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Tadesse K, Benhamou RI. Targeting MicroRNAs with Small Molecules. Noncoding RNA 2024; 10:17. [PMID: 38525736 PMCID: PMC10961812 DOI: 10.3390/ncrna10020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
MicroRNAs (miRs) have been implicated in numerous diseases, presenting an attractive target for the development of novel therapeutics. The various regulatory roles of miRs in cellular processes underscore the need for precise strategies. Recent advances in RNA research offer hope by enabling the identification of small molecules capable of selectively targeting specific disease-associated miRs. This understanding paves the way for developing small molecules that can modulate the activity of disease-associated miRs. Herein, we discuss the progress made in the field of drug discovery processes, transforming the landscape of miR-targeted therapeutics by small molecules. By leveraging various approaches, researchers can systematically identify compounds to modulate miR function, providing a more potent intervention either by inhibiting or degrading miRs. The implementation of these multidisciplinary approaches bears the potential to revolutionize treatments for diverse diseases, signifying a significant stride towards the targeting of miRs by precision medicine.
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Affiliation(s)
| | - Raphael I. Benhamou
- The Institute for Drug Research of the School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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2
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Talepoor AG, Doroudchi M. Regulatory RNAs in immunosenescence. Immun Inflamm Dis 2024; 12:e1209. [PMID: 38456619 PMCID: PMC10921898 DOI: 10.1002/iid3.1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Immunosenescence is a multifactorial stress response to different intrinsic and extrinsic insults that cause immune deterioration and is accompanied by genomic or epigenomic perturbations. It is now widely recognized that genes and proteins contributing in the process of immunosenescence are regulated by various noncoding (nc) RNAs, including microRNAs (miRNAs), long ncRNAs, and circular RNAs. AIMS This review article aimed to evaluate the regulatore RNAs roles in the process of immunosenescence. METHODS We analyzed publications that were focusing on the different roles of regulatory RNAs on the several aspects of immunosenescence. RESULTS In the immunosenescence setting, ncRNAs have been found to play regulatory roles at both transcriptional and post-transcriptional levels. These factors cooperate to regulate the initiation of gene expression programs and sustaining the senescence phenotype and proinflammatory responses. CONCLUSION Immunosenescence is a complex process with pivotal alterations in immune function occurring with age. The extensive network that drive immunosenescence-related features are are mainly directed by a variety of regulatory RNAs such as miRNAs, lncRNAs, and circRNAs. Latest findings about regulation of senescence by ncRNAs in the innate and adaptive immune cells as well as their role in the immunosenescence pathways, provide a better understanding of regulatory RNAs function in the process of immunosenescence.
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Affiliation(s)
- Atefe Ghamar Talepoor
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
- Autoimmune Diseases Research CenterUniversity of Medical SciencesShirazIran
| | - Mehrnoosh Doroudchi
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
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3
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Mecca M, Picerno S, Cortellino S. The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer. Int J Mol Sci 2024; 25:2750. [PMID: 38473997 DOI: 10.3390/ijms25052750] [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: 12/20/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.
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Affiliation(s)
- Marisabel Mecca
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Simona Picerno
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), 85028 Rionero in Vulture, PZ, Italy
| | - Salvatore Cortellino
- Laboratory of Preclinical and Translational Research, Responsible Research Hospital, 86100 Campobasso, CB, Italy
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, 80138 Naples, NA, Italy
- S.H.R.O. Italia Foundation ETS, 10060 Candiolo, TO, Italy
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Liu Z, Liu F, Petinrin OO, Wang F, Zhang Y, Wong KC. Uncovering the ceRNA Network Related to the Prognosis of Stomach Adenocarcinoma Among 898 Patient Samples. Biochem Genet 2024:10.1007/s10528-023-10656-7. [PMID: 38361095 DOI: 10.1007/s10528-023-10656-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024]
Abstract
Stomach adenocarcinoma (STAD) patients are often associated with significantly high mortality rates and poor prognoses worldwide. Among STAD patients, competing endogenous RNAs (ceRNAs) play key roles in regulating one another at the post-transcriptional stage by competing for shared miRNAs. In this study, we aimed to elucidate the roles of lncRNAs in the ceRNA network of STAD, uncovering the molecular biomarkers for target therapy and prognosis. Specifically, a multitude of differentially expressed lncRNAs, miRNAs, and mRNAs (i.e., 898 samples in total) was collected and processed from TCGA. Cytoplasmic lncRNAs were kept for evaluating overall survival (OS) time and constructing the ceRNA network. Differentially expressed mRNAs in the ceRNA network were also investigated for functional and pathological insights. Interestingly, we identified one ceRNA network including 13 lncRNAs, 25 miRNAs, and 9 mRNAs. Among them, 13 RNAs were found related to the patient survival time; their individual risk score can be adopted for prognosis inference. Finally, we constructed a comprehensive ceRNA regulatory network for STAD and developed our own risk-scoring system that can predict the OS time of STAD patients by taking into account the above.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Fang Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | | | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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5
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Banerjee S, Sarkar R, Mukherjee A, Mitra S, Gope A, Chawla-Sarkar M. Rotavirus-induced lncRNA SLC7A11-AS1 promotes ferroptosis by targeting cystine/glutamate antiporter xCT (SLC7A11) to facilitate virus infection. Virus Res 2024; 339:199261. [PMID: 37923170 PMCID: PMC10684390 DOI: 10.1016/j.virusres.2023.199261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Rotavirus (RV) is the primary etiological agent of virus-associated gastroenteritis in infants, causing 200,000 childhood death annually. Despite the availability of vaccines, rotaviral diarrhea continues to be a severe issue in underdeveloped nations in Asia and Africa. The situation demands continual studies on host-rotavirus interactions to understand disease pathogenesis and develop effective antiviral therapeutics. Long non-coding RNAs (lncRNAs), which are a subset of non-coding RNAs of more than 200 nucleotides in length, are reported to play a regulatory function in numerous viral infections. Virus infection often alters the host transcriptome including lncRNA that are differentially expressed either to play an antiviral role or to be advantageous towards virus propagation. In the current study, qPCR array-based expression profiling of host lncRNAs was performed in rotavirus-infected HT-29 cells that identified the lncRNA SLC7A11-AS1 to be upregulated during RV infection. Knockdown of SLC7A11-AS1 conspicuously reduced RV titers implying its pro-viral significance. RV-induced SLC7A11-AS1 downregulates the gene SLC7A11/xCT that encodes the light chain subunit of the system XC- cystine-glutamate exchange transporter, leading to decrease in intracellular glutathione level and increase in lipid peroxidation, which are signature features of ferroptotic pathway. Ectopic expression of xCT also abrogated RV infection by reversing the virus optimized levels of intracellular GSH and lipid ROS levels. Cumulatively, the study reveals that RV infection triggers ferroptotic cell death via SLC7A11-AS1/xCT axis to facilitate its own propagation.
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Affiliation(s)
- Shreya Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rakesh Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Arpita Mukherjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India.
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Pant P, Kumarswamy R. Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions. RNA Biol 2024; 21:1-9. [PMID: 38105541 PMCID: PMC10730167 DOI: 10.1080/15476286.2023.2287302] [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] [Accepted: 11/17/2023] [Indexed: 12/19/2023] Open
Abstract
Understanding RNA-protein interactions is crucial for deciphering the cellular functions and molecular mechanisms of regulatory RNAs. Consequently, there is a constant need to develop innovative and cost-effective methods to uncover such interactions. We developed a simple and cost-effective technique called Multiple Oligo assisted RNA Pulldown via Hybridization (MORPH) to identify proteins interacting with a specific RNA. MORPH employs a tiling array of antisense oligos (ASOs) to efficiently capture the RNA of interest along with proteins associated with it. Unlike existing techniques that rely on multiple individually biotinylated oligos spanning the entire RNA length, MORPH stands out by utilizing a single biotinylated oligo to capture all the ASOs. To evaluate MORPH's efficacy, we applied this technique combined with mass spectrometry to identify proteins interacting with lncRNA NEAT1, which has previously been studied using various methods. Our results demonstrate that despite being a simple and inexpensive procedure, MORPH performs on par with existing methods.Abbreviations: ASO, Antisense oligo; lncRNA, long non-coding RNA; MORPH, Multiple Oligo assisted RNA Pulldown via Hybridization.
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Affiliation(s)
- Priyanka Pant
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Regalla Kumarswamy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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7
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Zhang D, Zhang M, Zhang L, Wang W, Hua S, Zhou C, Sun X. Long non-coding RNAs and immune cells: Unveiling the role in viral infections. Biomed Pharmacother 2024; 170:115978. [PMID: 38056234 DOI: 10.1016/j.biopha.2023.115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
Viral infections present significant challenges to human health, underscoring the importance of understanding the immune response for effective therapeutic strategies. Immune cell activation leads to dynamic changes in gene expression. Numerous studies have demonstrated the crucial role of long noncoding RNAs (lncRNAs) in immune activation and disease processes, including viral infections. This review provides a comprehensive overview of lncRNAs expressed in immune cells, including CD8 T cells, CD4 T cells, B cells, monocytes, macrophages, dendritic cells, and granulocytes, during both acute and chronic viral infections. LncRNA-mediated gene regulation encompasses various mechanisms, including the modulation of viral replication, the establishment of latency, activation of interferon pathways and other critical signaling pathways, regulation of immune exhaustion and aging, and control of cytokine and chemokine production, as well as the modulation of interferon-stimulated genes. By highlighting specific lncRNAs in different immune cell types, this review enhances our understanding of immune responses to viral infections from a lncRNA perspective and suggests potential avenues for exploring lncRNAs as therapeutic targets against viral diseases.
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Affiliation(s)
- Dan Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengna Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liqin Zhang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Weijuan Wang
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stéphane Hua
- Laboratory of Cellular Immunology and Biotechnology, Molecular Engineering for Health Unit CEA Saclay, 91191 Gif-sur-Yvette cedex, France
| | - Chan Zhou
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xiaoming Sun
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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8
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Yang ZZ, Parchem RJ. The role of noncoding RNAs in pancreatic birth defects. Birth Defects Res 2023; 115:1785-1808. [PMID: 37066622 PMCID: PMC10579456 DOI: 10.1002/bdr2.2178] [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: 01/18/2023] [Revised: 03/19/2023] [Accepted: 04/03/2023] [Indexed: 04/18/2023]
Abstract
Congenital defects in the pancreas can cause severe health issues such as pancreatic cancer and diabetes which require lifelong treatment. Regenerating healthy pancreatic cells to replace malfunctioning cells has been considered a promising cure for pancreatic diseases including birth defects. However, such therapies are currently unavailable in the clinic. The developmental gene regulatory network underlying pancreatic development must be reactivated for in vivo regeneration and recapitulated in vitro for cell replacement therapy. Thus, understanding the mechanisms driving pancreatic development will pave the way for regenerative therapies. Pancreatic progenitor cells are the precursors of all pancreatic cells which use epigenetic changes to control gene expression during differentiation to generate all of the distinct pancreatic cell types. Epigenetic changes involving DNA methylation and histone modifications can be controlled by noncoding RNAs (ncRNAs). Indeed, increasing evidence suggests that ncRNAs are indispensable for proper organogenesis. Here, we summarize recent insight into the role of ncRNAs in the epigenetic regulation of pancreatic development. We further discuss how disruptions in ncRNA biogenesis and expression lead to developmental defects and diseases. This review summarizes in vivo data from animal models and in vitro studies using stem cell differentiation as a model for pancreatic development.
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Affiliation(s)
- Ziyue Zoey Yang
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald J Parchem
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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9
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Liu B, Zhong Y, Huang D, Yang L, Wang P, Yang L, Zhang F, Li X, Liang M, Huang K, Du M. LncRNA Nron deficiency protects mice from diet-induced adiposity and hepatic steatosis. Metabolism 2023; 148:155609. [PMID: 37277059 DOI: 10.1016/j.metabol.2023.155609] [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: 02/11/2023] [Revised: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
Obesity, as a worldwide healthcare problem, has attracted more and more attention. Here we identify a long non-coding RNA NRON, which is highly conserved across species, as an important regulator of glucose/lipid metabolism and whole-body energy expenditure. Depletion of Nron leads to metabolic benefits in DIO (diet-induced obesity) mice, including reduced body weight and fat mass, improved insulin sensitivity and serum lipid parameters, attenuated hepatic steatosis and enhanced adipose function. Mechanistically, Nron deletion improves hepatic lipid homeostasis via PER2/Rev-Erbα/FGF21 axis coupled with AMPK activation, and enhances adipose function via activating the process of triacylglycerol hydrolysis and fatty acid re-esterification (TAG/FA cycling) and coupled metabolic network. These interactive and integrative effects cooperatively account for a healthier metabolic phenotype in NKO (Nron knockout) mice. Genetic or pharmacological inhibition of Nron may have potential for future therapy of obesity.
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Affiliation(s)
- Bing Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yi Zhong
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dandan Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liuye Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengchao Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liu Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Fengxiao Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoguang Li
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Minglu Liang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China.
| | - Meng Du
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, China; Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China.
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Horai Y, Shimizu T, Umeda M, Nishihata SY, Nakamura H, Kawakami A. Current Views on Pathophysiology and Potential Therapeutic Targets in Sjögren's Syndrome: A Review from the Perspective of Viral Infections, Toll-like Receptors, and Long-Noncoding RNAs. J Clin Med 2023; 12:5873. [PMID: 37762814 PMCID: PMC10531551 DOI: 10.3390/jcm12185873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Sjögren's syndrome (SS) is a rheumatic disease characterized by sicca and extraglandular symptoms, such as interstitial lung disease and renal tubular acidosis. SS potentially affects the prognosis of patients, especially in cases of complicated extraglandular symptoms; however, only symptomatic therapies against xerophthalmia and xerostomia are currently included in the practice guidelines as recommended therapies for SS. Considering that SS is presumed to be a multifactorial entity caused by genetic and environmental factors, a multidisciplinary approach is necessary to clarify the whole picture of its pathogenesis and to develop disease-specific therapies for SS. This review discusses past achievements and future prospects for pursuing the pathophysiology and therapeutic targets for SS, especially from the perspectives of viral infections, toll-like receptors (TLRs), long-noncoding RNAs (lncRNAs), and related signals. Based on the emerging roles of viral infections, TLRs, long-noncoding RNAs and related signals, antiviral therapy, hydroxychloroquine, and vitamin D may lower the risk of or mitigate SS. Janus-kinase (JAK) inhibitors are also potential novel therapeutic options for several rheumatic diseases involving the JAK-signal transducer and activator of transcription pathways, which are yet to be ascertained in a randomized controlled study targeting SS.
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Affiliation(s)
- Yoshiro Horai
- Department of Rheumatology, Sasebo City General Hospital, Sasebo 857-8511, Japan
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
- Clinical Research Center, Nagasaki University Hospital, Nagasaki 852-8501, Japan
| | - Masataka Umeda
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
| | - Shin-Ya Nishihata
- Department of Rheumatology, National Hospital Organization Ureshino Medical Center, Ureshino 843-0393, Japan;
| | - Hideki Nakamura
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Tokyo 173-8610, Japan;
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan; (T.S.); (M.U.); (A.K.)
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11
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Guo Q, Li Y, Zhang Y, Shen L, Lin H, Chen J, Song E, Luo M. LncRNA NRON promotes tumorigenesis by enhancing MDM2 activity toward tumor suppressor substrates. EMBO J 2023; 42:e112414. [PMID: 37382239 PMCID: PMC10425849 DOI: 10.15252/embj.2022112414] [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: 08/21/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
The E3 ligase MDM2 promotes tumor growth and progression by inducing ubiquitin-mediated degradation of P53 and other tumor-suppressing proteins. Here, we identified an MDM2-interacting lncRNA NRON, which promotes tumor formation by suppressing both P53-dependent and independent pathways. NRON binds to MDM2 and MDMX (MDM4) via two different stem-loops, respectively, and induces their heterogenous dimerization, thereby enhancing the E3 ligase activity of MDM2 toward its tumor-suppressing substrates, including P53, RB1, and NFAT1. NRON knockdown dramatically inhibits tumor cell growth in vitro and in vivo. More importantly, NRON overexpression promotes oncogenic transformation by inducing anchorage-independent growth in vitro and facilitating tumor formation in immunocompromised mice. Clinically, NRON expression is significantly associated with poor clinical outcome in breast cancer patients. Together, our data uncover a pivotal role of lncRNA that induces malignant transformation of epithelial cells by inhibiting multiple tumor suppressor proteins.
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Affiliation(s)
- Qiannan Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Department of Thyroid Surgery, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yihui Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Medical Research CenterNanhai Translational Innovation Center of Precision Immunology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yunmei Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Breast Tumor Center, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Liping Shen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Breast Tumor Center, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Huayue Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Breast Tumor Center, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Jianing Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Breast Tumor Center, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Breast Tumor Center, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Man‐Li Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA Medicine, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
- Medical Research CenterNanhai Translational Innovation Center of Precision Immunology, Sun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhouChina
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12
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Erber J, Herndler-Brandstetter D. Regulation of T cell differentiation and function by long noncoding RNAs in homeostasis and cancer. Front Immunol 2023; 14:1181499. [PMID: 37346034 PMCID: PMC10281531 DOI: 10.3389/fimmu.2023.1181499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) increase in genomes of complex organisms and represent the largest group of RNA genes transcribed in mammalian cells. Previously considered only transcriptional noise, lncRNAs comprise a heterogeneous class of transcripts that are emerging as critical regulators of T cell-mediated immunity. Here we summarize the lncRNA expression landscape of different T cell subsets and highlight recent advances in the role of lncRNAs in regulating T cell differentiation, function and exhaustion during homeostasis and cancer. We discuss the different molecular mechanisms of lncRNAs and highlight lncRNAs that can serve as novel targets to modulate T cell function or to improve the response to cancer immunotherapies by modulating the immunosuppressive tumor microenvironment.
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13
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Wang Y, Gong H, Cao Y. LncRNA WAC-AS1 expression in human tumors correlates with immune infiltration and affects prognosis. Hereditas 2023; 160:26. [PMID: 37248547 DOI: 10.1186/s41065-023-00290-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND WAC-antisense RNA1 (WAC-AS1) is a newly identified long non-coding RNA (lncRNA) implicated in the prognosis and development of a few types of tumors. However, the correlations of WAC-AS1 with immune infiltration and patient prognosis in pan-cancer remain unclear. In the present study, we aimed to investigate the prognostic value and immunological functions of WAC-AS1 across 33 different types of cancers. METHODS To investigate the potential oncogenic roles of WAC-AS1, bioinformatics analyses were performed using the Cancer Genome Atlas (TCGA) and Genotype Tissue-Expression (GTEx) datasets. The correlations of WAC-AS1 with prognosis, clinical phenotype, tumor mutational burden (TMB), microsatellite instability (MSI), tumor regulation-related genes, tumor microenvironment, immune cell infiltration, and drug resistance to commonly used chemotherapy drugs in different types of tumors were explored. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed to explore the biological functions of WAC-AS1 in tumors. In situ hybridization (ISH) was performed in tissue microarray (TMA) to confirm the expression of WAC-AS1 in multiple tumor tissues. RESULTS WAC-AS1 showed aberrant expression in most cancers when compared to the normal tissues. It also has prognostic value in multiple types of cancers. Elevated WAC-AS1 expression was associated with poor prognosis and overall survival in adrenocortical carcinoma (ACC), breast invasive carcinoma (BRCA), and liver hepatocellular carcinoma (LIHC). A significant negative correlation between WAC-AS1 expression and overall survival was observed in brain lower-grade glioma (LGG), pancreatic adenocarcinoma (PAAD), and skin cutaneous melanoma (SKCM). The expression of WAC-AS1 also showed a correlation with clinical stage in six types of tumors, and with tumor mutational burden and microsatellite instability in several different types of cancers. The immune scores of those cancers were found to be significant. Additionally, the effectiveness of fluorouracil and four other anticancer drugs was significantly different based on the expression of WAC-AS1 in these cancers. Moreover, the ISH results showed in six types of tumors, the expression of WAC-AS1 was consistent with the Pan-cancer analysis using TCGA and GTEx database. CONCLUSIONS These results indicate an intensive involvement of WAC-AS1 in the regulation of immune responses, immune cell infiltration, and malignant properties in various types of cancers, suggesting that WAC-AS1 may serve as a prognostic marker across diverse types of cancers.
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Affiliation(s)
- Yanyang Wang
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University , Nanjing, 210008, China
| | - Haiyan Gong
- Medical Examination Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Yue Cao
- The Laboratory Center for Basic Medical Science, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu, 211166, China.
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Yan X, Li Q, Wu S, Liang J, Li Y, Zhang T, Chen D, Pan X. Acrylamide induces the activation of BV2 microglial cells through TLR2/4-mediated LRRK2-NFATc2 signaling cascade. Food Chem Toxicol 2023; 176:113775. [PMID: 37037409 DOI: 10.1016/j.fct.2023.113775] [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: 12/13/2022] [Revised: 03/26/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
Acrylamide (ACR), a potential neurotoxin, is generated from the Maillard reaction between reducing sugars and free amino acids during food processing. Our work focuses on clarifying the role of the leucine-rich repeat kinase 2 (LRRK2) and nuclear factor of activated T cells, cytoplasmic 2 (NFATc2) in the polarization of BV2 cells to the M1 proinflammatory type induced by ACR. Specifically, ACR promoted the phosphorylation of LRRK2 and NFATc2 in BV2 microglia. Furthermore, selectively phosphorylated LRRK2 by ACR induced nuclear translocation of NFATc2 to trigger a neuroinflammatory cascade. Knock-down of LRRK2 by silencing significantly diminished ACR-induced microglial neurotoxic effect with the decline of IL-1β, IL-6, and iNOS levels and the decrease of NFATc2 expression in BV2 cells. After pretreated with Toll-Like Receptor 2 (TLR2) and TLR4 inhibitors separately, both the activation of LRRK2 and the release of pro-inflammatory factors were inhibited in BV2 cells. Gallic acid (GA) is ubiquitous in most parts of the medicinal plant. GA alleviated the increased CD11b expression, IL-6 and iNOS levels induced by ACR in BV2 microglia. In conclusion, this study shows that ACR leads to the cascade activation of LRRK2-NFATc2 mediated by TLR2 and TLR4 to induce microglial toxicity.
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Affiliation(s)
- Xiaoyu Yan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Qiuju Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Sichuan, 610075, China; School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Shuangyue Wu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Jie Liang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Yuanyuan Li
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Tingting Zhang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Dayi Chen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
| | - Xiaoqi Pan
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Sichuan, 610075, China.
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15
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Dominguez-Alonso S, Carracedo A, Rodriguez-Fontenla C. The non-coding genome in Autism Spectrum Disorders. Eur J Med Genet 2023; 66:104752. [PMID: 37023975 DOI: 10.1016/j.ejmg.2023.104752] [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: 10/24/2022] [Revised: 03/10/2023] [Accepted: 03/19/2023] [Indexed: 04/08/2023]
Abstract
Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders (NDDs) characterized by difficulties in social interaction and communication, repetitive behavior, and restricted interests. While ASD have been proven to have a strong genetic component, current research largely focuses on coding regions of the genome. However, non-coding DNA, which makes up for ∼99% of the human genome, has recently been recognized as an important contributor to the high heritability of ASD, and novel sequencing technologies have been a milestone in opening up new directions for the study of the gene regulatory networks embedded within the non-coding regions. Here, we summarize current progress on the contribution of non-coding alterations to the pathogenesis of ASD and provide an overview of existing methods allowing for the study of their functional relevance, discussing potential ways of unraveling ASD's "missing heritability".
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Affiliation(s)
- S Dominguez-Alonso
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - C Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
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16
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Wu J, Zhang Z, Ma X, Liu X. Advances in Research on the Regulatory Roles of lncRNAs in Osteoarthritic Cartilage. Biomolecules 2023; 13:biom13040580. [PMID: 37189327 DOI: 10.3390/biom13040580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Osteoarthritis (OA) is the most common degenerative bone and joint disease that can lead to disability and severely affect the quality of life of patients. However, its etiology and pathogenesis remain unclear. It is currently believed that articular cartilage lesions are an important marker of the onset and development of osteoarthritis. Long noncoding RNAs (lncRNAs) are a class of multifunctional regulatory RNAs that are involved in various physiological functions. There are many differentially expressed lncRNAs between osteoarthritic and normal cartilage tissues that play multiple roles in the pathogenesis of OA. Here, we reviewed lncRNAs that have been reported to play regulatory roles in the pathological changes associated with osteoarthritic cartilage and their potential as biomarkers and a therapeutic target in OA to further elucidate the pathogenesis of OA and provide insights for the diagnosis and treatment of OA.
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Changes in the Transcriptome-Associated Co-Expression Profile of Embryonic External Ear Development After the BMP5 Gene Mutation. J Craniofac Surg 2023; 34:797-803. [PMID: 36192835 DOI: 10.1097/scs.0000000000009031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/21/2022] [Indexed: 11/26/2022] Open
Abstract
This study aimed to perform an association analysis of the full transcriptome in Bmp5 short-ear mice during the development of the external ear in mouse embryos using advanced sequencing techniques. To understand the changes in gene regulation and expression of BMP5 gene mutations involved in the external ear embryonic development of mice, external ear tissues of mouse embryos developed to E15.5 and E17.5 were obtained using a BMP5 short-ear mouse model. The association analysis of the full transcriptome mainly involved the analysis of lncRNA and mRNA associations, the analysis of lncRNA and miRNA associations, the analysis of miRNA and mRNA associations, the analysis of circRNA and mRNA associations and circRNA, miRNA, and mRNA associations. The results showed that regulation of the full transcriptome is associated with external ear development in BMP5 short-ear mouse embryos, and some key regulatory changes in full transcriptome after BMP5 gene point mutation are different. This study will provide a new clue to investigate the mechanism underlying the regulation of mouse external ear development by the full transcriptome.
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18
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Zou ZL, Ye Y, Zhou B, Zhang Y. Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder. World J Psychiatry 2023; 13:36-49. [PMID: 36925948 PMCID: PMC10011943 DOI: 10.5498/wjp.v13.i2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/06/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence; however, the interplay among RNA species, including protein-coding RNAs and ncRNAs, in MDD remains unclear.
AIM To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA (lncRNAs), microRNAs (miRNAs), and mRNAs between MDD and controls.
METHODS Gene expression data were searched in NCBI Gene Expression Omnibus using the search term “major depressive disorder.” Six array datasets from humans were related to the search term: GSE19738, GSE32280, GSE38206, GSE52790, GSE76826, and GSE81152. These datasets were processed for initial assessment and subjected to quality control and differential expression analysis. Differentially expressed lncRNAs, miRNAs, and mRNAs were determined, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction network was generated. The results were analyzed for their association with MDD.
RESULTS After analysis, 3 miRNAs, 12 lncRNAs, and 33 mRNAs were identified in the competing endogenous RNA network. Two of these miRNAs were earlier shown to be involved in psychiatric disorders, and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The expression of hub gene fatty acid 2-hydroxylase was enriched, and the encoded protein was found to be involved in myelin formation, indicating that neurological development and signal transduction are involved in MDD pathogenesis.
CONCLUSION The present study presents candidate ncRNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.
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Affiliation(s)
- Zhi-Li Zou
- Department of Psychosomatic, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
| | - Yu Ye
- Sichuan Provincial Center for Mental Health, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 611130, Sichuan Province, China
| | - Bo Zhou
- Department of Psychosomatic, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
| | - Yuan Zhang
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu 610072, Sichuan Province, China
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19
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Zhao NN, Yu XD, Tian X, Xu Q, Zhang CY. Mix-and-Detection Assay with Multiple Cyclic Enzymatic Repairing Amplification for Rapid and Ultrasensitive Detection of Long Noncoding RNAs in Breast Tissues. Anal Chem 2023; 95:3082-3088. [PMID: 36692970 DOI: 10.1021/acs.analchem.2c05353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Long noncoding RNAs (lncRNAs) are valuable biomarkers and therapeutic targets, and they play essential roles in various pathological and biological processes. So far, the reported lncRNA assays usually suffer from unsatisfactory sensitivity and time-consuming procedures. Herein, we develop a mix-and-read assay based on multiple cyclic enzymatic repairing amplification (ERA) for sensitive and rapid detection of mammalian metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1). In this assay, we design two three-way junction (3WJ) probes including a 3WJ template and a 3WJ primer to specifically recognize lncRNA MALAT1, and the formation of a stable 3WJ structure induces cyclic ERA to generate triggers. The resulting triggers subsequently hybridize with a free 3WJ template and act as primers to initiate new rounds of cyclic ERA, generating abundant triggers. The hybridization of triggers with signal probes forms stable double-stranded DNA duplexes that can be specifically cleaved by apurinic/apyrimidinic endonuclease 1 to produce a high fluorescence signal. This assay can be carried out in a mix-and-read manner within 10 min under an isothermal condition (50 °C), which is the rapidest and simplest method reported so far for the lncRNA MALAT1 assay. This method can sensitively detect lncRNA MALAT1 with a limit of detection of 0.87 aM, and it can accurately measure endogenous lncRNA MALAT1 at the single-cell level. Moreover, this method can distinguish lncRNA MALAT1 expression in breast cancer patient tissues and their corresponding healthy adjacent tissues. Importantly, the extension of this assay to different RNAs detection can be achieved by simply replacing the corresponding target recognition sequences.
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Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiao-Di Yu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
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20
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Wang A, Wang J, Mao M, Zhao X, Li Q, Xuan R, Li F, Chao T. Analyses of lncRNAs, circRNAs, and the Interactions between ncRNAs and mRNAs in Goat Submandibular Glands Reveal Their Potential Function in Immune Regulation. Genes (Basel) 2023; 14:187. [PMID: 36672927 PMCID: PMC9859278 DOI: 10.3390/genes14010187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
As part of one of the main ruminants, goat salivary glands hardly secrete digestive enzymes, but play an important role in immunity. The immune function of goat salivary glands significantly changes with age, while the expression profile and specific function of non-coding RNA during this process are unknown. In this study, transcriptome sequencing was performed on submandibular gland (SMG) tissues of 1-month-old, 12-month-old, and 24-month-old goats, revealing the expression patterns of lncRNA and circRNA at different ages. A total of 369 lncRNAs and 1699 circRNAs were found to be differentially expressed. Functional enrichment analyses showed that the lncRNA regulated target mRNAs and circRNA host genes were significantly enriched in immune-related GO terms and pathways. CeRNA network analysis showed that the key differentially expressed circRNAs and lncRNAs mainly regulate the key immune-related genes ITGB2, LCP2, PTPRC, SYK, and ZAP70 through competitive binding with miR-141-x, miR-29-y, and chi-miR-29b-3p, thereby affecting the natural killer cell-mediated cytotoxicity pathway, the T cell receptor signaling pathway, and other immune-related pathways. It should be noted that the expression of key circRNAs, lncRNAs, and key immune-related genes in goat SMGs decreased significantly with the growth of the goat. This is the first reporting of lncRNAs, circRNAs, and ceRNA network regulation in goat SMGs. Our study contributes to the knowledge of changes in the expression of non-coding RNAs during SMG development in goats and provides new insights into the relationship between non-coding RNAs and salivary gland immune function in goats.
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Affiliation(s)
- Aili Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271000, China
| | - Meina Mao
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang 262700, China
| | - Xiaodong Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
- Shandong Vocational Animal Science and Veterinary College, Weifang 261000, China
| | - Qing Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271000, China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271000, China
| | - Fajun Li
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang 262700, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271000, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271000, China
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Liu Q, Bao H, Zhang S, Song T, Li C, Sun G, Sun X, Fu T, Wang Y, Liang P. Identification of a cellular senescence-related-lncRNA (SRlncRNA) signature to predict the overall survival of glioma patients and the tumor immune microenvironment. Front Genet 2023; 14:1096792. [PMID: 36911393 PMCID: PMC9998504 DOI: 10.3389/fgene.2023.1096792] [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: 11/12/2022] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Background: Gliomas are brain tumors that arise from glial cells, and they are the most common primary intracranial tumors with a poor prognosis. Cellular senescence plays a critical role in cancer, especially in glioma. In this study, we constructed a senescence-related lncRNA (SRlncRNA) signature to assess the prognosis of glioma. Methods: The Cancer Genome Atlas was used to collect SRlncRNA transcriptome profiles and clinical data about glioma. Patients were randomized to training, testing, and whole cohorts. LASSO and Cox regression analyses were employed to construct the SRlncRNA signature, and Kaplan-Meier (K-M) analysis was performed to determine each cohort's survival. Receiver operating characteristic (ROC) curves were applied to verify the accuracy of this signature. Gene set enrichment analysis was used to visualize functional enrichment (GSEA). The CIBERSORT algorithm, ESTIMATE and TIMER databases were utilized to evaluate the differences in the infiltration of 22 types of immune cells and their association with the signature. RT-qPCR and IHC were used to identify the consistency of the signature in tumor tissue. Results: An SRlncRNA signature consisting of six long non-coding RNAs (lncRNAs) was constructed, and patients were divided into high-risk and low-risk groups by the median of their riskscore. The KM analysis showed that the high-risk group had worse overall survival, and the ROC curve confirmed that the riskscore had more accurate predictive power. A multivariate Cox analysis and its scatter plot with clinical characteristics confirmed the riskscore as an independent risk factor for overall survival. GSEA showed that the GO and KEGG pathways were mainly enriched in the immune response to tumor cells, p53 signaling pathway, mTOR signaling pathway, and Wnt signaling pathway. Further validation also yielded significant differences in the risk signature in terms of immune cell infiltration, which may be closely related to prognostic differences, and qRT-PCR and IHC confirmed the consistency of the expression differences in the major lncRNAs with those in the prediction model. Conclusion Our findings indicated that the SRlncRNA signature might be used as a predictive biomarker and that there is a link between it and immune infiltration. This discovery is consistent with the present categorization system and may open new avenues for research and personalized therapy.
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Affiliation(s)
- Qing Liu
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongbo Bao
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Sibin Zhang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianjun Song
- Department of Medicine II, University Hospital LMU Munich, Munich, Germany
| | - Chenlong Li
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guiyin Sun
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaoyang Sun
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianjiao Fu
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yujie Wang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Peng Liang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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Zhao Y, Bai L, Yao X, Hang R, Xiao Y. Understanding LncRNAs in Biomaterials Development for Osteointegration. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Wu W, Cao L, Jia Y, Xiao Y, Zhang X, Gui S. Emerging Roles of miRNA, lncRNA, circRNA, and Their Cross-Talk in Pituitary Adenoma. Cells 2022; 11:cells11182920. [PMID: 36139495 PMCID: PMC9496700 DOI: 10.3390/cells11182920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Pituitary adenoma (PA) is a common intracranial tumor without specific biomarkers for diagnosis and treatment. Non-coding RNAs (ncRNAs), including microRNAs (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA), regulate a variety of cellular processes, such as cell proliferation, differentiation, and apoptosis. Increasing studies have shown that the dysregulation of ncRNAs, especially the cross-talk between lncRNA/circRNA and miRNA, is related to the pathogenesis, diagnosis, and prognosis of PA. Therefore, ncRNAs can be considered as promising biomarkers for PA. In this review, we summarize the roles of ncRNAs from different specimens (i.e., tissues, biofluids, cells, and exosomes) in multiple subtypes of PA and highlight important advances in understanding the contribution of the cross-talk between ncRNAs (e.g., competing endogenous RNAs) to PA disease.
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Affiliation(s)
- Wentao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119 South Forth West Ring, Beijing 100070, China
| | - Lei Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119 South Forth West Ring, Beijing 100070, China
| | - Yanfei Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119 South Forth West Ring, Beijing 100070, China
| | - Youchao Xiao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119 South Forth West Ring, Beijing 100070, China
| | - Xu Zhang
- Department of Oncology, First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei 230032, China
- Correspondence: (X.Z.); (S.G.)
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119 South Forth West Ring, Beijing 100070, China
- Correspondence: (X.Z.); (S.G.)
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25
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Wu S, Ren K, Zhao J, Li J, Jia B, Wu X, Dou Y, Fei X, Huan Y, He X, Wang T, Lv W, Wang L, Wang Y, Zhao J, Fei Z, Li S. LncRNA GAS5 represses stemness and malignancy of gliomas via elevating the SPACA6-miR-125a/let-7e Axis. Front Oncol 2022; 12:803652. [PMID: 36106122 PMCID: PMC9465381 DOI: 10.3389/fonc.2022.803652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is a highly invasive neurological malignancy with poor prognosis. LncRNA-GAS5 (growth arrest-specific transcript 5) is a tumor suppressor involved in multiple cancers. In this study, we explored the clinical significance, biological function, and underlying mechanisms of GAS5 in GBM. We showed that lncRNA-GAS5 expression decreased in high-grade glioma tissues and cells, which might be associated with poor prognosis. GAS5 overexpression lowered cell viability, suppressed GBM cell migration and invasion, and impaired the stemness and proliferation of glioma stem cells (GSCs). We further discovered that GAS5 inhibited the viability of glioma cells through miR-let-7e and miR-125a by protecting SPACA6 from degradation. Moreover, GAS5 played an anti-oncogenic role in GBM through the combined involvement of let-7e and miR-125a in vivo and in vitro. Notably, these two miRNAs block the IL-6/STAT3 pathway in tumor tissues extracted from a xenograft model. Taken together, our study provides evidence for an important role of GAS5 in GBM by affecting the proliferation and migration of GSCs, thus providing a new potential prognostic biomarker and treatment strategy for GBM.
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Affiliation(s)
- Shuang Wu
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Kaixi Ren
- Department of Neurology, Tangdu Hospital, Air Force Military Medical University, Xi’an, China
| | - Jing Zhao
- Department of Anesthesiology, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Juan Li
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Bo Jia
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Xiuquan Wu
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Yanan Dou
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Xiaowei Fei
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Yu Huan
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Xin He
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Tingting Wang
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Weihao Lv
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Li Wang
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Yan’gang Wang
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
| | - Junlong Zhao
- State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Air Force Military Medical University, Xi’an, China
- *Correspondence: Sanzhong Li, ; Zhou Fei, ; Junlong Zhao,
| | - Zhou Fei
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
- *Correspondence: Sanzhong Li, ; Zhou Fei, ; Junlong Zhao,
| | - Sanzhong Li
- Department of Neurosurgery, Xijing Hospital, Air Force Military Medical University, Xi’an, China
- *Correspondence: Sanzhong Li, ; Zhou Fei, ; Junlong Zhao,
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26
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Zhao X, Lan Y, Chen D. Exploring long non-coding RNA networks from single cell omics data. Comput Struct Biotechnol J 2022; 20:4381-4389. [PMID: 36051880 PMCID: PMC9403499 DOI: 10.1016/j.csbj.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022] Open
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27
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Karimi B, Dehghani Firoozabadi A, Peymani M, Ghaedi K. Circulating long noncoding RNAs as novel bio-tools: Focus on autoimmune diseases. Hum Immunol 2022; 83:618-627. [PMID: 35717260 DOI: 10.1016/j.humimm.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs that do not encode proteins. These RNAs have various essential regulatory functions. Irregular expression of lncRNAs has been related to the pathological process of varied diseases, and are considered promising diagnostic biomarkers. LncRNAs can release into the circulation and be stable in body fluids as circulating lncRNAs. A subset of circulating lncRNAs that exist in exosomes are referred to as exosomal lncRNA molecules. These lncRNAs are highly stable and resist RNases. Exosomes have captured a great deal of attention due to their involvement in regulating communications between cells. In conditions of autoimmune disease, exosomes play critical roles in the pathological processes. In this context, circulating lncRNAs have been shown to modulate the immune response and indicated as prognosis and diagnostic biomarkers for autoimmune diseases. This review highlights the role of circulating lncRNAs (particularly exosomal) as diagnostic biomarkers for autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis, psoriasis, and Sjögren's syndrome.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Kamran Ghaedi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Jiang S, Zhang Q, Li J, Raziq K, Kang X, Liang S, Sun C, Liang X, Zhao D, Fu S, Cai M. New Sights Into Long Non-Coding RNA LINC01133 in Cancer. Front Oncol 2022; 12:908162. [PMID: 35747817 PMCID: PMC9209730 DOI: 10.3389/fonc.2022.908162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
LINC01133 is a long intergenic non-coding RNA that regulates malignancy in several cancers, including those of the digestive, female reproductive, respiratory, and urinary system. LINC01133 is an extensively studied lncRNA that is highly conserved, and its relatively stable expression is essential for its robust biological function. Its expression is highly tissue-specific with a distinct subcellular localization. It functions as an oncogene or a tumor suppressor gene in different cancers via multiple mechanisms, such as those that involve competing with endogenous RNA and binding to RNA-binding proteins or DNA. Moreover, the secretion and transportation of LINC01133 by extracellular vesicles in the tumor micro-environment is regulated by other cells in the tumor micro-environment. To date, two mechanisms, an increase in copy number and regulation of transcription elements, have been found to regulate LINC01133 expression. Clinically, LINC01133 is an ideal marker for cancer prognosis and a potential therapeutic target in cancer treatment regimes. In this review, we aimed to summarize the aforementioned information as well as posit future directions for LINC01133 research.
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Affiliation(s)
- Shengnan Jiang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Qian Zhang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jiaqi Li
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Khadija Raziq
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xinyu Kang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Shiyin Liang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chaoyue Sun
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Xiao Liang
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Di Zhao
- Department of Genecology and Obstetrics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Key Laboratory of Preservation of Human Genetic Resources and DiseaseControl, Ministry of Education, Harbin Medical University, Harbin, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- *Correspondence: Mengdi Cai,
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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30
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Juni RP, ’t Hart KC, Houtkooper RH, Boon R. Long non‐coding RNAs in cardiometabolic disorders. FEBS Lett 2022; 596:1367-1387. [DOI: 10.1002/1873-3468.14370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Rio P. Juni
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
| | - Kelly C. ’t Hart
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Reinier Boon
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Institute for Cardiovascular Regeneration Centre for Molecular Medicine Goethe University Frankfurt am Main Frankfurt am Main Germany
- German Centre for Cardiovascular Research DZHK Partner site Frankfurt Rhein/Main Frankfurt am Main Germany
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31
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Zhou H, Li S, Pan W, Wu S, Ma F, Jin P. Interaction of lncRNA-CR33942 with Dif/Dorsal Facilitates Antimicrobial Peptide Transcriptions and Enhances Drosophila Toll Immune Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1978-1988. [PMID: 35379744 DOI: 10.4049/jimmunol.2100658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/02/2022] [Indexed: 01/08/2023]
Abstract
The Drosophila Toll signaling pathway mainly responds to Gram-positive (G+) bacteria or fungal infection, which is highly conserved with mammalian TLR signaling pathway. Although many positive and negative regulators involved in the immune response of the Toll pathway have been identified in Drosophila, the roles of long noncoding RNAs (lncRNAs) in Drosophila Toll immune responses are poorly understood to date. In this study, our results demonstrate that lncRNA-CR33942 is mainly expressed in the nucleus and upregulated after Micrococcus luteus infection. Especially, lncRNA-CR33942 not only modulates differential expressions of multiple antimicrobial peptide genes but also affects the Drosophila survival rate during response to G+ bacterial infection based on the transiently overexpressing and the knockdown lncRNA-CR33942 assays in vivo. Mechanically, lncRNA-CR33942 interacts with the NF-κB transcription factors Dorsal-related immunity factor/Dorsal to promote the transcriptions of antimicrobial peptides drosomycin and metchnikowin, thus enhancing Drosophila Toll immune responses. Taken together, this study identifies lncRNA-CR33942 as a positive regulator of Drosophila innate immune response to G+ bacterial infection to facilitate Toll signaling via interacting with Dorsal-related immunity factor/Dorsal. It would be helpful to reveal the roles of lncRNAs in Toll immune response in Drosophila and provide insights into animal innate immunity.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and.,Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, People's Republic of China
| | - Wanwan Pan
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics and Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, People's Republic of China; and
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Bioactive glass nanoparticles inhibit osteoclast differentiation and osteoporotic bone loss by activating lncRNA NRON expression in the extracellular vesicles derived from bone marrow mesenchymal stem cells. Biomaterials 2022; 283:121438. [DOI: 10.1016/j.biomaterials.2022.121438] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022]
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Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
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Liu X, Xu M, Li P, Zhang W, Zeng LH, Yang Y, Yang G. Roles of lncRNAs in the transcription regulation of HIV-1. Biomed J 2022; 45:580-593. [PMID: 35364293 PMCID: PMC9486250 DOI: 10.1016/j.bj.2022.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) is a class of RNA molecules that are more than 200bp but cannot be translated into proteins. More and more studies have proved that lncRNA plays a crucial role in various biological functions and disease processes, including virus infection. It's worth noting that studies have also shown that lncRNAs play an essential role in the pathogenesis of human immunodeficiency virus 1 (HIV-1), one of the lethal virus that can destroy immune system. Although lncRNA-mediated gene regulation involves a variety of mechanisms, such as transcription regulation, translation regulation, protein modification, and the formation of RNA-protein complexes, in this review, we primarily focus on the role of lncRNAs in HIV-1 transcription regulation, which is one of the most important mechanisms that control the activation and development of HIV-1. This review also briefly summarizes the latest research progress of lncRNAs related to HIV-1 infection and its potential application in HIV-1 therapy. Although there are antiretroviral drugs that interfere with the function of HIV-1 virus-encoded proteins, this treatment for the HIV-1 virus is limited by its ability to produce drug resistance. Hence, a further understanding of HIV-1 transcription regulation by lncRNAs might help develop non-traditional antiviral therapy strategies.
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Affiliation(s)
- Xingzhu Liu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Mengjiao Xu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ping Li
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wenyuan Zhang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ling-Hui Zeng
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
| | - Yadong Yang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
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The role of long noncoding RNA Nron in atherosclerosis development and plaque stability. iScience 2022; 25:103978. [PMID: 35295812 PMCID: PMC8919297 DOI: 10.1016/j.isci.2022.103978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/31/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
The major clinical consequences of atherosclerosis such as myocardial infarction or stroke are because of thrombotic events associated with acute rupture or erosion of an unstable plaque. Here, we identify an lncRNA Noncoding Repressor of NFAT (Nron) as a critical regulator of atherosclerotic plaque stability. Nron overexpression (OE) in vascular smooth muscle cells (VSMC) induces a highly characteristic architecture of more-vulnerable plaques, while Nron knockdown (KD) suppresses the development of atherosclerosis and favors plaque stability. Mechanistically, Nron specifically binds to and negatively regulates NFATc3, thus inhibiting the proliferation and promoting the apoptosis of VSMCs. Moreover, we also provide evidence that Nron increases the production and secretion of VEGFA from VSMCs, which functions as a paracrine factor to enhance intra-plaque angiogenesis. All of these effects contribute to plaque instability. Genetic or pharmacological inhibition of Nron may have potential for future therapy of atherosclerosis. Nron promotes atherosclerosis progression and contributes to plaque instability Nron negatively regulates NFATc3 activity and impairs VSMC function Nron increases VEGFA production and promotes intra-plaque angiogenesis
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Hoepfner J, Leonardy J, Lu D, Schmidt K, Hunkler HJ, Biß S, Foinquinos A, Xiao K, Regalla K, Ramanujam D, Engelhardt S, Bär C, Thum T. The long non-coding RNA NRON promotes the development of cardiac hypertrophy in the murine heart. Mol Ther 2022; 30:1265-1274. [PMID: 34856383 PMCID: PMC8899598 DOI: 10.1016/j.ymthe.2021.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/13/2021] [Accepted: 11/27/2021] [Indexed: 10/19/2022] Open
Abstract
Physiological and pathological cardiovascular processes are tightly regulated by several cellular mechanisms. Non-coding RNAs, including long non-coding RNAs (lncRNAs), represent one important class of molecules involved in regulatory processes within the cell. The lncRNA non-coding repressor of NFAT (NRON) was described as a repressor of the nuclear factor of activated T cells (NFAT) in different in vitro studies. Although the calcineurin/NFAT-signaling pathway is one of the most important pathways in pathological cardiac hypertrophy, a potential regulation of hypertrophy by NRON in vivo has remained unclear. Applying subcellular fractionation and RNA fluorescence in situ hybridization (RNA-FISH), we found that, unlike what is known from T cells, in cardiomyocytes, NRON predominantly localizes to the nucleus. Hypertrophic stimulation in neonatal mouse cardiomyocytes led to a downregulation of NRON, while NRON overexpression led to an increase in expression of hypertrophic markers. To functionally investigate NRON in vivo, we used a mouse model of transverse aortic constriction (TAC)-induced hypertrophy and performed NRON gain- and loss-of-function experiments. Cardiomyocyte-specific NRON overexpression in vivo exacerbated TAC-induced hypertrophy, whereas cardiomyocyte-specific NRON deletion attenuated cardiac hypertrophy in mice. Heart weight, cardiomyocyte cell size, hypertrophic marker gene expression, and left ventricular mass showed a NRON-dependent regulation upon TAC-induced hypertrophy. In line with this, transcriptome profiling revealed an enrichment of anti-hypertrophic signaling pathways upon NRON-knockout during TAC-induced hypertrophy. This set of data refutes the hypothesized anti-hypertrophic role of NRON derived from in vitro studies in non-cardiac cells and suggests a novel regulatory function of NRON in the heart in vivo.
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Affiliation(s)
- Jeannine Hoepfner
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Julia Leonardy
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Dongchao Lu
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Kevin Schmidt
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Hannah J. Hunkler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sinje Biß
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Ariana Foinquinos
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Kumarswamy Regalla
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology, Technical University Munich, 80802 Munich, Germany,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University Munich, 80802 Munich, Germany,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, 80802 Munich, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, 30625 Hannover, Germany.
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, 30625 Hannover, Germany.
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Cao M, Luo H, Li D, Wang S, Xuan L, Sun L. Research advances on circulating Long noncoding RNAs as biomarkers of cardiovascular diseases. Int J Cardiol 2022; 353:109-117. [PMID: 35143876 DOI: 10.1016/j.ijcard.2022.01.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
Cardiovascular diseases (CVD) such as myocardial ischemia, myocardial infarction, heart failure, atherosclerosis, hypertension, arrhythmia, and their complications diseases are associated with increased morbidity and mortality, it is necessary to develop new diagnostic markers for CVD. LncRNAs have become a new class of biomarkers in CVD with good development prospects. Numerous studies have confirmed lncRNAs feasibility as diagnostic, prognostic and predictive tools for different types of CVD. In this review, we summarized the available knowledge regarding the clinical application value and pathophysiological mechanism of circulating lncRNA as potential biomarkers of cardiovascular disease. We reviewed the scope of application and changes of circulating lncRNAs such as ZFAS1, CDR1AS, CHAST, UCA1, HOTAIR, MIAT, NEAT1, LIPCAR, H19, NRF, NRON, MHRT, PVT1, Heat2, CASC7, GAS5, MALAT1, APPAT, HIF1A-AS1, KCNQ1OT1, NEXN in different kinds of CVD and discussed their clinical application potential as biomarker, which can help us better understand the mechanism of CVD.
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Affiliation(s)
- Mingyi Cao
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Huishan Luo
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Danning Li
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shengjie Wang
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lina Xuan
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lihua Sun
- Department of Pharmacology, Harbin Medical University (the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China.
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38
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Emerging Role of LncRNAs in Autoimmune Lupus. Inflammation 2022; 45:937-948. [DOI: 10.1007/s10753-021-01607-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/11/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022]
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Abstract
Recently an explosion in the discovery of long noncoding RNAs (lncRNAs) was obtained by high-throughput sequencing. Genome-wide transcriptome analyses, in conjugation with research for epigenetic modifications of chromatins, identified a novel type of non-protein coding transcripts longer than 200 nucleotides named lncRNAs . They are gradually emerging as functional and critical participants in many physiological processes. Here we gave an overview of the characteristics, biological functions, and working mechanism for this new class of noncoding RNA molecules.
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Zuo Q, Jing J, Zhou J, Zhang Y, Wei W, Chen G, Li B. Dual regulatory actions of LncBMP4 on BMP4 promote chicken primordial germ cell formation. EMBO Rep 2022; 23:e52491. [PMID: 34747116 PMCID: PMC8728602 DOI: 10.15252/embr.202152491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
The unique characteristics of chicken primordial germ cells (PGCs) provide potential strategies for transgenic animal generation; however, insufficient PGC availability has limited their application. Regulation of bone morphogenic protein 4 (BMP4), a crucial factor for PGCs formation, may provide new strategies for PGC generation. We here identify a long noncoding RNA (lncRNA) that targets BMP4 (LncBMP4). LncBMP4 has similar functions as BMP4, in that it facilitates the formation and migration of PGCs. LncBMP4 promotes BMP4 expression by adsorbing the miRNA gga-mir-12211, thus reducing its inhibitory effect on BMP4 expression. In addition, the small peptide EPC5 encoded by LncBMP4 promotes the transcription of BMP4. The competing endogenous RNA (ceRNA) effect of LncBMP4 requires N6-methyladenosine (m6A) modification, in a dose-dependent manner, and high levels of m6A modification hinder EPC5 translation. Understanding the molecular mechanisms through which LncBMP4 promotes BMP4 expression during PGC formation may provide new avenues for efficient PGC generation.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jin Jing
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jing Zhou
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Wanhong Wei
- Department of Biological SciencesCollege of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
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Morrison TA, Hudson WH, Chisolm DA, Kanno Y, Shih HY, Ahmed R, Henao-Mejia J, Hafner M, O'Shea JJ. Evolving Views of Long Noncoding RNAs and Epigenomic Control of Lymphocyte State and Memory. Cold Spring Harb Perspect Biol 2022; 14:a037952. [PMID: 34001528 PMCID: PMC8725624 DOI: 10.1101/cshperspect.a037952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Not simply an attribute of the adaptive immune system, immunological memory can be viewed on multiple levels. Accordingly, the molecular basis of memory comprises multiple mechanisms. The advent of new sequencing technologies has greatly enhanced the understanding of gene regulation and lymphocyte specification, and improved measurement of chromatin states affords new insights into the epigenomic and transcriptomic programs that underlie memory. Beyond canonical genes, the involvement of long noncoding RNAs (lncRNAs) is becoming increasingly apparent, and it appears that there are more than two to three times as many lncRNAs as protein-coding genes. lncRNAs can directly interact with DNA, RNA, and proteins, and a single lncRNA can contain multiple modular domains and thus interact with different classes of molecules. Yet, most lncRNAs have not been tested for function, and even fewer knockout mice have been generated. It is therefore timely to consider new potential mechanisms that may contribute to immune memory.
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Affiliation(s)
- Tasha A Morrison
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William H Hudson
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Danielle A Chisolm
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jorge Henao-Mejia
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Dey S, Misra A, Selvi Bharathavikru R. Long Non-coding RNAs, Lnc (ing) RNA Metabolism to Cancer Biology. Subcell Biochem 2022; 100:175-199. [PMID: 36301495 DOI: 10.1007/978-3-031-07634-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The eukaryotic genome is represented by a vast proportion of non-coding regions, which in recent years have been attributed to have important functional roles in gene regulation through a myriad of processes, ranging from proper localization, correct folding and, most importantly, spatial and temporally regulated expression of genes. One of the major contributing factors in these processes is ribonucleic acid (RNA) metabolism, which comprises the RNA-nucleoprotein (RNP) complexes that interact with and instruct the genome to function. Long non-coding RNAs are an integral component of several RNPs, and herein we provide an overview of the understanding of the long non-coding RNAs, their characteristics, their function and their balancing act as dual modulators in cancer manifestation and progression.
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Affiliation(s)
- Sourav Dey
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - Arushi Misra
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - R Selvi Bharathavikru
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India.
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Li C, Cao M, Zhou X. Role of epigenetics in parturition and preterm birth. Biol Rev Camb Philos Soc 2021; 97:851-873. [PMID: 34939297 DOI: 10.1111/brv.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022]
Abstract
Preterm birth occurs worldwide and is associated with high morbidity, mortality, and economic cost. Although several risk factors associated with parturition and preterm birth have been identified, mechanisms underlying this syndrome remain unclear, thereby limiting the implementation of interventions for prevention and management. Known triggers of preterm birth include conditions related to inflammatory and immunological pathways, as well as genetics and maternal history. Importantly, epigenetics, which is the study of heritable phenotypic changes that occur without alterations in the DNA sequence, may play a role in linking social and environmental risk factors for preterm birth. Epigenetic approaches to the study of preterm birth, including analyses of the effects of microRNAs, long non-coding RNAs, DNA methylation, and histone modification, have contributed to an improved understanding of the molecular bases of both term and preterm birth. Additionally, epigenetic modifications have been linked to factors already associated with preterm birth, including obesity and smoking. The prevention and management of preterm birth remains a challenge worldwide. Although epigenetic analysis provides valuable insights into the causes and risk factors associated with this syndrome, further studies are necessary to determine whether epigenetic approaches can be used routinely for the diagnosis, prevention, and management of preterm birth.
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Affiliation(s)
- Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
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Wu KX, Wang XT, Hu XL, Jiang XY, Zhuang JC, Xu YZ, Lin LR, Tong ML, Yang TC, Liu LL. LncRNA-ENST00000421645 Upregulates Kank1 to Inhibit IFN-γ Expression and Promote T Cell Apoptosis in Neurosyphilis. Front Microbiol 2021; 12:749171. [PMID: 34917045 PMCID: PMC8669649 DOI: 10.3389/fmicb.2021.749171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs are involved in many infectious diseases. Our previous studies showed that lncRNA-ENST00000421645 expression is increased in T lymphocytes of neurosyphilis patients compared to healthy controls. However, whether lncRNA-ENST00000421645 has biological functions remains unclear. The current study was undertaken to understand the mechanism of lncRNA-ENST00000421645 in T lymphocyte function in neurosyphilis patients. The lncRNA-ENST00000421645 pull-down assay showed that lncRNA-ENST00000421645 acted on the acetylase NAT10. The chromatin immunoprecipitation (ChIP)-PCR results showed that lncRNA-ENST00000421645 promoted the acetylation of histone H3K27 adjacent to the Kank1 promoter, thereby promoting Kank1 protein expression. Kank1 promotes 14-3-3 protein expression, inhibits NF-kB activation, inhibits IFN-γ secretion by T lymphocytes, and promotes T lymphocyte apoptosis. Taken together, our findings suggest a novel mechanism that LncRNA-ENST00000421645 upregulates Kank1 to inhibit IFN-γ expression and promote T cell apoptosis in neurosyphilis.
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Affiliation(s)
- Kai-Xuan Wu
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Xiao-Tong Wang
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Xin-Lin Hu
- Department of Dermatology, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Xiao-Yong Jiang
- Department of Dermatology, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Jing-Cong Zhuang
- Department of Neurology, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yan-Zhu Xu
- Department of Dermatology, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Li-Rong Lin
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Man-Li Tong
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Tian-Ci Yang
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Li-Li Liu
- Center of Clinical Laboratory, School of Medical, Zhongshan Hospital, Xiamen University, Xiamen, China
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45
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Park EG, Pyo SJ, Cui Y, Yoon SH, Nam JW. Tumor immune microenvironment lncRNAs. Brief Bioinform 2021; 23:6458113. [PMID: 34891154 PMCID: PMC8769899 DOI: 10.1093/bib/bbab504] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.
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Affiliation(s)
- Eun-Gyeong Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sung-Jin Pyo
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Youxi Cui
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sang-Ho Yoon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
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Meessen JMTA, Bär C, di Dona FM, Staszewsky LI, Di Giulio P, Di Tano G, Costa A, Leonardy J, Novelli D, Nicolis EB, Masson S, Pinet F, Thum T, Latini R. LIPCAR Is Increased in Chronic Symptomatic HF Patients. A Sub-Study of the GISSI-HF Trial. Clin Chem 2021; 67:1721-1731. [PMID: 34751777 DOI: 10.1093/clinchem/hvab197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND The long noncoding RNA LIPCAR (Long Intergenic noncoding RNA Predicting CARdiac remodeling) has emerged as a promising biomarker in cardiac disease and cardiac remodeling. To determine whether LIPCAR levels help for a molecular phenotyping of chronic heart failure (HF) patients, this study assessed the association of LIPCAR with severity of the disease and its progression, and with risk of death or hospitalization in HF patients. METHODS LIPCAR was measured in plasma of 967 HF patients with symptomatic heart failure participating in the Gruppo Italiano per lo Studio della Sopravvivenza nell'Insufficienza Cardiaca - Heart Failure (GISSI-HF) biohumoral sub-study. RESULTS Plasma levels of LIPCAR were significantly associated with functional impairment as assessed by the New York Heart Association (NYHA) class, kidney function as reflected by estimated glomerular filtration rate, and creatinine, hemoglobin and mitral insufficiency. In females, these associations were more marked as compared to males. LIPCAR plasma levels were significantly related to the two cardiac markers, N-terminal pro-B type natriuretic peptide and high-sensitivity cardiac troponin T, but not to inflammatory markers such as high sensitivity C-reactive protein and pentraxin-3, nor to patient reported outcomes such as depression and quality of life. HF patients with high LIPCAR levels univariately showed significantly higher incidence of cardiovascular hospitalizations but not of death; after adjusting for covariates, no significant effects of LIPCAR were found for cardiovascular hospitalizations. CONCLUSION The circulating long noncoding RNA LIPCAR was increased in HF patients with higher NYHA class, impaired kidney function, and lower hemoglobin, which are indicators of patients' overall state.
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Affiliation(s)
- Jennifer M T A Meessen
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Filippo M di Dona
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Lidia I Staszewsky
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Paola Di Giulio
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | | | - Alessia Costa
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Julia Leonardy
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Deborah Novelli
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Enrico B Nicolis
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Serge Masson
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
| | - Florence Pinet
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, Lille, France
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Roberto Latini
- Department of Cardiovascular Medicine, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
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Reichard J, Zimmer-Bensch G. The Epigenome in Neurodevelopmental Disorders. Front Neurosci 2021; 15:776809. [PMID: 34803599 PMCID: PMC8595945 DOI: 10.3389/fnins.2021.776809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Neurodevelopmental diseases (NDDs), such as autism spectrum disorders, epilepsy, and schizophrenia, are characterized by diverse facets of neurological and psychiatric symptoms, differing in etiology, onset and severity. Such symptoms include mental delay, cognitive and language impairments, or restrictions to adaptive and social behavior. Nevertheless, all have in common that critical milestones of brain development are disrupted, leading to functional deficits of the central nervous system and clinical manifestation in child- or adulthood. To approach how the different development-associated neuropathologies can occur and which risk factors or critical processes are involved in provoking higher susceptibility for such diseases, a detailed understanding of the mechanisms underlying proper brain formation is required. NDDs rely on deficits in neuronal identity, proportion or function, whereby a defective development of the cerebral cortex, the seat of higher cognitive functions, is implicated in numerous disorders. Such deficits can be provoked by genetic and environmental factors during corticogenesis. Thereby, epigenetic mechanisms can act as an interface between external stimuli and the genome, since they are known to be responsive to external stimuli also in cortical neurons. In line with that, DNA methylation, histone modifications/variants, ATP-dependent chromatin remodeling, as well as regulatory non-coding RNAs regulate diverse aspects of neuronal development, and alterations in epigenomic marks have been associated with NDDs of varying phenotypes. Here, we provide an overview of essential steps of mammalian corticogenesis, and discuss the role of epigenetic mechanisms assumed to contribute to pathophysiological aspects of NDDs, when being disrupted.
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Affiliation(s)
- Julia Reichard
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
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Horai Y, Nakamura H, Shimizu T, Nishihata S, Iwamoto N, Kuroki T, Okano S, Kawakami A. Increased Expression of the lncRNA NRON Along With NFATc1/PIM-1 in Labial Salivary Glands of Sjögren's Syndrome Patients. Appl Immunohistochem Mol Morphol 2021; 29:734-740. [PMID: 34261974 PMCID: PMC8579987 DOI: 10.1097/pai.0000000000000959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/10/2021] [Indexed: 11/30/2022]
Abstract
The aim of our study was to analyze the expressions of nuclear factor of activated T cells (NFAT)-related substances including long noncoding RNA NRON which participates in pathophysiology of Sjögren's syndrome (SS), and to assess the histologic findings in individuals with SS. In this study, the expressions of NRON, NFATc1, CD3/CD4, and proviral integration site for Moloney murine leukemia virus (PIM)-1 were examined by in situ hybridization, immunohistochemical analysis, and immunofluorescence in labial salivary glands (LSGs) obtained from 16 patients with SS and five controls. The microcell count method has been applied to calculate the NFATc1-positive area/infiltrating cell area in LSGs, and we compared those results to the infiltrating cell area, focus score, serum immunoglobulin G, and the European League Against Rheumatism Sjögren's Syndrome Disease Activity Index. The NRON expression in the nuclei of cell-infiltration lesions of the SS patients were prominent. The NFATc1 expression was strong in the cytoplasm of infiltrating mononuclear cells and weak in ducts of both SS and controls. In SS, the NFATc1-positive area/infiltrating cell area was positively correlated with the infiltrating cell area and focus score. CD3/CD4 was expressed in infiltrating mononuclear cells, and PIM-1 colocalized with NFATc1 in the cytoplasm. These results suggest NRON along with NFATc1/PIM-1 in SS LSGs might participate in SS pathophysiology.
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Affiliation(s)
- Yoshiro Horai
- Departments of Rheumatology
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Hideki Nakamura
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
- Department of Medicine, Division of Hematology and Rheumatology, Nihon University School of Medicine, Tokyo, Japan
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
- Clinical Research Center
| | - Shinya Nishihata
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Naoki Iwamoto
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
| | - Tamotsu Kuroki
- Surgery
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura
| | - Shinji Okano
- Department of Pathology, Nagasaki University Hospital, Nagasaki
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences
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Wang S, Wang Y, Zhang Z, Zhu C, Wang C, Yu F, Zhao E. Long Non-Coding RNA NRON promotes Tumor Proliferation by regulating ALKBH5 and Nanog in Gastric Cancer. J Cancer 2021; 12:6861-6872. [PMID: 34659574 PMCID: PMC8518016 DOI: 10.7150/jca.60737] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) act as tumor suppressors or oncogenes in tumor development and progression. In this study, we explored the expression and biological role of lncRNA NRON in gastric cancer (GC). We observed that lncNRON was upregulated in GC tissues and cell lines, and high lncNRON expression was associated with malignant features and poor prognosis in GC patients. LncNRON was found to promote the proliferation and tumorigenicity of GC cells. Mechanistically, lncNRON exerted its oncogenic functions by binding to the N6-methyladenosine eraser ALKHB5 and mediating Nanog mRNA decay. In conclusion, our results suggest that lncNRON serves as an oncogenic lncRNA in GC and thus may be a promising prognostic factor and potential therapeutic target for GC patients.
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Affiliation(s)
- Shuchang Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yangyang Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chaojie Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Fengrong Yu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Enhao Zhao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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50
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Sun L, Xu A, Li M, Xia X, Li P, Han R, Fei G, Zhou S, Wang R. Effect of Methylation Status of lncRNA-MALAT1 and MicroRNA-146a on Pulmonary Function and Expression Level of COX2 in Patients With Chronic Obstructive Pulmonary Disease. Front Cell Dev Biol 2021; 9:667624. [PMID: 34604205 PMCID: PMC8479795 DOI: 10.3389/fcell.2021.667624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/19/2021] [Indexed: 12/25/2022] Open
Abstract
This study aimed to investigate the role of methylation of MALAT1 and miR-146a in the pathogenesis of chronic obstructive pulmonary disease (COPD). COPD patients were grouped according to their methylation status of MALAT1 and miR-146a promoters, and we found that forced vital capacity, volume that has been exhaled at the end of the first second of forced expiration, and diffusion capacity for carbon monoxide were the highest in the MALAT1 HYPO + miR-146a HYPER group and lowest in the MALAT1 HYPER + miR-146a HYPO group, and COPD patients with hypermethylated MALAT1 showed lower expression of MALAT1 than that in the COPD patients with hypomethylated MALAT1. Meanwhile, miR-146a was the most significantly upregulated in the MALAT1 HYPER + miR-146a HYPO group and the most significantly downregulated in the MALAT1 HYPO + miR-146a HYPER group. Both prostaglandin E1 and cyclooxygenase 2 (COX2) expression were the highest in the MALAT1 HYPO + miR-146a HYPER group and the lowest in the MALAT1 HYPER + miR-146a HYPO group. In conclusion, our results established a MALAT1/miR-146a/COX2 signaling axis. The overexpression of MALAT1 could increase the expression of COX2 by inhibiting the expression of miR-146a, thus affecting the pulmonary function of COPD patients.
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Affiliation(s)
- Li Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Aiqun Xu
- Department of General Medicine, Hefei Second People's Hospital, Hefei, China
| | - Min Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xingyuan Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Pulin Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Rui Han
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Guanghe Fei
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Sijing Zhou
- Hefei Third Clinical College of Anhui Medical University, Hefei, China.,Hefei Prevention and Treatment Center for Occupational Diseases, Hefei, China
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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