the human transcriptome indicate pervasive transcription in
previously unannotated regions of the genome and that many RNA transcripts have
short or lack 3′ poly(A) ends. We hypothesized that using ENCODE tiling
arrays (1% of the genome) in combination with affinity purifying Pol II
RNAs by their unique 5′ m7GpppN cap would identify previously
undescribed annotated and unannotated genes that are differentially expressed in
liver during hepatitis C virus (HCV) infection. Both 5′-capped and
poly(A)+ populations of RNA were analyzed using ENCODE tiling arrays.
Sixty-four annotated genes were significantly increased in HCV cirrhotic as
compared to control liver; twenty-seven (42%) of these genes were
identified only by analyzing 5′ capped RNA. Thirty-one annotated genes
were significantly decreased; sixteen (50%) of these were identified only
by analyzing 5′ capped RNA. Bioinformatic analysis showed that capped RNA
produced more consistent results, provided a more extensive expression profile
of intronic regions and identified upregulated Pol II transcriptionally active
regions in unannotated areas of the genome in HCV cirrhotic liver. Two of these
regions were verified by PCR and RACE analysis. qPCR analysis of liver biopsy
specimens demonstrated that these unannotated transcripts, as well as IRF1,
TRIM22 and MET, were also upregulated in hepatitis C with mild inflammation and
no fibrosis. The analysis of 5′ capped RNA in combination with ENCODE
tiling arrays provides additional gene expression information and identifies
novel upregulated Pol II transcripts not previously described in HCV infected
liver. This approach, particularly when combined with new RNA sequencing
technologies, should also be useful in further defining Pol II transcripts
differentially regulated in specific disease states and in studying RNAs
regulated by changes in pre-mRNA splicing or 3′ polyadenylation
status.
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Affiliation(s)
- Milan E. Folkers
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
| | - Don A. Delker
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Christopher I. Maxwell
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Cassie A. Nelson
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
| | - Jason J. Schwartz
- Department of Surgery, University of Utah,
Salt Lake City, Utah, United States of America
| | - David A. Nix
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
| | - Curt H. Hagedorn
- Department of Medicine, University of Utah,
Salt Lake City, Utah, United States of America
- Huntsman Cancer Institute, University of Utah,
Salt Lake City, Utah, United States of America
- Department of Experimental Pathology,
University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines. BMC Mol Biol 2010; 11:99. [PMID: 21162727 PMCID: PMC3023731 DOI: 10.1186/1471-2199-11-99] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 12/16/2010] [Indexed: 12/13/2022] Open
Abstract
Background Postgenomic transcriptome analyses have identified large numbers of noncoding (nc)RNAs in mammalian cells. However, the biological function of long ncRNAs in mammalian cells remains largely unknown. Our recent expression profiling of selected human long ncRNAs revealed that a majority were expressed in an organ-specific manner, suggesting their function was linked to specific physiological phenomena in each organ. We investigated the characteristics and function of ncRNAs that were specifically expressed in the thymus, the site of T-cell selection and maturation. Results Expression profiling of 10 thymus-specific ncRNAs in 17 T-cell leukemia cell lines derived from various stages of T-cell maturation revealed that HIT14168 ncRNA, named Thy-ncR1, was specifically expressed in cell lines derived from stage III immature T cells in which the neighbouring CD1 gene cluster is also specifically activated. The Thy-ncR1 precursor exhibited complex alternative splicing patterns and differential usage of the 5' terminus leading to the production of an estimated 24 isoforms, which were predominantly located in the cytoplasm. Selective RNAi knockdown of each Thy-ncR1 isoform demonstrated that microfibril-associated glycoprotein 4 (MFAP4) mRNA was negatively regulated by two major Thy-ncR1 isoforms. Intriguingly, the MFAP4 mRNA level was controlled by a hUPF1-dependent mRNA degradation pathway in the cytoplasm distinct from nonsense-mediated decay. Conclusions This study identified Thy-ncR1 ncRNA to be specifically expressed in stage III immature T cells in which the neighbouring CD1 gene cluster was activated. Complex alternative splicing produces multiple Thy-ncR1 isoforms. Two major Thy-ncR1 isoforms are cytoplasmic riboregulators that suppress the expression of MFAP4 mRNA, which is degraded by an uncharacterized hUPF1-dependent pathway.
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Sousa JF, Torrieri R, Silva RR, Pereira CG, Valente V, Torrieri E, Peronni KC, Martins W, Muto N, Francisco G, Brohem CA, Carlotti CG, Maria-Engler SS, Chammas R, Espreafico EM. Novel primate-specific genes, RMEL 1, 2 and 3, with highly restricted expression in melanoma, assessed by new data mining tool. PLoS One 2010; 5:e13510. [PMID: 20975957 PMCID: PMC2958148 DOI: 10.1371/journal.pone.0013510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 09/15/2010] [Indexed: 01/07/2023] Open
Abstract
Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.
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Affiliation(s)
- Josane F. Sousa
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Raul Torrieri
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rodrigo R. Silva
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cristiano G. Pereira
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Valeria Valente
- Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Erico Torrieri
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Kamila C. Peronni
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Waleska Martins
- Clinical Staff, Molecular Biology Group, Pathology Division, AC Camargo Hospital Melanoma Group, São Paulo, São Paulo, Brazil
| | - Nair Muto
- Clinical Staff, Molecular Biology Group, Pathology Division, AC Camargo Hospital Melanoma Group, São Paulo, São Paulo, Brazil
| | - Guilherme Francisco
- Departamento de Radiologia e Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Abdo Brohem
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Carlos G. Carlotti
- Departamento de Cirurgia e Anatomia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Silvya S. Maria-Engler
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Roger Chammas
- Departamento de Radiologia e Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Enilza M. Espreafico
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- * E-mail:
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Motaln H, Schichor C, Lah TT. Human mesenchymal stem cells and their use in cell-based therapies. Cancer 2010; 116:2519-30. [PMID: 20301117 DOI: 10.1002/cncr.25056] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human population is increasingly facing various diseases, including types of cancer, that cannot be cured with conventional drugs. Advanced drug targeting of tumor cells is also often impossible when treating highly invasive and infiltrative tumors such as glioblastoma or pulmonary cancer, because of tumor cells' high migration and invasiveness. Pluripotent human mesenchymal stem cells (hMSCs) have been extensively studied, and strategies are being proposed for treating "incurable" cancers and injury/disease-affected organs. Because of their own intrinsic properties, involving homing and immunomodulatory potency, hMSCs could be used as an excellent cell/drug delivery vehicle in those cell-based therapies. Their unprecedented use has been shadowed, however, by their spontaneous transformation, which links them to cancer-initiating cells during tumor development. How malignant initiation proceeds in vivo, and what are the exact characteristics of the cancer-initiating cells, still remain to be investigated. In the present review, the authors summed up the most recent knowledge about hMSC characteristics, their malignant transformation, and outlined the possibilities of their safe use in novel cell-based therapies.
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Affiliation(s)
- Helena Motaln
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia.
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Fujii YR. RNA Genes: Retroelements and Virally Retroposable microRNAs in Human Embryonic Stem Cells. Open Virol J 2010; 4:63-75. [PMID: 20835360 PMCID: PMC2936035 DOI: 10.2174/1874357901004010063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 04/15/2010] [Accepted: 04/20/2010] [Indexed: 11/29/2022] Open
Abstract
Embryonic stem cells (ESCs) are capable of undergoing self-renewal, and their developmental ability is known as the stemness. Recently, microRNAs (miRNAs) as regulators have been isolated from ESCs. Although Dicer and DiGeorge syndrome critical region gene 8 (DGCR8) are essential factors for the biogeneration of miRNA, Dicer-knockout (KO) ESCs have showed to fail to express differentiation markers and DGCR8-KO ESCs have showed to be arrest in the G1 phase. Furthermore, Dicer-KO ESCs lost the ability to epigenetically silence retroelemtns (REs). REs are expressed and transposed in ESCs, whose transcripts control expression of miRNAs, and their transposable retroelement (TE) expression is, therefore related to ESC proliferation and differentiation, suggesting that the interplay between miRNAs and REs may have a deep responsibility for the stemness including a short G1/S transition and for RE regulation in ESCs.
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Affiliation(s)
- Yoichi R. Fujii
- Retroviral Genetics Group, Nagoya City University, Nagoya, 467-8603, Japan
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Takizawa T, Gemma A, Ui-Tei K, Aizawa Y, Sadovsky Y, Robinson JM, Seike M, Miyake K. Basic and Clinical Studies on Functional RNA Molecules for Advanced Medical Technologies. J NIPPON MED SCH 2010; 77:71-9. [DOI: 10.1272/jnms.77.71] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Toshihiro Takizawa
- Division of Molecular Medicine and Anatomy, Graduate School of Medicine, Nippon Medical School
| | - Akihiko Gemma
- Division of Pulmonary Medicine, Infection Diseases and Oncology, Graduate School of Medicine, Nippon Medical School
| | - Kumiko Ui-Tei
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo
| | - Yasunori Aizawa
- Center for Biological Resources and Informatics, Tokyo Institute of Technology
| | - Yoel Sadovsky
- Magee-Womens Research Institute, University of Pittsburgh
| | - John M. Robinson
- Department of Physiology and Cell Biology, Ohio State University
| | - Masahiro Seike
- Division of Pulmonary Medicine, Infection Diseases and Oncology, Graduate School of Medicine, Nippon Medical School
| | - Koichi Miyake
- Division of Biochemistry and Molecular Biology, Graduate School of Medicine, and Division of Gene Therapy Research Center for Advanced Medical Technology, Nippon Medical School
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