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Hussain S, Gupta G, Shahwan M, Bansal P, Kaur H, Deorari M, Pant K, Ali H, Singh SK, Rama Raju Allam VS, Paudel KR, Dua K, Kumarasamy V, Subramaniyan V. Non-coding RNA: A key regulator in the Glutathione-GPX4 pathway of ferroptosis. Noncoding RNA Res 2024; 9:1222-1234. [PMID: 39036600 PMCID: PMC11259992 DOI: 10.1016/j.ncrna.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/26/2024] [Accepted: 05/19/2024] [Indexed: 07/23/2024] Open
Abstract
Ferroptosis, a form of regulated cell death, has emerged as a crucial process in diverse pathophysiological states, encompassing cancer, neurodegenerative ailments, and ischemia-reperfusion injury. The glutathione (GSH)-dependent lipid peroxidation pathway, chiefly governed by glutathione peroxidase 4 (GPX4), assumes an essential part in driving ferroptosis. GPX4, as the principal orchestrator of ferroptosis, has garnered significant attention across cancer, cardiovascular, and neuroscience domains over the past decade. Noteworthy investigations have elucidated the indispensable functions of ferroptosis in numerous diseases, including tumorigenesis, wherein robust ferroptosis within cells can impede tumor advancement. Recent research has underscored the complex regulatory role of non-coding RNAs (ncRNAs) in regulating the GSH-GPX4 network, thus influencing cellular susceptibility to ferroptosis. This exhaustive review endeavors to probe into the multifaceted processes by which ncRNAs control the GSH-GPX4 network in ferroptosis. Specifically, we delve into the functions of miRNAs, lncRNAs, and circRNAs in regulating GPX4 expression and impacting cellular susceptibility to ferroptosis. Moreover, we discuss the clinical implications of dysregulated interactions between ncRNAs and GPX4 in several conditions, underscoring their capacity as viable targets for therapeutic intervention. Additionally, the review explores emerging strategies aimed at targeting ncRNAs to modulate the GSH-GPX4 pathway and manipulate ferroptosis for therapeutic advantage. A comprehensive understanding of these intricate regulatory networks furnishes insights into innovative therapeutic avenues for diseases associated with perturbed ferroptosis, thereby laying the groundwork for therapeutic interventions targeting ncRNAs in ferroptosis-related pathological conditions.
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Affiliation(s)
- Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, 346, United Arab Emirates
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Moyad Shahwan
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, 346, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, United Arab Emirates
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka, 560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh, 247341, India
- Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand, 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Kumud Pant
- Graphic Era (Deemed to be University), Clement Town, Dehradun, 248002, India
- Graphic Era Hill University, Clement Town, Dehradun, 248002, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- School of Medical and Life Sciences, Sunway University, 47500 Sunway City, Malaysia
| | | | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, 2007, Australia
| | - Kamal Dua
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, P.O. Box: 123 Broadway, Ultimo, NSW, 2007, Australia
| | - Vinoth Kumarasamy
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
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He Y, Ma L, Zeng X, Xie J, Ning X. Systematic identification and analysis of immune-related circRNAs of Pelteobagrus fulvidraco involved in Aeromonas veronii infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 51:101256. [PMID: 38797004 DOI: 10.1016/j.cbd.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Circular RNA (circRNA) represents a type of newly discovered non-coding RNA, distinguished by its closed loop structure formed through covalent bonds. Recent studies have revealed that circRNAs have crucial influences on host anti-pathogen responses. Yellow catfish (Pelteobagrus fulvidraco), an important aquaculture fish with great economic value, is susceptible to Aeromonas veronii, a common aquatic pathogen that can cause acute death. Here, we reported the first systematic investigation of circRNAs in yellow catfish, especially those associated with A. veronii infection at different time points. A total of 1205 circRNAs were identified, which were generated from 875 parental genes. After infection, 47 circRNAs exhibited differential expression patterns (named DEcirs). The parental genes of these DEcirs were functionally engaged in immune-related processes. Accordingly, seven DEcirs (novel_circ_000226, 278, 401, 522, 736, 843, and 975) and six corresponding parental genes (ADAMTS13, HAMP1, ANG3, APOA1, FGB, and RALGPS1) associated with immunity were obtained, and their expression was confirmed by RT-qPCR. Moreover, we found that these DEcir-gene pairs likely acted through pathways, such as platelet activation, antimicrobial humoral response, and regulation of Ral protein signal transduction, to influence host immune defenses. Additionally, integrated analysis showed that, of the 7 immune-related DEcirs, three targeted 16 miRNAs, which intertwined into circRNA-miRNA networks. These findings revealed that circRNAs, by targeting genes or miRNAs are highly involved in anti-bacterial responses in yellow catfish. Our study comprehensively illustrates the roles of circRNAs in yellow catfish immune defenses. The identified DEcirs and the circRNA-miRNA network will contribute to the further investigations on the molecular mechanisms underlying yellow catfish immune responses.
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Affiliation(s)
- Yongxin He
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lina Ma
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xueyu Zeng
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Jingjing Xie
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China.
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Jurj A, Fontana B, Varani G, Calin GA. Small molecules targeting microRNAs: new opportunities and challenges in precision cancer therapy. Trends Cancer 2024:S2405-8033(24)00121-3. [PMID: 39107162 DOI: 10.1016/j.trecan.2024.06.006] [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: 11/27/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 08/09/2024]
Abstract
Noncoding RNAs, especially miRNAs, play a pivotal role in cancer initiation and metastasis, underscoring their susceptibility to precise modulation via small molecule inhibitors. This review examines the innovative strategy of targeting oncogenic miRNAs with small drug-like molecules, an approach that can reshape the cancer treatment landscape. We review the current understanding of the multifaceted roles of miRNAs in oncogenesis, highlighting emerging therapeutic paradigms that have the potential to expand cancer treatment options. As research on small molecule inhibitors of miRNA is still in its early stages, ongoing investigative efforts and the development of new technologies and chemical matter are essential to fulfill the significant potential of this innovative approach to cancer treatment.
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Affiliation(s)
- Ancuta Jurj
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beatrice Fontana
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Musgrove MRB, Mikhaylova M, Bredy TW. Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non-coding RNAs spanning learning, memory and adaptive immunity. J Neurochem 2024; 168:961-976. [PMID: 38339812 DOI: 10.1111/jnc.16071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs (ncRNAs) are highly plastic RNA molecules that can sequester cellular proteins and other RNAs, serve as transporters of cellular cargo and provide spatiotemporal feedback to the genome. Mounting evidence indicates that ncRNAs are central to biology, and are critical for neuronal development, metabolism and intra- and intercellular communication in the brain. Their plasticity arises from state-dependent dynamic structure states that can be influenced by cell type and subcellular environment, which can subsequently enable the same ncRNA with discrete functions in different contexts. Here, we highlight different classes of brain-enriched ncRNAs, including microRNA, long non-coding RNA and other enigmatic ncRNAs, that are functionally important for both learning and memory and adaptive immunity, and describe how they may promote cross-talk between these two evolutionarily ancient biological systems.
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Affiliation(s)
- Mason R B Musgrove
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Marina Mikhaylova
- AG Optobiologie, Institute für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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5
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Kong J, Lyu H, Ouyang Q, Shi H, Zhang R, Xiao S, Guo D, Zhang Q, Chen XZ, Zhou C, Tang J. Insights into the Roles of Epigenetic Modifications in Ferroptosis. BIOLOGY 2024; 13:122. [PMID: 38392340 PMCID: PMC10886775 DOI: 10.3390/biology13020122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Ferroptosis is a non-apoptotic mode of cell death driven by membrane lipid peroxidation and is characterized by elevated intracellular levels of Fe2+, ROS, and lipid peroxidation. Studies have shown that ferroptosis is related to the development of multiple diseases, such as cancer, neurodegenerative diseases, and acute myeloid leukemia. Ferroptosis plays a dual role in the occurrence and development of these diseases. Ferroptosis mainly involves iron metabolism, ROS, and lipid metabolism. Various mechanisms, including epigenetic regulation, have been reported to be deeply involved in ferroptosis. Abnormal epigenetic modifications have been reported to promote tumor onset or other diseases and resistance to chemotherapy drugs. In recent years, diversified studies have shown that epigenetic modification is involved in ferroptosis. In this review, we reviewed the current resistance system of ferroptosis and the research progress of epigenetic modification, such as DNA methylation, RNA methylation, non-coding RNAs, and histone modification in cancer and other diseases by regulating ferroptosis.
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Affiliation(s)
- Jinghua Kong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Qian Ouyang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Shi
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Rui Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Shuai Xiao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Dong Guo
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Qi Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
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Li K, Ma L, Lu Z, Yan L, Chen W, Wang B, Xu H, Asemi Z. Apoptosis and heart failure: The role of non-coding RNAs and exosomal non-coding RNAs. Pathol Res Pract 2023; 248:154669. [PMID: 37422971 DOI: 10.1016/j.prp.2023.154669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023]
Abstract
Heart failure is a condition that affects the cardio vascular system and occurs if the heart cannot adequately pump the oxygen and blood to the body. Myocardial infarction, reperfusion injury, and this disease is the only a few examples of the numerous cardiovascular illnesses that are impacted by the closely controlled cell deletion process known as apoptosis. Attention has been paid to the creation of alternative diagnostic and treatment modalities for the condition. Recent evidences have shown that some non-coding RNAs (ncRNAs) influence the stability of proteins, control of transcription factors, and HF apoptosis through a variety of methods. Exosomes make a significant paracrine contribution to the regulation of illnesses as well as to the communication between nearby and distant organs. However, it has not yet been determined whether exosomes regulate the cardiomyocyte-tumor cell interaction in ischemia HF to limit the vulnerability of malignancy to ferroptosis. Here, we list the numerous ncRNAs in HF that are connected to apoptosis. In addition, we emphasize the significance of exosomal ncRNAs in the HF.
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Affiliation(s)
- Ketao Li
- Department of cardiology, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, Zhejiang 310022, China
| | - Liping Ma
- Department of cardiology, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, Zhejiang 310022, China
| | - Zhiwei Lu
- Hangzhou Heyunjia Hospital, Hangzhou, Zhe'jiang 310000, China
| | - Laixing Yan
- Department of cardiology, Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, Zhejiang 310022, China
| | - Wan Chen
- Department of Cardiology, Jiulongpo First People's Hospital, Chongqing 400051, China
| | - Bing Wang
- Department of cardiology, Zouping People's Hospital, Zouping, Shandong 256299, China
| | - Huiju Xu
- Department of cardiology, Hangzhou Mingzhou Hospital, Hangzhou, Zhe'jiang 311215, China.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
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Wang Q, Long Z, Zhu F, Li H, Xiang Z, Liang H, Wu Y, Dai X, Zhu Z. Integrated analysis of lncRNA/circRNA-miRNA-mRNA in the proliferative phase of liver regeneration in mice with liver fibrosis. BMC Genomics 2023; 24:417. [PMID: 37488484 PMCID: PMC10364436 DOI: 10.1186/s12864-023-09478-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Non-coding RNAs play important roles in liver regeneration; however, their functions and mechanisms of action in the regeneration of fibrotic liver have not been elucidated. We aimed to clarify the expression patterns and regulatory functions of lncRNAs, circRNAs, miRNAs, and mRNAs in the proliferative phase of fibrotic liver regeneration. METHODS Based on a mouse model of liver fibrosis with 70% hepatectomy, whole-transcriptome profiling was performed using high-throughput sequencing on samples collected at 0, 12, 24, 48, and 72 h after hepatectomy. Hub genes were selected by weighted gene co-expression network analysis and subjected to enrichment analysis. Integrated analysis was performed to reveal the interactions of differentially expressed (DE) lncRNAs, circRNAs, miRNAs, and mRNAs, and to construct lncRNA-mRNA cis- and trans-regulatory networks and lncRNA/circRNA-miRNA-mRNA ceRNA regulatory networks. Real-Time quantitative PCR was used to validate part of the ceRNA network. RESULTS A total of 1,329 lncRNAs, 48 circRNAs, 167 miRNAs, and 6,458 mRNAs were differentially expressed, including 812 hub genes. Based on these DE RNAs, we examined several mechanisms of ncRNA regulatory networks, including lncRNA cis and trans interactions, circRNA parental genes, and ceRNA pathways. We constructed a cis-regulatory core network consisting of 64 lncRNA-mRNA pairs (53 DE lncRNAs and 58 hub genes), a trans-regulatory core network consisting of 103 lncRNA-mRNA pairs (18 DE lncRNAs and 85 hub genes), a lncRNA-miRNA-mRNA ceRNA core regulatory network (20 DE lncRNAs, 12 DE miRNAs, and 33 mRNAs), and a circRNA-miRNA-mRNA ceRNA core regulatory network (5 DE circRNAs, 5 DE miRNAs, and 39 mRNAs). CONCLUSIONS These results reveal the expression patterns of lncRNAs, circRNAs, miRNAs, and mRNAs in the proliferative phase of fibrotic liver regeneration, as well as core regulatory networks of mRNAs and non-coding RNAs underlying liver regeneration. The findings provide insights into molecular mechanisms that may be useful in developing new therapeutic approaches to ameliorate diseases that are characterized by liver fibrosis, which would be beneficial for the prevention of liver failure and treatment of liver cancer.
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Affiliation(s)
- Qian Wang
- The First Affiliated Hospital, Department of Reproductive Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhangtao Long
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Fengfeng Zhu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Huajian Li
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhiqiang Xiang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hao Liang
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yachen Wu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaoming Dai
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Zhu Zhu
- The First Affiliated Hospital, Department of Hepatobiliary Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- The First Affiliated Hospital, Department of Education and Training, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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Dunkel H, Wehrmann H, Jensen LR, Kuss AW, Simm S. MncR: Late Integration Machine Learning Model for Classification of ncRNA Classes Using Sequence and Structural Encoding. Int J Mol Sci 2023; 24:8884. [PMID: 37240230 PMCID: PMC10218863 DOI: 10.3390/ijms24108884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Non-coding RNA (ncRNA) classes take over important housekeeping and regulatory functions and are quite heterogeneous in terms of length, sequence conservation and secondary structure. High-throughput sequencing reveals that the expressed novel ncRNAs and their classification are important to understand cell regulation and identify potential diagnostic and therapeutic biomarkers. To improve the classification of ncRNAs, we investigated different approaches of utilizing primary sequences and secondary structures as well as the late integration of both using machine learning models, including different neural network architectures. As input, we used the newest version of RNAcentral, focusing on six ncRNA classes, including lncRNA, rRNA, tRNA, miRNA, snRNA and snoRNA. The late integration of graph-encoded structural features and primary sequences in our MncR classifier achieved an overall accuracy of >97%, which could not be increased by more fine-grained subclassification. In comparison to the actual best-performing tool ncRDense, we had a minimal increase of 0.5% in all four overlapping ncRNA classes on a similar test set of sequences. In summary, MncR is not only more accurate than current ncRNA prediction tools but also allows the prediction of long ncRNA classes (lncRNAs, certain rRNAs) up to 12.000 nts and is trained on a more diverse ncRNA dataset retrieved from RNAcentral.
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Affiliation(s)
- Heiko Dunkel
- Institute of Bioinformatics, University Medicine Greifswald, Walther-Rathenau Str. 48, 17489 Greifswald, Germany
| | - Henning Wehrmann
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt am Main, Germany
| | - Lars R. Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Andreas W. Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Walther-Rathenau Str. 48, 17489 Greifswald, Germany
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Lv X, Luo Q, Xin S, Zheng W, Xu T, Sun Y. Circular RNA circPlce1 regulates innate immune response in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108561. [PMID: 36690265 DOI: 10.1016/j.fsi.2023.108561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
In recent years, more and more researchers have devoted to the study of circular RNAs (circRNAs) in noncoding RNAs. As an important regulator in a variety of biological processes, circRNAs are relatively abundant in the study of mammals, while research in lower vertebrates is still lacking. In this study, we found a circRNA, circPlce1, related to innate immune response in Miichthys miiuy (miiuy croaker). The experimental results confirmed that circPlce1 could promote the production of antiviral genes and inflammatory response under the stimulation of poly (I: C) and LPS. We also confirmed that circPlce1 can promote NF-κB and IRF3 pathways through luciferase reporter assay experiment. In addition, we also found that circPlce1 can promote cell proliferation and improve cell viability. In conclusion, our results showed that circPlce1 plays an active role in regulating inflammatory response, cell proliferation and cell viability, providing a foundation for the study of the biological function of circRNAs in the innate immune response in teleost fish.
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Affiliation(s)
- Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qiang Luo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China.
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10
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Andrews RJ, Rouse WB, O’Leary CA, Booher NJ, Moss WN. ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes. PeerJ 2022; 10:e14361. [PMID: 36389431 PMCID: PMC9651051 DOI: 10.7717/peerj.14361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural stability, evidence of sequence-ordered (potentially evolved) structure, and unique model structures comprised of recurring base pairs with the greatest structural bias. A key step in quantifying this propensity for ordered structure is the prediction of secondary structural stability for randomized sequences which, in the original implementation of ScanFold, is explicitly evaluated. This slow process has limited the rapid identification of ordered structures in large genomes/transcriptomes, which we seek to overcome in this current work introducing ScanFold 2.0. In this revised version of ScanFold, we no longer explicitly evaluate randomized sequence folding energy, but rather estimate it using a machine learning approach. For high randomization numbers, this can increase prediction speeds over 100-fold compared to ScanFold 1.0, allowing for the analysis of large sequences, as well as the use of additional folding algorithms that may be computationally expensive. In the testing of ScanFold 2.0, we re-evaluate the Zika, HIV, and SARS-CoV-2 genomes and compare both the consistency of results and the time of each run to ScanFold 1.0. We also re-evaluate the SARS-CoV-2 genome to assess the quality of ScanFold 2.0 predictions vs several biochemical structure probing datasets and compare the results to those of the original ScanFold program.
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Affiliation(s)
- Ryan J. Andrews
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
| | - Warren B. Rouse
- The Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States
| | - Collin A. O’Leary
- The Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States
| | - Nicholas J. Booher
- Infrastructure and Research IT Services, Iowa State University, Ames, IA, United States
| | - Walter N. Moss
- The Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States
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11
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Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int J Mol Sci 2022; 23:ijms23179630. [PMID: 36077037 PMCID: PMC9455975 DOI: 10.3390/ijms23179630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/19/2023] Open
Abstract
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
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Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Antczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Ryszard W. Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Jun Li
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Computational Biology, Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | | | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sicheng Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- Correspondence: (Z.M.); (A.R.)
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
- Correspondence: (Z.M.); (A.R.)
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12
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Balihodzic A, Prinz F, Dengler MA, Calin GA, Jost PJ, Pichler M. Non-coding RNAs and ferroptosis: potential implications for cancer therapy. Cell Death Differ 2022; 29:1094-1106. [PMID: 35422492 PMCID: PMC9177660 DOI: 10.1038/s41418-022-00998-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022] Open
Abstract
Ferroptosis is a recently defined form of regulated cell death, which is biochemically and morphologically distinct from traditional forms of programmed cell death such as apoptosis or necrosis. It is driven by iron, reactive oxygen species, and phospholipids that are oxidatively damaged, ultimately resulting in mitochondrial damage and breakdown of membrane integrity. Numerous cellular signaling pathways and molecules are involved in the regulation of ferroptosis, including enzymes that control the cellular redox status. Alterations in the ferroptosis-regulating network can contribute to the development of various diseases, including cancer. Evidence suggests that ferroptosis is commonly suppressed in cancer cells, allowing them to survive and progress. However, cancer cells which are resistant to common chemotherapeutic drugs seem to be highly susceptible to ferroptosis inducers, highlighting the great potential of pharmacologic modulation of ferroptosis for cancer treatment. Non-coding RNAs (ncRNAs) are considered master regulators of various cellular processes, particularly in cancer where they have been implicated in all hallmarks of cancer. Recent work also demonstrated their involvement in the molecular control of ferroptosis. Hence, ncRNA-based therapeutics represent an exciting alternative to modulate ferroptosis for cancer therapy. This review summarizes the ncRNAs implicated in the regulation of ferroptosis in cancer and highlights their underlying molecular mechanisms in the light of potential therapeutic applications.
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Affiliation(s)
- Amar Balihodzic
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - Felix Prinz
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - Michael A Dengler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Philipp J Jost
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria.,Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036, Graz, Austria. .,Research Unit "Non-Coding RNAs and Genome Editing in Cancer", Division of Oncology, Medical University of Graz, 8036, Graz, Austria. .,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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13
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Lodde V, Floris M, Muroni MR, Cucca F, Idda ML. Non-coding RNAs in malaria infection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1697. [PMID: 34651456 PMCID: PMC9286032 DOI: 10.1002/wrna.1697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 12/31/2022]
Abstract
Malaria is one of the most severe infectious diseases affecting humans and it is caused by protozoan pathogens of the species Plasmodium (spp.). The malaria parasite Plasmodium is characterized by a complex, multistage life cycle that requires tight gene regulation which allows for host invasion and defense against host immune responses. Unfortunately, the mechanisms regulating gene expression during Plasmodium infection remain largely elusive, though several lines of evidence implicate a major involvement of non-coding RNAs (ncRNAs). The ncRNAs have been found to play a key role in regulating transcriptional and post-transcriptional events in a broad range of organisms including Plasmodium. In Plasmodium ncRNAs have been shown to regulate key events in the multistage life cycle and virulence ability. Here we review recent progress involving ncRNAs (microRNAs, long non-coding RNAs, and circular RNAs) and their role as regulators of gene expression during Plasmodium infection in human hosts with focus on the possibility of using these molecules as biomarkers for monitoring disease status. We also discuss the surprising function of ncRNAs in mediating the complex interplay between parasite and human host and future perspectives of the field. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Matteo Floris
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Rosaria Muroni
- Department of Medical, Surgical, and Experimental SciencesUniversity of SassariSassariItaly
| | - Francesco Cucca
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Laura Idda
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR)SassariItaly
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14
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Najafi S. Circular RNAs as emerging players in cervical cancer tumorigenesis; A review to roles and biomarker potentials. Int J Biol Macromol 2022; 206:939-953. [PMID: 35318084 DOI: 10.1016/j.ijbiomac.2022.03.103] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 03/16/2022] [Indexed: 01/10/2023]
Abstract
Cervical cancer is the most lethal gynecological cancer among women worldwide. Most of the patients are diagnosed at the advanced stages due to late diagnosis and lack of accessible and valuable approaches for early detection of the disease. Circular RNAs (circRNAs) are a distinguishable class of non-coding RNAs with characteristic loop structures. Although their function has not been completely elucidated; however, recent evidence has suggested regulatory functions for circRNAs on gene expression controlling various biological functions like cell growth and apoptosis, development, embryogenesis, and pathogenesis of human diseases particularly cancers. Studies show the role of dysregulated circRNAs in biological processes including cell proliferation, migration, invasion, apoptosis, angiogenesis, and chemoresistance contributing to affect tumorigenesis in ovarian cancer cells, animal, and clinical studies. These effects can be defined as consistent with several tumorigenesis characteristics, which are defined as "hallmarks of cancer". Additionally, dysregulated circRNAs exhibit prognostic, and diagnostic potentials both in the prediction of prognosis in ovarian cancer patients, and also their discrimination from healthy individuals. Furthermore, targeting circRNAs has shown positive results in the suppression of malignant features of cancer cells, and also in overcoming chemoresistance. In this review, I have gathered the majority of studies evaluating the role of circRNAs in the development, and progression of cervical cancer, and also have discussed prognostic, diagnostic, and therapeutic potentials of circRNAs for clinical applications in cervical cancer patients.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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15
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Martinez-Arroyo O, Ortega A, Forner MJ, Cortes R. Mesenchymal Stem Cell-Derived Extracellular Vesicles as Non-Coding RNA Therapeutic Vehicles in Autoimmune Diseases. Pharmaceutics 2022; 14:pharmaceutics14040733. [PMID: 35456567 PMCID: PMC9028692 DOI: 10.3390/pharmaceutics14040733] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/26/2022] [Indexed: 02/07/2023] Open
Abstract
Autoimmune diseases (ADs) are characterized by the activation of the immune system against self-antigens. More common in women than in men and with an early onset, their incidence is increasing worldwide, and this, combined with their chronic nature, is contributing to an enlarged medical and economic burden. Conventional immunosuppressive agents are designed to alleviate symptoms but do not constitute an effective therapy, highlighting a need to develop new alternatives. In this regard, mesenchymal stem cells (MSCs) have demonstrated powerful immunosuppressive and regenerative effects. MSC-derived extracellular vesicles (MSC-EVs) have shown some advantages, such as less immunogenicity, and are proposed as novel therapies for ADs. In this review, we summarize current perspectives on therapeutic options for ADs based on MSCs and MSC-EVs, focusing particularly on their mechanism of action exerted through their non-coding RNA (ncRNA) cargo. A complete state-of-the-art review was performed, centralized on some of the most severe ADs (rheumatoid arthritis, autoimmune type 1 diabetes mellitus, and systemic lupus erythematosus), giving evidence that a promising field is evolving to overcome the current knowledge and provide new therapeutic possibilities centered on MSC-EVs and their role as ncRNA delivery vehicles for AD gene therapy.
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Affiliation(s)
- Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (O.M.-A.); (M.J.F.)
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (O.M.-A.); (M.J.F.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-96398-3916 (R.C.); Fax: +34-96398-7860 (R.C.)
| | - Maria J. Forner
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (O.M.-A.); (M.J.F.)
- Internal Medicine Unit, Hospital Clinico Universitario, 46010 Valencia, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (O.M.-A.); (M.J.F.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-96398-3916 (R.C.); Fax: +34-96398-7860 (R.C.)
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16
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Zhao G, Li P, Qiao X, Han X, Liu ZP. Predicting lncRNA–Protein Interactions by Heterogenous Network Embedding. Front Genet 2022; 12:814073. [PMID: 35186016 PMCID: PMC8854746 DOI: 10.3389/fgene.2021.814073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022] Open
Abstract
lncRNA–protein interactions play essential roles in a variety of cellular processes. However, the experimental methods for systematically mapping of lncRNA–protein interactions remain time-consuming and expensive. Therefore, it is urgent to develop reliable computational methods for predicting lncRNA–protein interactions. In this study, we propose a computational method called LncPNet to predict potential lncRNA–protein interactions by embedding an lncRNA–protein heterogenous network. The experimental results indicate that LncPNet achieves promising performance on benchmark datasets extracted from the NPInter database with an accuracy of 0.930 and area under ROC curve (AUC) of 0.971. In addition, we further compare our method with other eight state-of-the-art methods, and the results illustrate that our method achieves superior prediction performance. LncPNet provides an effective method via a new perspective of representing lncRNA–protein heterogenous network, which will greatly benefit the prediction of lncRNA–protein interactions.
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Affiliation(s)
- Guoqing Zhao
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, China
| | - Pengpai Li
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, China
| | - Xu Qiao
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, China
| | - Xianhua Han
- Faculty of Science, Yamaguchi University, Yamaguchi, Japan
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, China
- *Correspondence: Zhi-Ping Liu,
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17
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Potemkin N, Cawood SMF, Treece J, Guévremont D, Rand CJ, McLean C, Stanton JAL, Williams JM. A method for simultaneous detection of small and long RNA biotypes by ribodepleted RNA-Seq. Sci Rep 2022; 12:621. [PMID: 35022475 PMCID: PMC8755727 DOI: 10.1038/s41598-021-04209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was extremely efficient, resulting in less than 1.5% rRNA content in the final library. We identified > 30,000 unique transcripts from all samples, including protein-coding genes and many species of non-coding RNA, in biologically-relevant proportions. Furthermore, the normalized sequencing read count for select genes significantly negatively correlated with Ct values from qRT-PCR analysis from the same samples. These results indicate that this protocol accurately and consistently identifies and quantifies a wide variety of transcripts simultaneously. The highly efficient rRNA depletion, coupled with minimized sample handling and without complicated and high-loss size selection protocols, makes this protocol useful to researchers wishing to investigate whole transcriptomes.
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Affiliation(s)
- Nikita Potemkin
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Sophie M F Cawood
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Jackson Treece
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Diane Guévremont
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Christy J Rand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Catriona McLean
- Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
- Anatomical Pathology, The Alfred Hospital, Melbourne, VIC, Australia
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Joanna M Williams
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand.
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand.
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18
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Dysregulation of PER3 clock gene and its only pseudogene in colorectal cancer and type 2 diabetes. ARCH BIOL SCI 2022. [DOI: 10.2298/abs220223009n] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The period (PER) family genes (PER1, PER2, and PER3) play a fundamental role
in regulating the day/night cycle. PER3 has a pseudogene variant, PER3P1 or
PER4, whose role and expression pattern is unclear in human health and
diseases. This study was performed to evaluate the expression levels of
normal PER family members and the PER3P1 pseudogene in colorectal cancer
(CRC) and type 2 diabetes (T2D). Blood samples were taken from 50 diabetic
patients and analyzed using real-time PCR for quantification of PER3 and
PER3P1 expression. Colorectal tumor tissues of 50 individuals were also used
to evaluate the expression of PER members. All PER members, including
PER3P1, were found to be downregulated in colorectal tumor samples. Blood
samples collected from diabetic subjects revealed an opposite expression
pattern; both PER3 and its pseudogene were found to be upregulated when
compared to the control group. Our results reveal coordination between the
expression pattern of PER3P1 and normal PER family genes. Based on our
findings and the pathological importance of this pseudogene, it can be
suggested that PER3P1 may be one of the key regulators of the molecular
clock network and PER family expression. This hypothesis needs to be
confirmed by further studies.
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19
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Fan W, Pang H, Xie Z, Huang G, Zhou Z. Circular RNAs in diabetes mellitus and its complications. Front Endocrinol (Lausanne) 2022; 13:885650. [PMID: 35979435 PMCID: PMC9376240 DOI: 10.3389/fendo.2022.885650] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
Diabetes mellitus (DM) is an endocrine disorder characterized by a relative or absolute lack of insulin due to the dysfunction or destruction of β-cells. DM is one of the fastest growing challenges to global health in the 21st century and places a tremendous burden on affected individuals and their families and countries. Although insulin and antidiabetic drugs have been used to treat DM, a radical cure for the disease is unavailable. The pathogenesis of DM remains unclear. Emerging roles of circular RNAs (circRNAs) in DM have become a subject of global research. CircRNAs have been verified to participate in the onset and progression of DM, implying their potential roles as novel biomarkers and treatment tools. In the present review, we briefly introduce the characteristics of circRNAs. Next, we focus on specific roles of circRNAs in type 1 diabetes mellitus, type 2 diabetes mellitus, gestational diabetes mellitus and diabetes-associated complications.
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20
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Long Noncoding RNAs: Recent Insights into Their Role in Male Infertility and Their Potential as Biomarkers and Therapeutic Targets. Int J Mol Sci 2021; 22:ijms222413579. [PMID: 34948376 PMCID: PMC8708977 DOI: 10.3390/ijms222413579] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are composed of nucleotides located in the nucleus and cytoplasm; these are transcribed by RNA polymerase II and are greater than 200 nt in length. LncRNAs fulfill important functions in a variety of biological processes, including genome imprinting, cell differentiation, apoptosis, stem cell pluripotency, X chromosome inactivation and nuclear transport. As high throughput sequencing technology develops, a substantial number of lncRNAs have been found to be related to a variety of biological processes, such as development of the testes, maintaining the self-renewal and differentiation of spermatogonial stem cells, and regulating spermatocyte meiosis. These indicate that lncRNAs can be used as biomarkers and potential therapeutic targets for male infertility. However, only a few comprehensive reviews have described the role of lncRNAs in male reproduction. In this paper, we summarize recent findings relating to the role of lncRNAs in spermatogenesis, their potential as biomarkers for male infertility and the relationship between reproductive arrest and transgenerational effects. Finally, we suggest specific targets for the treatment of male infertility from the perspective of lncRNAs.
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21
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Su H, Zheng W, Pan J, Lv X, Xin S, Xu T. Circular RNA circSamd4a Regulates Antiviral Immunity in Teleost Fish by Upregulating STING through Sponging miR-29a-3p. THE JOURNAL OF IMMUNOLOGY 2021; 207:2770-2784. [PMID: 34697227 DOI: 10.4049/jimmunol.2100469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/21/2021] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) are a subgroup of endogenous noncoding RNA that is covalently closed rings and widely expressed. In recent years, there is accumulating evidence indicating that circRNAs are a class of important regulators, which play an important role in various biological processes. However, the biological functions and regulation mechanism of circRNAs in lower vertebrates are little known. In this study, we discovered a circRNA Samd4a (circSamd4a) that is related to the antiviral immune response of teleost fish. It can act as a key regulator of the host's antiviral response and play a key role in inhibiting Sininiperca chuatsi rhabdovirus replication. Further studies have shown that circSamd4a may act as a competing endogenous RNA, which can enhance the STING-mediated NF-κB/IRF3 signaling pathway by adsorbing miR-29a-3p, thereby enhancing the antiviral immune response. Therefore, circSamd4a plays an active regulatory role in the antiviral immune response of bony fish. Our research results provide a strong foundation for circular RNA to play a regulatory role in the antiviral immune response of teleost fish.
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Affiliation(s)
- Hui Su
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiajia Pan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; .,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China; and.,National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
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22
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Circular RNA circPIKfyve acts as a sponge of miR-21-3p to enhance antiviral immunity through regulating MAVS in teleost fish. J Virol 2021; 95:JVI.02296-20. [PMID: 33536171 PMCID: PMC8103680 DOI: 10.1128/jvi.02296-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of widespread and diverse covalently closed circular endogenous RNAs that exert crucial functions in regulating gene expression in mammals. However, the function and regulation mechanism of circRNAs in lower vertebrates are still unknown. Here, we discovered a novel circRNA derived from PIKfyve, named circPIKfyve, that is related to the antiviral responses in teleost fish. The results showed that circPIKfyve plays essential roles in host antiviral immunity and inhibition of SCRV replication. Moreover, we also found that the antiviral effect inhibited by miR-21-3p could be reversed with the addition of circPIKfyve. In mechanism, our data revealed that circPIKfyve is a competitive endogenous RNA (ceRNA) of MAVS by sponging miR-21-3p, leading to activation of NF-κB/IRF3 pathway, which then enhance the innate antiviral responses. In addition, we firstly found that RNA binding protein QKI is involved in the formation and regulation of circPIKfyve. Our results provided a strong basis that circRNAs to play a regulatory role in antiviral immune responses in teleost fish.Importance: Here, we identified a novel circRNA, namely, circPIKfyve, that can act as a key regulator of the innate immune response in teleost fish. circPIKfyve acts as a molecular sponge by competitive adsorbing of miR-21-3p, thereby increasing the abundance of MAVS and activating the downstream NF-κB/IRF3 pathway to enhance the antiviral response. In addition, this study was the first to find that QKI protein is involved in regulating the formation of circPIKfyve in fish. The overall results of this study suggest that circPIKfyve plays an active regulatory role in the antiviral immune response of teleost fish.
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23
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Sun Y, Cao Z, Shan J, Gao Y, Liu X, Ma D, Li Z. Hsa_circ_0020095 Promotes Oncogenesis and Cisplatin Resistance in Colon Cancer by Sponging miR-487a-3p and Modulating SOX9. Front Cell Dev Biol 2021; 8:604869. [PMID: 33520987 PMCID: PMC7844065 DOI: 10.3389/fcell.2020.604869] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022] Open
Abstract
Objectives Colon cancer (CC) currently ranks as the third most common human cancer worldwide with an increasing incidence and a poor prognosis. Recently, circular RNAs have been reported to regulate the progression of diverse human cancers. However, the role of circRNA hsa_circ_0020095 in CC remains largely unclear. Methods Expression levels of the related circRNAs, microRNAs and mRNA in CC tissues and cells were determined. The impacts of circ_0020095 or miR-487a-3p on CC cells were examined at the indicated times after transfection. Meanwhile, a luciferase-reporter experiment was employed to validate the interplay between miR-487a-3p and circ_002009695 or SOX9. Moreover, the in vivo tumor growth assay was applied to further evaluate the effects of circ_0020095 knockdown on CC progression. Results We demonstrated that circ_0020095 was highly expressed in CC tissues and cells. The proliferation, migration, invasion, and cisplatin resistance of CC were suppressed by silencing circ_0020095 in vitro and in vivo or by ectopic expression of miR-487a-3p in vitro. Mechanistically, circ_0020095 could directly bind to miR-487a-3p and subsequently act as a miR-487a-3p sponge to modulate the activity by targeting the 3′-UTR of SOX9. Interestingly, overexpression of circ_0020095 dramatically reversed the suppressive effects of miR-487a-3p mimics on CC cells. Conclusion Circ_0020095 functions as an oncogene to accelerate CC cell proliferation, invasion, migration and cisplatin resistance through the miR-487a-3p/SOX9 axis, which could be a promising target for CC treatment.
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Affiliation(s)
- Yanlai Sun
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhen Cao
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Junqi Shan
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yang Gao
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xin Liu
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Dejian Ma
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zengjun Li
- Department of Gastrointestinal Cancer Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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24
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Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020; 10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022] Open
Abstract
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Yu Luo
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
| | - Otilia Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
- Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daniela Verga
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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25
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Falker-Gieske C, Mott A, Preuß S, Franzenburg S, Bessei W, Bennewitz J, Tetens J. Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking. BMC Genomics 2020; 21:595. [PMID: 32854615 PMCID: PMC7457272 DOI: 10.1186/s12864-020-07002-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Background Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the gut microbiome, and the immune system. To identify genes and biological pathways responsible for FP behavior we compared the brain transcriptomes of 48 hens divergently selected for FP. In addition, we tested if high feather peckers (HFP) and low feather peckers (LFP) respond differently to light since light has been shown to trigger FP behavior. Results Of approximately 48 million reads/sample an average of 98.4% were mapped to the chicken genome (GRCg6a). We found 13,070 expressed genes in the analyzed brains of which 423 showed differential expression between HFP and LFP. Genes of uncertain function and non-coding RNAs were overrepresented among those transcripts. Functional analyses revealed the involvement of cholinergic signaling, postsynaptic activity, membrane channels, and the immune system. After the light stimulus, 28 genes were found to be differentially expressed. These included an interaction cluster of core components of the circadian clock. However, differences in the response to light between HFP and LFP were not detectable. Conclusions Genes involved in cholinergic signaling, channel activity, synaptic transmission, and immune response were found to be involved in FP behavior. We propose a model in which the gut microbiota modulates the immune system, which in turn affects cholinergic signaling. This might have an influence on monoamine signaling with possible involvement of GABA or glutamate signaling.
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Affiliation(s)
- Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.
| | - Andrea Mott
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Siegfried Preuß
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Werner Bessei
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.,Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
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26
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Xie Y, Chen L. Epigenetic Regulation of Gibberellin Metabolism and Signaling. ACTA ACUST UNITED AC 2020; 61:1912-1918. [DOI: 10.1093/pcp/pcaa101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
Abstract
Abstract
The precise regulation of gibberellin (GA) metabolism and signaling is essential for plant development and environmental responses. Epigenetic regulatory mechanisms, such as histone modification, noncoding RNA-mediated regulation, chromatin remodeling and DNA methylation, are emerging as important means of fine-tuning gene expression. Recent studies have significantly improved our understanding of the relationships between epigenetic regulation and GA metabolism and signaling. Here, we summarize the molecular mechanisms by which epigenetic modifications affect GA metabolism and signaling pathways and provide new insight into an unfolding avenue of research related to the epigenetic regulation of GA pathways.
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Affiliation(s)
- Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
- Department of Genetics, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
- Department of Genetics, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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27
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Ke ZP, Xu YJ, Wang ZS, Sun J. RNA sequencing profiling reveals key mRNAs and long noncoding RNAs in atrial fibrillation. J Cell Biochem 2020; 121:3752-3763. [PMID: 31680326 DOI: 10.1002/jcb.29504] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/08/2019] [Indexed: 01/24/2023]
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of RNA species that could participate in some critical pathways and disease pathogenesis. However, the underlying molecular mechanism of lncRNAs in atrial fibrillation (AF) is still not fully understood. In the present study, we analyzed RNA-seq data of paired left and right atrial appendages from five patients with AF and other five patients without AF. Based on the gene expression profiles of 20 samples, we found that a majority of genes were aberrantly expressed in both left and right atrial appendages of patients with AF. Similarly, the dysregulated pathways in the left and right atrial appendages of patients with AF also bore a close resemblance. Moreover, we predicted regulatory lncRNAs that regulated the expression of adjacent protein-coding genes (PCGs) or interacted with proteins. We identified that NPPA and its antisense RNA NPPA-AS1 may participate in the pathogenesis of AF by regulating the muscle contraction. We also identified that RP11 - 99E15.2 and RP3 - 523K23.2 could interact with proteins ITGB3 and HSF2, respectively. RP11 - 99E15.2 and RP3 - 523K23.2 may participate in the pathogenesis of AF via regulating the extracellular matrix binding and the transcription of HSF2 target genes, respectively. The close association of the lncRNA-interacting proteins with AF further demonstrated that these two lncRNAs were also associated with AF. In conclusion, we have identified key regulatory lncRNAs implicated in AF, which not only improves our understanding of the lncRNA-related molecular mechanism underlying AF but also provides computationally predicted regulatory lncRNAs for AF researchers.
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Affiliation(s)
- Zun-Ping Ke
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Ying-Jia Xu
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Zhang-Sheng Wang
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Clinical Research Unit, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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28
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Lodde V, Murgia G, Simula ER, Steri M, Floris M, Idda ML. Long Noncoding RNAs and Circular RNAs in Autoimmune Diseases. Biomolecules 2020; 10:E1044. [PMID: 32674342 PMCID: PMC7407480 DOI: 10.3390/biom10071044] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 02/07/2023] Open
Abstract
Immune responses are essential for the clearance of pathogens and the repair of injured tissues; however, if these responses are not properly controlled, autoimmune diseases can occur. Autoimmune diseases (ADs) are a family of disorders characterized by the body's immune response being directed against its own tissues, with consequent chronic inflammation and tissue damage. Despite enormous efforts to identify new drug targets and develop new therapies to prevent and ameliorate AD symptoms, no definitive solutions are available today. Additionally, while substantial progress has been made in drug development for some ADs, most treatments only ameliorate symptoms and, in general, ADs are still incurable. Hundreds of genetic loci have been identified and associated with ADs by genome-wide association studies. However, the whole list of molecular factors that contribute to AD pathogenesis is still unknown. Noncoding (nc)RNAs, such as microRNAs, circular (circ)RNAs, and long noncoding (lnc)RNAs, regulate gene expression at different levels in various diseases, including ADs, and serve as potential drug targets as well as biomarkers for disease progression and response to therapy. In this review, we will focus on the potential roles and genetic regulation of ncRNA in four autoimmune diseases-systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes mellitus.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.L.); (G.M.); (E.R.S.); (M.F.)
| | - Giampaolo Murgia
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.L.); (G.M.); (E.R.S.); (M.F.)
| | - Elena Rita Simula
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.L.); (G.M.); (E.R.S.); (M.F.)
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, SS554 km 4,500, 09042 Monserrato-Cagliari, Italy;
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (V.L.); (G.M.); (E.R.S.); (M.F.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, SS554 km 4,500, 09042 Monserrato-Cagliari, Italy;
| | - Maria Laura Idda
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Traversa La Crucca 3, 07100 Sassari, Italy
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29
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Queen NJ, Hassan QN, Cao L. Improvements to Healthspan Through Environmental Enrichment and Lifestyle Interventions: Where Are We Now? Front Neurosci 2020; 14:605. [PMID: 32655354 PMCID: PMC7325954 DOI: 10.3389/fnins.2020.00605] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Environmental enrichment (EE) is an experimental paradigm that is used to explore how a complex, stimulating environment can impact overall health. In laboratory animal experiments, EE housing conditions typically include larger-than-standard cages, abundant bedding, running wheels, mazes, toys, and shelters which are rearranged regularly to further increase stimulation. EE has been shown to improve multiple aspects of health, including but not limited to metabolism, learning and cognition, anxiety and depression, and immunocompetence. Recent advances in lifespan have led some researchers to consider aging as a risk factor for disease. As such, there is a pressing need to understand the processes by which healthspan can be increased. The natural and predictable changes during aging can be reversed or decreased through EE and its underlying mechanisms. Here, we review the use of EE in laboratory animals to understand mechanisms involved in aging, and comment on relative areas of strength and weakness in the current literature. We additionally address current efforts toward applying EE-like lifestyle interventions to human health to extend healthspan. Although increasing lifespan is a clear goal of medical research, improving the quality of this added time also deserves significant attention. Despite hurdles in translating experimental results toward clinical application, we argue there is great potential in using features of EE toward improving human healthy life expectancy or healthspan, especially in the context of increased global longevity.
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Affiliation(s)
- Nicholas J. Queen
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Quais N. Hassan
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Medical Scientist Training Program, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lei Cao
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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30
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Da Fonseca BHR, Domingues DS, Paschoal AR. mirtronDB: a mirtron knowledge base. Bioinformatics 2020; 35:3873-3874. [PMID: 30874795 PMCID: PMC6761972 DOI: 10.1093/bioinformatics/btz153] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/21/2019] [Accepted: 03/14/2019] [Indexed: 01/12/2023] Open
Abstract
Motivation Mirtrons arise from short introns with atypical cleavage by using the splicing mechanism. In the current literature, there is no repository centralizing and organizing the data available to the public. To fill this gap, we developed mirtronDB, the first knowledge database dedicated to mirtron, and it is available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB currently contains a total of 1407 mirtron precursors and 2426 mirtron mature sequences in 18 species. Results Through a user-friendly interface, users can now browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource that provides free and user-friendly access to knowledge on mirtron data. Availability and implementation MirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bruno Henrique Ribeiro Da Fonseca
- Bioinformatics Graduation Program (PPGBIOINFO), Department of Computer Science, Federal University of Technology - Paraná, Cornélio Procópio, Paraná, Brazil
| | - Douglas Silva Domingues
- Bioinformatics Graduation Program (PPGBIOINFO), Department of Computer Science, Federal University of Technology - Paraná, Cornélio Procópio, Paraná, Brazil.,Department of Botany, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, São Paulo, Brazil
| | - Alexandre Rossi Paschoal
- Bioinformatics Graduation Program (PPGBIOINFO), Department of Computer Science, Federal University of Technology - Paraná, Cornélio Procópio, Paraná, Brazil
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31
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Bustelo M, Barkhuizen M, van den Hove DLA, Steinbusch HWM, Bruno MA, Loidl CF, Gavilanes AWD. Clinical Implications of Epigenetic Dysregulation in Perinatal Hypoxic-Ischemic Brain Damage. Front Neurol 2020; 11:483. [PMID: 32582011 PMCID: PMC7296108 DOI: 10.3389/fneur.2020.00483] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Placental and fetal hypoxia caused by perinatal hypoxic-ischemic events are major causes of stillbirth, neonatal morbidity, and long-term neurological sequelae among surviving neonates. Brain hypoxia and associated pathological processes such as excitotoxicity, apoptosis, necrosis, and inflammation, are associated with lasting disruptions in epigenetic control of gene expression contributing to neurological dysfunction. Recent studies have pointed to DNA (de)methylation, histone modifications, and non-coding RNAs as crucial components of hypoxic-ischemic encephalopathy (HIE). The understanding of epigenetic dysregulation in HIE is essential in the development of new clinical interventions for perinatal HIE. Here, we summarize our current understanding of epigenetic mechanisms underlying the molecular pathology of HI brain damage and its clinical implications in terms of new diagnostic, prognostic, and therapeutic tools.
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Affiliation(s)
- Martín Bustelo
- Department of Pediatrics, Maastricht University Medical Center (MUMC), Maastricht, Netherlands.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, Netherlands.,Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina.,Laboratorio de Neuropatología Experimental, Facultad de Medicina, Instituto de Biología Celular y Neurociencias "Prof. E. De Robertis" (IBCN), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Melinda Barkhuizen
- Department of Pediatrics, Maastricht University Medical Center (MUMC), Maastricht, Netherlands
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Harry Wilhelm M Steinbusch
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, Netherlands
| | - Martín A Bruno
- Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina
| | - C Fabián Loidl
- Instituto de Ciencias Biomédicas, Facultad de Ciencias Médicas, Universidad Católica de Cuyo, San Juan, Argentina.,Laboratorio de Neuropatología Experimental, Facultad de Medicina, Instituto de Biología Celular y Neurociencias "Prof. E. De Robertis" (IBCN), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
| | - Antonio W Danilo Gavilanes
- Department of Pediatrics, Maastricht University Medical Center (MUMC), Maastricht, Netherlands.,Facultad de Ciencias Médicas, Instituto de Investigación e Innovación de Salud Integral, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
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Morgado S, Antunes D, Caffarena E, Vicente AC. The rare lncRNA GOLLD is widespread and structurally conserved among Mycobacterium tRNA arrays. RNA Biol 2020; 17:1001-1008. [PMID: 32275844 DOI: 10.1080/15476286.2020.1748922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from Lactobacillales and Actinomycetales orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of Mycobacterium and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. Mycobacterium GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) Mycobacterium exclusive; (ii) Mycobacterium and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3' half conserved structure, including utter E-loops pseudoknots substructures, also shared by non-Mycobacterium GOLLD while the 5' half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in Mycobacterium within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.
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Affiliation(s)
- Sergio Morgado
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) , Rio de Janeiro, Brazil
| | - Deborah Antunes
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute (IOC - FIOCRUZ) , Rio de Janeiro, Brazil
| | - Ernesto Caffarena
- Computational Biophysics and Molecular Modeling Group, Scientific Computing Program (PROCC - FIOCRUZ) , Rio de Janeiro, Brazil
| | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute (IOC - FIOCRUZ) , Rio de Janeiro, Brazil
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33
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Lu X, Yu Y, Liao F, Tan S. Homo Sapiens Circular RNA 0079993 (hsa_circ_0079993) of the POLR2J4 Gene Acts as an Oncogene in Colorectal Cancer Through the microRNA-203a-3p.1 and CREB1 Axis. Med Sci Monit 2019; 25:6872-6883. [PMID: 31515467 PMCID: PMC6755939 DOI: 10.12659/msm.916064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Worldwide, dietary changes have resulted in an increased incidence of colorectal cancer (CRC). Circular RNAs (circRNAs) are involved in tumorigenesis of several human tumors, but their role in CRC remains unknown. This study aimed to investigate the expression and effects of Homo sapiens (hsa)_circ_0079993 of POLR2J4 and its impact on CRC. Material/Methods Paired CRC tissue and adjacent normal colorectal tissue samples (N=41), and HCT116 and SW620 human CRC cells were studied. The expression of circ_0079993 and its parental gene, POLR2J4, were examined using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Two small-interfering RNAs (siRNAs) against circ_0079993 were used to silence circ_0079993 expression in HCT116 and SW620 CRC cells. Cell proliferation was evaluated using the cell counting kit-8 (CCK-8) assay, colony formation, and in vivo tumor growth assays. The target miRNAs of circ_0079993 was predicted using TargetScan, and the interaction between circ_0079993 and its target miRNAs were verified by the dual-luciferase reporter (DLR) assay. Results In CRC tissue POLR2J4 expression was reduced, and circ_0079993 expression was increased compared with normal tissue. Knockdown of circ_0079993 significantly inhibited the proliferation of CRC cells in vitro. Also, circ_0079993 was predicted to sponge multiple miRNAs, miR-203a-3p.1 was verified as a target of circ_0079993, and circ_0079993 indirectly regulated mRNA expression of the CREB1 gene by sponging miR-203a-3p.1 in CRC cells. The use of anti-miR-203a-3p.1 reversed the inhibitory effects of circ_0079993 knockdown on CRC cell proliferation. Conclusions The findings supported that hsa_circ_0079993 acts as an oncogene in CRC through the miRNA-203a-3p.1/CREB1 axis.
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Affiliation(s)
- Xiaohong Lu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System Disease, Wuhan, Hubei, China (mainland)
| | - Yuanjie Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System Disease, Wuhan, Hubei, China (mainland)
| | - Fei Liao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System Disease, Wuhan, Hubei, China (mainland)
| | - Shiyun Tan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System Disease, Wuhan, Hubei, China (mainland)
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34
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Jiang H, Wu F, Jiang N, Gao J, Zhang J. Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. Mol Med Rep 2019; 20:4091-4100. [PMID: 31545470 PMCID: PMC6797987 DOI: 10.3892/mmr.2019.10682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Hepatic fibrosis (HF), one of the leading global health problems, is defined as aberrant and excess production of extracellular matrix components. The pathogenesis of HF is complex and poorly understood. Long non‑coding RNAs (LncRNAs) can interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate the expression of target genes, which play a significant role in the initiation and progression of HF. In the present study, the LncRNA‑associated ceRNA network was reconstructed based on LncRNA, miRNA and mRNA expression profiles that were downloaded from National Center for Biotechnology Information Gene Expression Omnibus. Bioinformatics assessments including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed with Database for Annotation, Visualization and Integration Discovery. The ceRNA network was composed of 220 LncRNA nodes, 24 miRNA nodes, 164 mRNA nodes and 1,149 edges. Functional assays identified that a total of 338 GO terms and 25 pathways, including regulation of cytokine and collagen, and the transforming growth factor‑β and Toll‑like receptor signaling pathways, were significantly enriched. In addition, 4 LncRNAs (NONMMUT036242, XR_877072, XR_378619 and XR_378418) were highly related to HF and thereby chosen as key LncRNAs. The present study uncovered a ceRNA network that could further the understanding of the mechanisms underlying HF development and provide potential novel markers for clinical diagnosis and targets for treatment.
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Affiliation(s)
- Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Furong Wu
- Department of Pharmacy, Anhui Provincial Hospital, Hefei, Anhui 230001, P.R. China
| | - Nannan Jiang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Jiarong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
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35
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Chen H, Zhang Z, Jiang S, Li R, Li W, Zhao C, Hong H, Huang X, Li H, Bo X. New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. Brief Bioinform 2019; 21:1397-1410. [PMID: 31504171 PMCID: PMC7373178 DOI: 10.1093/bib/bbz072] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/13/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
Essential genes are those whose loss of function compromises organism viability or results in profound loss of fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic and regulatory characteristics of human essential genes. First, we found that essential genes act as ‘hubs’ in protein–protein interaction networks, chromatin structure and epigenetic modification. Second, essential genes represent conserved biological processes across species, although gene essentiality changes differently among species. Third, essential genes are important for cell development due to their discriminate transcription activity in embryo development and oncogenesis. In addition, we developed an interactive web server, the Human Essential Genes Interactive Analysis Platform (http://sysomics.com/HEGIAP/), which integrates abundant analytical tools to enable global, multidimensional interpretation of gene essentiality. Our study provides new insights that improve the understanding of human essential genes.
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Affiliation(s)
- Hebing Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhuo Zhang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shuai Jiang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ruijiang Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wanying Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Chenghui Zhao
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Hong
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
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36
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Kim SS, Lee SJV. Non-Coding RNAs in Caenorhabditis elegans Aging. Mol Cells 2019; 42:379-385. [PMID: 31094164 PMCID: PMC6537654 DOI: 10.14348/molcells.2019.0077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 01/04/2023] Open
Abstract
Non-coding RNAs (ncRNAs) comprise various RNA species, including small ncRNAs and long ncRNAs (lncRNAs). ncRNAs regulate various cellular processes, including transcription and translation of target messenger RNAs. Recent studies also indicate that ncRNAs affect organismal aging and conversely aging influences ncRNA levels. In this review, we discuss our current understanding of the roles of ncRNAs in aging and longevity, focusing on recent advances using the roundworm Caenorhabditis elegans. Expression of various ncRNAs, including microRNA (miRNA), tRNA-derived small RNA (tsRNA), ribosomal RNA (rRNA), PIWI-interacting RNA (piRNA), circular RNA (circRNA), and lncRNA, is altered during aging in C. elegans. Genetic modulation of specific ncRNAs affects longevity and aging rates by modulating established aging-regulating protein factors. Because many aging-regulating mechanisms in C. elegans are evolutionarily conserved, these studies will provide key information regarding how ncRNAs modulate aging and lifespan in complex organisms, including mammals.
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Affiliation(s)
- Sieun S. Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,
Korea
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37
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Turner AW, Wong D, Khan MD, Dreisbach CN, Palmore M, Miller CL. Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. Front Cardiovasc Med 2019; 6:9. [PMID: 30838214 PMCID: PMC6389617 DOI: 10.3389/fcvm.2019.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.
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Affiliation(s)
- Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Caitlin N. Dreisbach
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- School of Nursing, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
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38
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Zhang W, Yue X, Tang G, Wu W, Huang F, Zhang X. SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions. PLoS Comput Biol 2018; 14:e1006616. [PMID: 30533006 PMCID: PMC6331124 DOI: 10.1371/journal.pcbi.1006616] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 01/14/2019] [Accepted: 11/02/2018] [Indexed: 01/12/2023] Open
Abstract
LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. Existing computational methods utilize multiple lncRNA features or multiple protein features to predict lncRNA-protein interactions, but features are not available for all lncRNAs or proteins; most of existing methods are not capable of predicting interacting proteins (or lncRNAs) for new lncRNAs (or proteins), which don’t have known interactions. In this paper, we propose the sequence-based feature projection ensemble learning method, “SFPEL-LPI”, to predict lncRNA-protein interactions. First, SFPEL-LPI extracts lncRNA sequence-based features and protein sequence-based features. Second, SFPEL-LPI calculates multiple lncRNA-lncRNA similarities and protein-protein similarities by using lncRNA sequences, protein sequences and known lncRNA-protein interactions. Then, SFPEL-LPI combines multiple similarities and multiple features with a feature projection ensemble learning frame. In computational experiments, SFPEL-LPI accurately predicts lncRNA-protein associations and outperforms other state-of-the-art methods. More importantly, SFPEL-LPI can be applied to new lncRNAs (or proteins). The case studies demonstrate that our method can find out novel lncRNA-protein interactions, which are confirmed by literature. Finally, we construct a user-friendly web server, available at http://www.bioinfotech.cn/SFPEL-LPI/. LncRNA-protein interactions play important roles in post-transcriptional gene regulation, poly-adenylation, splicing and translation. Identification of lncRNA-protein interactions helps to understand lncRNA-related activities. In this paper, we propose a novel computational method “SFPEL-LPI” to predict lncRNA-protein interactions. SFPEL-LPI makes use of lncRNA sequences, protein sequences and known lncRNA-protein associations to extract features and calculate similarities for lncRNAs and proteins, and then combines them with a feature projection ensemble learning frame. SFPEL-LPI can predict unobserved interactions between lncRNAs and proteins, and also can make predictions for new lncRNAs (or proteins), which have no interactions with any proteins (or lncRNAs). SFPEL-LPI produces high-accuracy performances on the benchmark dataset when evaluated by five-fold cross validation, and outperforms state-of-the-art methods. The case studies demonstrate that SFPEL-LPI can find out novel associations, which are confirmed by literature. To facilitate the lncRNA-protein interaction prediction, we develop a user-friendly web server, available at http://www.bioinfotech.cn/SFPEL-LPI/.
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Affiliation(s)
- Wen Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan, China
- School of Computer Science, Wuhan University, Wuhan, China
- * E-mail: , (WZ); (XZ)
| | - Xiang Yue
- Department of Computer Science and Engineering, The Ohio State University, Columbus, United States of America
| | - Guifeng Tang
- School of Computer Science, Wuhan University, Wuhan, China
| | - Wenjian Wu
- Electronic Information School, Wuhan University, Wuhan, China
| | - Feng Huang
- School of Computer Science, Wuhan University, Wuhan, China
| | - Xining Zhang
- School of Computer Science, Wuhan University, Wuhan, China
- * E-mail: , (WZ); (XZ)
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Naidoo V, Naidoo M, Ghai M. Cell- and tissue-specific epigenetic changes associated with chronic inflammation in insulin resistance and type 2 diabetes mellitus. Scand J Immunol 2018; 88:e12723. [PMID: 30589455 DOI: 10.1111/sji.12723] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/29/2018] [Accepted: 09/29/2018] [Indexed: 12/15/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by hyperglycaemia, which can cause micro- and macrovascular complications. Chronic inflammation may be the cause and result of T2DM, and its related complications as an imbalance between pro- and anti-inflammatory cytokines can affect immune functions. Apart from genetic changes occurring within the body resulting in inflammation in T2DM, epigenetic modifications can modify gene expression in response to environmental cues such as an unhealthy diet, lack of exercise and obesity. The most widely studied epigenetic modification, DNA methylation (DNAm), regulates gene expression and may manipulate inflammatory genes to increase or decrease inflammation associated with T2DM. This review explores the studies related to epigenetic changes, more specifically DNAm, associated with chronic inflammation in T2DM, at both the cell and tissue levels. Studying epigenetic alterations during inflammatory response, as a result of genetic and environmental signals, creates opportunities for the development of "early detection/relative risk" tests to aid in prevention of T2DM. Understanding inflammation in T2DM at the gene level in inflammation-associated cells and tissues may provide further insight for the development of specific therapeutic targets for the disorder.
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Affiliation(s)
- Velosha Naidoo
- Department of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Merusha Naidoo
- Department of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
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40
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George L, Indig FE, Abdelmohsen K, Gorospe M. Intracellular RNA-tracking methods. Open Biol 2018; 8:rsob.180104. [PMID: 30282659 PMCID: PMC6223214 DOI: 10.1098/rsob.180104] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/03/2018] [Indexed: 12/26/2022] Open
Abstract
RNA tracking allows researchers to visualize RNA molecules in cells and tissues, providing important spatio-temporal information regarding RNA dynamics and function. Methods such as fluorescent in situ hybridization (FISH) and molecular beacons rely on complementary oligonucleotides to label and view endogenous transcripts. Other methods create artificial chimeric transcripts coupled with bacteriophage-derived coat proteins (e.g. MS2, λN) to tag molecules in live cells. In other approaches, endogenous RNAs are recognized by complementary RNAs complexed with noncatalytic Cas proteins. Each technique has its own set of strengths and limitations that must be considered when planning an experiment. Here, we discuss the mechanisms, advantages, and weaknesses of in situ hybridization, molecular beacons, MS2 tagging and Cas-derived systems, as well as how RNA tracking can be employed to study various aspects of molecular biology.
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Affiliation(s)
- Logan George
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.,Confocal Core Facility, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Fred E Indig
- Confocal Core Facility, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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42
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Ding C, Lim YC, Chia SY, Walet ACE, Xu S, Lo KA, Zhao Y, Zhu D, Shan Z, Chen Q, Leow MKS, Xu D, Sun L. De novo reconstruction of human adipose transcriptome reveals conserved lncRNAs as regulators of brown adipogenesis. Nat Commun 2018; 9:1329. [PMID: 29626186 PMCID: PMC5889397 DOI: 10.1038/s41467-018-03754-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/08/2018] [Indexed: 12/13/2022] Open
Abstract
Obesity has emerged as an alarming health crisis due to its association with metabolic risk factors such as diabetes, dyslipidemia, and hypertension. Recent work has demonstrated the multifaceted roles of lncRNAs in regulating mouse adipose development, but their implication in human adipocytes remains largely unknown. Here we present a catalog of 3149 adipose active lncRNAs, of which 909 are specifically detected in brown adipose tissue (BAT) by performing deep RNA-seq on adult subcutaneous, omental white adipose tissue and fetal BATs. A total of 169 conserved human lncRNAs show positive correlation with their nearby mRNAs, and knockdown assay supports a role of lncRNAs in regulating their nearby mRNAs. The knockdown of one of those, lnc-dPrdm16, impairs brown adipocyte differentiation in vitro and a significant reduction of BAT-selective markers in in vivo. Together, our work provides a comprehensive human adipose catalog built from diverse fat depots and establishes a roadmap to facilitate the discovery of functional lncRNAs in adipocyte development. Long non-coding RNAs are known to regulate mouse white adipose tissue development and brown adipose tissue program expression. Here, the authors construct a roadmap for human long non-coding RNAs expressed in fetal brown adipose tissue, adult omental and subcutaneous white adipose tissues.
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Affiliation(s)
- Chunming Ding
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Yen Ching Lim
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.,Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Sook Yoong Chia
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Arcinas Camille Esther Walet
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Shaohai Xu
- Division of Bioengineering, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Kinyui Alice Lo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Yanling Zhao
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Dewen Zhu
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zhihui Shan
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Melvin Khee-Shing Leow
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Clinical Nutrition Research Centre (CNRC), Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR) and National University Health System (NUHS), Singapore, 117599, Singapore.,National University Health System (NUHS), Singapore, 119074, Singapore.,Department of Endocrinology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Dan Xu
- Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China. .,Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
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43
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Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018; 8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.
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Affiliation(s)
- Deborah Antunes
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natasha A N Jorge
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Ernesto R Caffarena
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
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44
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The linear neighborhood propagation method for predicting long non-coding RNA–protein interactions. Neurocomputing 2018. [DOI: 10.1016/j.neucom.2017.07.065] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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45
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Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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46
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Andrews RJ, Baber L, Moss WN. RNAStructuromeDB: A genome-wide database for RNA structural inference. Sci Rep 2017; 7:17269. [PMID: 29222504 PMCID: PMC5722888 DOI: 10.1038/s41598-017-17510-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
RNA plays important roles in almost every aspect of biology, and every aspect of RNA biology is influenced by its folding. This is a particularly important consideration in the era of high-throughput sequencing, when the discovery of novel transcripts far outpaces our knowledge of their functions. To gain a comprehensive picture of biology requires a structural framework for making functional inferences on RNA. To this end we have developed the RNA Structurome Database ( https://structurome.bb.iastate.edu ), a comprehensive repository of RNA secondary structural information that spans the entire human genome. Here, we compile folding information for every base pair of the genome that may be transcribed: coding, noncoding, and intergenic regions, as well as repetitive elements, telomeres, etc. This was done by fragmenting the GRCh38 reference genome into 154,414,320 overlapping sequence fragments and, for each fragment, calculating a set of metrics based on the sequence's folding properties. These data will facilitate a wide array of investigations: e.g. discovery of structured regulatory elements in differential gene expression data or noncoding RNA discovery, as well as allow genome-scale analyses of RNA folding.
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Affiliation(s)
- Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Levi Baber
- Biology Information Technology, Iowa State University, 2310 Pammel Drive, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA.
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47
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Qin N, Wang C, Lu Q, Ma Z, Dai J, Ma H, Jin G, Shen H, Hu Z. Systematic identification of long non-coding RNAs with cancer-testis expression patterns in 14 cancer types. Oncotarget 2017; 8:94769-94779. [PMID: 29212265 PMCID: PMC5706911 DOI: 10.18632/oncotarget.21930] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022] Open
Abstract
Cancer-testis (CT) genes are a group of genes that are potential targets of immunotherapy and candidate epi-drivers participating in the development of cancers. Previous studies mainly focused on protein-coding genes, neglecting long non-coding RNAs with the same expression patterns. In this study, we performed a systematic investigation of cancer-testis long non-coding RNAs (CT-lncRNAs) with multiple independent open-access databases.We identified 1,325 extremely highly expressed CT-lncRNAs (EECT-lncRNAs) in 14 cancer types. Functional annotation revealed that CT-lncRNAs reactivated in cancers could promote genome instability and the malignant potential of cancers. We observed a mutually exclusive pattern of EECT-lncRNA activation and mutation in known oncogenes, suggesting their potential role as drivers of cancer that complement known mut-driver genes. Additionally, we provided evidence that testis-specific regulatory elements and promoter hypo-methylation may be EECT-lncRNA activation mechanisms, and EECT-lncRNAs may regulate CT gene reactivation. Taken together, our study puts forth a new hypothesis in the research field of CT genes, whereby CT-lncRNAs/EECT-lncRNAs play important roles in the progression and maintenance of tumorigenesis, expanding candidate CT epi-driver genes from coding genes to non-coding RNAs.
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Affiliation(s)
- Na Qin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211116, China
| | - Qun Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zijian Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
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48
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Marcus JI, Hassoun S, Nair NU. Computational prediction of functional abortive RNA in E. coli. Genomics 2017; 109:196-203. [PMID: 28347827 DOI: 10.1016/j.ygeno.2017.03.003] [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: 09/30/2016] [Revised: 02/24/2017] [Accepted: 03/22/2017] [Indexed: 11/26/2022]
Abstract
Failure by RNA polymerase to break contacts with promoter DNA results in release of bound RNA and re-initiation of transcription. These abortive RNAs were assumed to be non-functional but have recently been shown to affect termination in bacteriophage T7. Little is known about the functional role of these RNA in other genetic models. Using a computational approach, we investigated whether abortive RNA could exert function in E. coli. Fragments generated from 3780 transcription units were used as query sequences within their respective transcription units to search for possible binding sites. Sites that fell within known regulatory features were then ranked based upon the free energy of hybridization to the abortive. We further hypothesize about mechanisms of regulatory action for a select number of likely matches. Future experimental validation of these putative abortive-mRNA pairs may confirm our findings and promote exploration of functional abortive RNAs (faRNAs) in natural and synthetic systems.
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Affiliation(s)
- Jeremy I Marcus
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Soha Hassoun
- Department of Computer Science, Tufts University, Medford, MA 02155, United States; Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States.
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49
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Busch A, Eken SM, Maegdefessel L. Prospective and therapeutic screening value of non-coding RNA as biomarkers in cardiovascular disease. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:236. [PMID: 27429962 DOI: 10.21037/atm.2016.06.06] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Non-coding RNA (ncRNA) is a class of genetic, epigenetic and translational regulators, containing short and long transcripts with intriguing abilities for use as biomarkers due to their superordinate role in disease development. In the past five years many of these have been investigated in cardiovascular diseases (CVD), mainly myocardial infarction (MI) and heart failure. To extend this view, we summarize the existing data about ncRNA as biomarker in the whole entity of CVDs by literature-based review and comparison of the identified candidates. The myomirs miRNA-1, -133a/b, -208a, -499 with well-defined cellular functions have proven equal to classic protein biomarkers for disease detection in MI. Other microRNAs (miRNAs) were reproducibly found to correlate with disease, disease severity and outcome in heart failure, stroke, coronary artery disease (CAD) and aortic aneurysm. An additional utilization has been discovered for therapeutic monitoring. The function of long non-coding transcripts is only about to be unraveled, yet shows great potential for outcome prediction. ncRNA biomarkers have a distinct role if no alternative test is available or has is performing poorly. With increasing mechanistic understanding, circulating miRNA and long non-coding transcripts will provide useful disease information with high predictive power.
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Affiliation(s)
- Albert Busch
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institute, Center for Molecular Medicine, Stockholm, Sweden
| | - Suzanne M Eken
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institute, Center for Molecular Medicine, Stockholm, Sweden
| | - Lars Maegdefessel
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institute, Center for Molecular Medicine, Stockholm, Sweden
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50
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Transcriptional regulation of long-term potentiation. Neurogenetics 2016; 17:201-210. [PMID: 27318935 DOI: 10.1007/s10048-016-0489-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
Abstract
Long-term potentiation (LTP), the persistent strengthening of synapses following high levels of stimulation, is a form of synaptic plasticity that has been studied extensively as a possible mechanism for learning and memory formation. The strengthening of the synapse that occurs during LTP requires cascades of complex molecular processes and the coordinated remodeling of pre-synaptic and post-synaptic neurons. Despite over four decades of research, our understanding of the transcriptional mechanisms and molecular processes underlying LTP remains incomplete. Identification of all the proteins and non-coding RNA transcripts expressed during LTP may provide greater insight into the molecular mechanisms involved in learning and memory formation.
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