1
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Zhang Q, Liu L. Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough. Cancer Lett 2024; 587:216691. [PMID: 38360139 DOI: 10.1016/j.canlet.2024.216691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Traditionally, non-coding RNAs (ncRNAs) are regarded as a class of RNA transcripts that lack encoding capability; however, advancements in technology have revealed that some ncRNAs contain small open reading frames (sORFs) that are capable of encoding micropeptides of approximately 150 amino acids in length. sORF-encoded micropeptides (SEPs) have emerged as intriguing entities in hepatocellular carcinoma (HCC) research, shedding light on this previously unexplored realm. Recent studies have highlighted the regulatory functions of SEPs in the occurrence and progression of HCC. Some SEPs exhibit inhibitory effects on HCC, but others facilitate its development. This discovery has revolutionized the landscape of HCC research and clinical management. Here, we introduce the concept and characteristics of SEPs, summarize their associations with HCC, and elucidate their carcinogenic mechanisms in HCC metabolism, signaling pathways, cell proliferation, and metastasis. In addition, we propose a step-by-step workflow for the investigation of HCC-associated SEPs. Lastly, we discuss the challenges and prospects of applying SEPs in the diagnosis and treatment of HCC. This review aims to facilitate the discovery, optimization, and clinical application of HCC-related SEPs, inspiring the development of early diagnostic, individualized, and precision therapeutic strategies for HCC.
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Affiliation(s)
- Qiangnu Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
| | - Liping Liu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China.
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2
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024; 15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Siyan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China.
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4
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Sadeghian I, Akbarpour M, Chafjiri FMA, Chafjiri PMA, Heidari R, Morowvat MH, Sadeghian R, Raee MJ, Negahdaripour M. Potential of oligonucleotide- and protein/peptide-based therapeutics in the management of toxicant/stressor-induced diseases. Naunyn Schmiedebergs Arch Pharmacol 2024; 397:1275-1310. [PMID: 37688622 DOI: 10.1007/s00210-023-02683-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
Exposure to toxicants/stressors has been linked to the development of many human diseases. They could affect various cellular components, such as DNA, proteins, lipids, and non-coding RNAs (ncRNA), thereby triggering various cellular pathways, particularly oxidative stress, inflammatory responses, and apoptosis, which can contribute to pathophysiological states. Accordingly, modulation of these pathways has been the focus of numerous investigations for managing related diseases. The involvement of various ncRNAs, such as small interfering RNA (siRNA), microRNAs (miRNA), and long non-coding RNAs (lncRNA), as well as various proteins and peptides in mediating these pathways, provides many target sites for pharmaceutical intervention. In this regard, various oligonucleotide- and protein/peptide-based therapies have been developed to treat toxicity-induced diseases, which have shown promising results in vitro and in vivo. This comprehensive review provides information about various aspects of toxicity-related diseases including their causing factors, main underlying mechanisms and intermediates, and their roles in pathophysiological states. Particularly, it highlights the principles and mechanisms of oligonucleotide- and protein/peptide-based therapies in the treatment of toxicity-related diseases. Furthermore, various issues of oligonucleotides and proteins/peptides for clinical usage and potential solutions are discussed.
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Affiliation(s)
- Issa Sadeghian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Incubator, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Akbarpour
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | | | - Reza Heidari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mohammad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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5
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Alharbi KS. Noncoding RNAs in hepatitis: Unraveling the apoptotic pathways. Pathol Res Pract 2024; 255:155170. [PMID: 38324964 DOI: 10.1016/j.prp.2024.155170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Hepatitis is a worldwide health issue that causes inflammation of the liver and is frequently brought on by viral infections, specifically those caused by the hepatitis B and C viruses. Although the pathophysiological causes of hepatitis are complex, recent research indicates that noncoding RNAs (ncRNAs) play a crucial role in regulating apoptosis, an essential process for maintaining liver homeostasis and advancing the illness. Noncoding RNAs have been linked to several biological processes, including apoptosis. These RNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). Distinct expression patterns characterising different stages of the disease have been discovered, indicating dysregulation of these non-coding RNAs in liver tissues infected with hepatitis. The complex interplay that exists between these noncoding RNAs and apoptotic effectors, including caspases and members of the Bcl-2 family, plays a role in the precarious equilibrium that regulates cell survival and death during hepatitis. The purpose of this review is to provide an overview of ncRNA-mediated apoptosis in hepatitis, as well as insights into possible therapeutic targets and diagnostic indicators.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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Khojali WMA, Khalifa NE, Alshammari F, Afsar S, Aboshouk NAM, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Syed RU, Nagaraju P. Pyroptosis-related non-coding RNAs emerging players in atherosclerosis pathology. Pathol Res Pract 2024; 255:155219. [PMID: 38401375 DOI: 10.1016/j.prp.2024.155219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Globally, atherosclerosis a persistent inflammatory condition of the artery walls continues to be the primary cause of cardiovascular illness and death. The ncRNAs are important regulators of important signalling pathways that affect pyroptosis and the inflammatory environment in atherosclerotic plaques. Comprehending the complex interaction between pyroptosis and non-coding RNAs (ncRNAs) offers fresh perspectives on putative therapeutic targets for ameliorating cardiovascular problems linked to atherosclerosis. The discovery of particular non-coding RNA signatures linked to the advancement of atherosclerosis could lead to the creation of novel biomarkers for risk assessment and customised treatment approaches. A thorough investigation of the regulatory networks regulated by these non-coding RNAs has been made possible by the combination of cutting-edge molecular methods and bioinformatics tools. Studying pyroptosis-related ncRNAs in detail appears to be a promising way to advance our understanding of disease pathophysiology and develop focused therapeutic methods as we work to unravel the complex molecular tapestry of atherosclerosis. This review explores the emerging significance of non-coding RNAs (ncRNAs) in the regulation of pyroptosis and their consequential impact on atherosclerosis pathology.
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Affiliation(s)
- Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman 14415, Republic of the Sudan
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11115, Republic of the Sudan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Amna Abakar Suleiman Khalifa
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia.
| | - Potnuri Nagaraju
- Department of Pharmaceutics, Mandesh Institute of Pharmaceutical Science and Research Center, Maharashtra, India
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Yaghoobi Z, Seyed Bagher Nazeri SS, Asadi A, Derafsh E, Talebi Taheri A, Tamtaji Z, Dadgostar E, Rahmati-Dehkordi F, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. Non-coding RNAs and Aquaporin 4: Their Role in the Pathogenesis of Neurological Disorders. Neurochem Res 2024; 49:583-596. [PMID: 38114727 DOI: 10.1007/s11064-023-04067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Neurological disorders are a major group of non-communicable diseases affecting quality of life. Non-Coding RNAs (ncRNAs) have an important role in the etiology of neurological disorders. In studies on the genesis of neurological diseases, aquaporin 4 (AQP4) expression and activity have both been linked to ncRNAs. The upregulation or downregulation of several ncRNAs leads to neurological disorder progression by targeting AQP4. The role of ncRNAs and AQP4 in neurological disorders is discussed in this review.
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Affiliation(s)
- Zahra Yaghoobi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | | | - Amir Asadi
- Psychiatry and Behavioral Sciences Research Center, School of Medicine, Addiction Institute, and Department of Psychiatry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ehsan Derafsh
- Windsor University School of Medicine, Cayon, St Kitts and Nevis
| | - Abdolkarim Talebi Taheri
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Tamtaji
- Student Research Committee, Kashan University of Medical Sciences, Kashan, I.R. of Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
| | - Fatemeh Rahmati-Dehkordi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. of Iran.
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| | - Fatemeh Nabavizadeh
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Jia L, Yang Y, Sun F, Tao H, Lu C, Yang JJ. Mitochondrial quality control in liver fibrosis: Epigenetic hallmarks and therapeutic strategies. Cell Signal 2024; 115:111035. [PMID: 38182067 DOI: 10.1016/j.cellsig.2024.111035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
BACKGROUND AND AIM Mitochondrial quality control (MQC) plays a significant role in the progression of liver fibrosis, with key processes such as mitochondrial fission, fusion, mitophagy and biogenesis maintaining mitochondrial homeostasis. To understand the molecular mechanisms underlying epigenetic regulation of mitochondrial quality control in liver fibrosis, with the aim of uncovering novel therapeutic targets for treating, mitigating, and potentially reversing liver fibrosis, in light of the most recent advances in this field. METHODS We searched PubMed, Web of Science, and Scopus for published manuscripts using terms "mitochondrial quality control" "mitochondrial fission" "mitochondrial fusion" "mitochondrial biogenesis" "mitophagy" "liver fibrosis" "epigenetic regulation" "DNA methylation" "RNA methylation" "histone modification" and "non-coding RNA". Manuscripts were collated, studied and carried forward for discussion where appropriate. RESULTS Mitochondrial fission, fusion, biogenesis, and mitophagy regulate the homeostasis of mitochondria, and the imbalance of mitochondrial homeostasis can induce liver fibrosis. Epigenetic regulation, including DNA methylation, RNA methylation, histone modifications, and non-coding RNAs, plays a significant role in regulating the processes of mitochondrial homeostasis. CONCLUSION Mitochondrial quality control and epigenetic mechanisms are intricately linked to the pathogenesis of liver fibrosis. Understanding these molecular interactions provides insight into potential therapeutic strategies. Further research is necessary to translate these findings into clinical applications, with a focus on developing epigenetic drugs to ameliorate liver fibrosis by modulating MQC and epigenetic pathways.
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Affiliation(s)
- Lin Jia
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- Department of General Surgery, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou 215153, China
| | - Feng Sun
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
| | - Chao Lu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; First Affiliated Hospital, Anhui University of Science & Technology, Huainan 232001, China.
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.
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10
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Shbeer AM. Mystery of COVID 19: Focusing on important ncRNAs and effective signaling pathways. Pathol Res Pract 2024; 255:155155. [PMID: 38354486 DOI: 10.1016/j.prp.2024.155155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
This article provides a thorough investigation of the essential role of non-coding RNAs (ncRNAs) in the context of COVID-19, emphasizing their impact on the complex molecular dynamics of the viral infection. By conducting a systematic review of existing literature, we identify key ncRNAs involved in different stages of the viral life cycle, modulation of host immune response, and disease progression. The importance of microRNAs, long non-coding RNAs, and other ncRNA types emerges as influential factors in shaping the interaction between the host and the virus. Additionally, the study delves into the effective signaling pathways linked to COVID-19 pathogenesis, uncovering intricate molecular cascades that govern viral entry, replication, and host cell response. This exploration encompasses established pathways such as IL-6/JAK/STAT signaling, highlighting their interplay within the context of COVID-19. By synthesizing this knowledge, our aim is not only to enhance our understanding of the molecular complexities of COVID-19 but also to reveal potential therapeutic targets. Through elucidating the interaction between ncRNAs and signaling pathways, our article seeks to contribute to ongoing efforts in developing targeted interventions against COVID-19, ultimately advancing our ability to address this global health crisis.
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Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
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11
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Xu S, Wang L, Zhao Y, Mo T, Wang B, Lin J, Yang H. Metabolism-regulating non-coding RNAs in breast cancer: roles, mechanisms and clinical applications. J Biomed Sci 2024; 31:25. [PMID: 38408962 PMCID: PMC10895768 DOI: 10.1186/s12929-024-01013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Breast cancer is one of the most common malignancies that pose a serious threat to women's health. Reprogramming of energy metabolism is a major feature of the malignant transformation of breast cancer. Compared to normal cells, tumor cells reprogram metabolic processes more efficiently, converting nutrient supplies into glucose, amino acid and lipid required for malignant proliferation and progression. Non-coding RNAs(ncRNAs) are a class of functional RNA molecules that are not translated into proteins but regulate the expression of target genes. NcRNAs have been demonstrated to be involved in various aspects of energy metabolism, including glycolysis, glutaminolysis, and fatty acid synthesis. This review focuses on the metabolic regulatory mechanisms and clinical applications of metabolism-regulating ncRNAs involved in breast cancer. We summarize the vital roles played by metabolism-regulating ncRNAs for endocrine therapy, targeted therapy, chemotherapy, immunotherapy, and radiotherapy resistance in breast cancer, as well as their potential as therapeutic targets and biomarkers. Difficulties and perspectives of current targeted metabolism and non-coding RNA therapeutic strategies are discussed.
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Affiliation(s)
- Shiliang Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Lingxia Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Tong Mo
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Bo Wang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Jun Lin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China.
| | - Huan Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China.
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12
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Tang C, Hu W. Non-coding RNA regulates the immune microenvironment in recurrent spontaneous abortion (RSA): new insights into immune mechanisms†. Biol Reprod 2024; 110:220-229. [PMID: 37956412 PMCID: PMC10873270 DOI: 10.1093/biolre/ioad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023] Open
Abstract
Recurrent spontaneous abortion (RSA) has various causes, including chromosomal abnormalities, prethrombotic state, and abnormal uterine anatomical factors. However, the pathogenesis of RSA is still unclear. Surprisingly, non-coding RNA can stably express at the maternal-fetal interface and regulate immune cells' proliferation, apoptosis, invasion, metastasis, and angiogenesis. Accumulating evidence suggests that the competing endogenous RNA (ceRNA) regulatory network between non-coding RNAs complicates RSA's pathological process and maybe a new starting point for exploring RSA. In this review, we mainly discuss the regulatory network and potential significance of non-coding RNA in the immune microenvironment of RSA patients. In addition, the cellular interactions of non-coding RNA transported through vesicles were introduced from aspects of trophoblast function and immune regulation. Finally, we analyze previous studies and further discuss that the stable expression of non-coding RNA may be used as a biomarker of some disease states and a prediction target of RSA.
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Affiliation(s)
- Cen Tang
- Obstetrics Department, Kunming Medical University Second Affiliated Hospital, Kunming, Yunnan, China
| | - Wanqin Hu
- Obstetrics Department, Kunming Medical University Second Affiliated Hospital, Kunming, Yunnan, China
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13
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Yilmaz Sukranli Z, Korkmaz Bayram K, Mehmetbeyoglu E, Doganyigit Z, Beyaz F, Sener EF, Taheri S, Ozkul Y, Rassoulzadegan M. Trans Species RNA Activity: Sperm RNA of the Father of an Autistic Child Programs Glial Cells and Behavioral Disorders in Mice. Biomolecules 2024; 14:201. [PMID: 38397438 PMCID: PMC10886764 DOI: 10.3390/biom14020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Recently, we described the alteration of six miRNAs in the serum of autistic children, their fathers, mothers, siblings, and in the sperm of autistic mouse models. Studies in model organisms suggest that noncoding RNAs participate in transcriptional modulation pathways. Using mice, approaches to alter the amount of RNA in fertilized eggs enable in vivo intervention at an early stage of development. Noncoding RNAs are very numerous in spermatozoa. Our study addresses a fundamental question: can the transfer of RNA content from sperm to eggs result in changes in phenotypic traits, such as autism? To explore this, we used sperm RNA from a normal father but with autistic children to create mouse models for autism. Here, we induced, in a single step by microinjecting sperm RNA into fertilized mouse eggs, a transcriptional alteration with the transformation in adults of glial cells into cells affected by astrogliosis and microgliosis developing deficiency disorders of the 'autism-like' type in mice born following these manipulations. Human sperm RNA alters gene expression in mice, and validates the possibility of non-Mendelian inheritance in autism.
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Affiliation(s)
- Zeynep Yilmaz Sukranli
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Keziban Korkmaz Bayram
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Yıldırım Beyazıt University, Ankara 06010, Turkey
| | - Ecmel Mehmetbeyoglu
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
| | - Zuleyha Doganyigit
- Histology and Embryology Department, Medical Faculty, Yozgat Bozok University, Yozgat 66700, Turkey
| | - Feyzullah Beyaz
- Histology and Embryology Department, Faculty of Veterinary, Erciyes University, Kayseri 38039, Turkey
| | - Elif Funda Sener
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Biology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Serpil Taheri
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Biology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Yusuf Ozkul
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | - Minoo Rassoulzadegan
- Betul-Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri 38039, Turkey
- The National Institute of Health and Medical Research (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Côte d’Azur, Inserm, 06000 Nice, France
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14
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Gu YY, Liu XS, Lan HY. Therapeutic potential for renal fibrosis by targeting Smad3-dependent noncoding RNAs. Mol Ther 2024; 32:313-324. [PMID: 38093516 PMCID: PMC10861968 DOI: 10.1016/j.ymthe.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024] Open
Abstract
Renal fibrosis is a characteristic hallmark of chronic kidney disease (CKD) that ultimately results in renal failure, leaving patients with few therapeutic options. TGF-β is a master regulator of renal fibrosis and mediates progressive renal fibrosis via both canonical and noncanonical signaling pathways. In the canonical Smad signaling, Smad3 is a key mediator in tissue fibrosis and mediates renal fibrosis via a number of noncoding RNAs (ncRNAs). In this regard, targeting Smad3-dependent ncRNAs may offer a specific therapy for renal fibrosis. This review highlights the significance and innovation of TGF-β/Smad3-associated ncRNAs as biomarkers and therapeutic targets in renal fibrogenesis. In addition, the underlying mechanisms of these ncRNAs and their future perspectives in the treatment of renal fibrosis are discussed.
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Affiliation(s)
- Yue-Yu Gu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Departments of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong; Department of Pharmacology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China; Departments of Nephrology and Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xu-Sheng Liu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Hui-Yao Lan
- Departments of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong; Departments of Nephrology and Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
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15
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Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proc Natl Acad Sci U S A 2024; 121:e2318008121. [PMID: 38306478 PMCID: PMC10861870 DOI: 10.1073/pnas.2318008121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/02/2023] [Indexed: 02/04/2024] Open
Abstract
Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "raiA motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.
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Affiliation(s)
- Lucas W. Soares
- Department of Microbial Pathogenesis, Yale University, New Haven, CT06536
| | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Chrishan M. Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
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16
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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17
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Zhu Y, Guan X, Geng X, Du Y, Jin S, Liu J. The signaling pathways involved in non-coding RNA regulation during osteogenic differentiation of periodontal tissue-derived cells in the field of periodontitis. J Periodontal Res 2024; 59:18-31. [PMID: 37961979 DOI: 10.1111/jre.13199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/07/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Periodontitis is a prevalent oral disease caused by chronic inflammation of the periodontal tissues surrounding the teeth, which can lead to bone loss, tooth loosening, and even tooth loss. This inflammation has a negative impact on the osteogenic differentiation capacity of periodontal tissue-derived cells. Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not encode proteins but can regulate various physiological processes. In this review, we summarized the critical signaling pathways that ncRNAs modulate in osteogenic differentiation of periodontal tissue-derived cells, such as the Wnt, BMP/Smad, NF-κB, and PI3-K/Akt/mTOR pathways. This comprehensive exploration of ncRNA-mediated modulation offers fresh and promising insights for prospective approaches in the management of periodontitis and the advancement of periodontal regeneration therapies.
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Affiliation(s)
- Yinci Zhu
- School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Xiaoyan Guan
- Department of Orthodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Xiaorui Geng
- Department of Otolaryngology. Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T, Institute of E.N.T Shenzhen, Shenzhen, China
| | - Yuanhang Du
- School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Suhan Jin
- Department of Orthodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Jianguo Liu
- School of Stomatology, Zunyi Medical University, Zunyi, China
- Special Key Laboratory of Oral Diseases Research, Higher Education Institution, Zunyi, China
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18
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Li S, Zhao Y, Tan S, Li Z. Non-coding RNAs and leaf senescence: Small molecules with important roles. Plant Physiol Biochem 2024; 207:108399. [PMID: 38277833 DOI: 10.1016/j.plaphy.2024.108399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.
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Affiliation(s)
- Shichun Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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19
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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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20
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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21
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Hao Q, Liu M, Daulatabad SV, Gaffari S, Song YJ, Srivastava R, Bhaskar S, Moitra A, Mangan H, Tseng E, Gilmore RB, Frier SM, Chen X, Wang C, Huang S, Chamberlain S, Jin H, Korlach J, McStay B, Sinha S, Janga SC, Prasanth SG, Prasanth KV. Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. eLife 2024; 13:e80684. [PMID: 38240312 PMCID: PMC10852677 DOI: 10.7554/elife.80684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Out of the several hundred copies of rRNA genes arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ~50% remain transcriptionally inactive. NOR-associated sequences and epigenetic modifications contribute to the differential expression of rRNAs. However, the mechanism(s) controlling the dosage of active versus inactive rRNA genes within each NOR in mammals is yet to be determined. We have discovered a family of ncRNAs, SNULs (Single NUcleolus Localized RNA), which form constrained sub-nucleolar territories on individual NORs and influence rRNA expression. Individual members of the SNULs monoallelically associate with specific NOR-containing chromosomes. SNULs share sequence similarity to pre-rRNA and localize in the sub-nucleolar compartment with pre-rRNA. Finally, SNULs control rRNA expression by influencing pre-rRNA sorting to the DFC compartment and pre-rRNA processing. Our study discovered a novel class of ncRNAs influencing rRNA expression by forming constrained nucleolar territories on individual NORs.
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Affiliation(s)
- Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Minxue Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Saba Gaffari
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Shivang Bhaskar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Anurupa Moitra
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Hazel Mangan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | | | - Rachel B Gilmore
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | | | - Xin Chen
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Chengliang Wang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern UniversityChicagoUnited States
| | - Stormy Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of MedicineFarmingtonUnited States
| | - Hong Jin
- Department of Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | | | - Brian McStay
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland GalwayGalwayIreland
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Department of Biomedical Engineering, Georgia TechAtlantaUnited States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUIIndianapolisUnited States
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Cancer Center at Illinois, University of Illinois at Urbana-ChampaignUrbanaUnited States
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22
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Grandchamp A, Czuppon P, Bornberg-Bauer E. Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Res 2024; 52:274-287. [PMID: 38000384 PMCID: PMC10783523 DOI: 10.1093/nar/gkad1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in genomic innovations. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate the de novo transcript turnover rate with an evolutionary model. We use DNA long reads and RNA short reads from seven geographically remote samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are gained on a short evolutionary time scale. Overall, each sampled individual contains around 2500 unspliced de novo transcripts, with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5× 10-5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rate estimates are essential to comprehend the process and timescale of de novo gene birth.
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Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
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23
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Cao X, Zhou X, Hou F, Huang YE, Yuan M, Long M, Chen S, Lei W, Zhu J, Chen J, Zhang T, Guo AY, Jiang W. ncRNADrug: a database for validated and predicted ncRNAs associated with drug resistance and targeted by drugs. Nucleic Acids Res 2024; 52:D1393-D1399. [PMID: 37953323 PMCID: PMC10767907 DOI: 10.1093/nar/gkad1042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/08/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
Drug resistance is a major barrier in cancer treatment and anticancer drug development. Growing evidence indicates that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play pivotal roles in cancer progression, therapy, and drug resistance. Furthermore, ncRNAs have been proven to be promising novel therapeutic targets for cancer treatment. Reversing dysregulated ncRNAs by drugs holds significant potential as an effective therapeutic strategy for overcoming drug resistance. Therefore, we developed ncRNADrug, an integrated and comprehensive resource that records manually curated and computationally predicted ncRNAs associated with drug resistance, ncRNAs targeted by drugs, as well as potential drug combinations for the treatment of resistant cancer. Currently, ncRNADrug collects 29 551 experimentally validated entries involving 9195 ncRNAs (2248 miRNAs, 4145 lncRNAs and 2802 circRNAs) associated with the drug resistance of 266 drugs, and 32 969 entries involving 10 480 ncRNAs (4338 miRNAs, 6087 lncRNAs and 55 circRNAs) targeted by 965 drugs. In addition, ncRNADrug also contains associations between ncRNAs and drugs predicted from ncRNA expression profiles by differential expression analysis. Altogether, ncRNADrug surpasses the existing related databases in both data volume and functionality. It will be a useful resource for drug development and cancer treatment. ncRNADrug is available at http://www.jianglab.cn/ncRNADrug.
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Affiliation(s)
- Xinyu Cao
- Fujian Key Laboratory of Precision Medicine for Cancer, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Xu Zhou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Fei Hou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Yu-e Huang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Mengqin Yuan
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Min Long
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Sina Chen
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Wanyue Lei
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Jicun Zhu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Jiahao Chen
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Tao Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - An-Yuan Guo
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Jiang
- Fujian Key Laboratory of Precision Medicine for Cancer, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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24
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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25
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Feng Y, Guo K, Jiang J, Lin S. Mesenchymal stem cell-derived exosomes as delivery vehicles for non-coding RNAs in lung diseases. Biomed Pharmacother 2024; 170:116008. [PMID: 38071800 DOI: 10.1016/j.biopha.2023.116008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
The burden of lung diseases is gradually increasing with an increase in the average human life expectancy. Therefore, it is necessary to identify effective methods to treat lung diseases and reduce their social burden. Currently, an increasing number of studies focus on the role of mesenchymal stem cell-derived exosomes (MSC-Exos) as a cell-free therapy in lung diseases. They show great potential for application to lung diseases as a more stable and safer option than traditional cell therapies. MSC-Exos are rich in various substances, including proteins, nucleic acids, and DNA. Delivery of Non-coding RNAs (ncRNAs) enables MSC-Exos to communicate with target cells. MSC-Exos significantly inhibit inflammatory factors, reduce oxidative stress, promote normal lung cell proliferation, and reduce apoptosis by delivering ncRNAs. Moreover, MSC-Exos carrying specific ncRNAs affect the proliferation, invasion, and migration of lung cancer cells, thereby playing a role in managing lung cancer. The detailed mechanisms of MSC-Exos in the clinical treatment of lung disease were explored by developing standardized culture, isolation, purification, and administration strategies. In summary, MSC-Exo-based delivery methods have important application prospects for treating lung diseases.
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Affiliation(s)
- Yuqian Feng
- Hangzhou School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Kaibo Guo
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, Zhejiang 310003, China
| | - Jing Jiang
- The Third Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Shengyou Lin
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, China.
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26
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Dong G, Yin X, Liang Y, Chen J, Wang J, Jiang F, Wang C, Guo W, Wang Y. A novel AluYb8 insertion-associated non-coding RNA, lncMUTYH, impairs mitochondrial function and dampens the M2-like polarization of macrophages. Free Radic Res 2024; 58:27-42. [PMID: 38145459 DOI: 10.1080/10715762.2023.2299333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023]
Abstract
An inverted AluYb8 insertion in the MUTYH intron 15 (AluYb8MUTYH variant) has been reported to be associated with reduced MUTYH1 expression and mitochondrial dysfunction with age. However, the underlying mechanism remains unknown. In this study, we identified a novel transcript associated with the AluYb8MUTYH variant, which revealed that this transcript is about 780 nucleotides in length with a poly-A tail, lacks protein-coding potential, referred to as lncMUTYH. The results from the reporter gene system confirmed that the lncMUTYH down-regulates MUTYH1 expression at the translational level. Site-directed mutagenesis on the 5'-terminal exon sequences of α-MUTYH and lncMUTYH constructs revealed that lncMUTYH can act as a trans-regulator that depends on the partial base pairing between its exonized AluYb8 sequence and the 5'UTR of α-MUTYH to impede MUTYH 1 expression. Furthermore, we have demonstrated a correlation between decreased mitochondrion-localized MUTYH1 caused by lncMUTYH and lowered levels of mitochondrial biological function indicators, such as mtDNA content, mitochondrial regulatory gene expression, oxygen consumption rate, ATP product, and mitochondrial respiratory capacity. Notably, we found that lncMUTYH inhibited the M2-like polarization of macrophages, and CD68/CD206-positive cell fractions were significantly lower in lncMUTYH ectopically expressing cells. The results confirmed that the AluYb8MUTYH-associated lncMUTYH, derived from an AluYb8 insertion mutation, acts as a trans-regulatory factor that inhibits the MUTYH1 protein expression, leading to a progressive mitochondrial dysfunction that may disrupt macrophage differentiation. In summary, lncMUTYH can contribute to AluYb8MUTYH-associated mitochondrial dysfunction with age and hamper the macrophage polarization process, potentially increasing the risk of developing age-related diseases.
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Affiliation(s)
- Gaochao Dong
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Xuewen Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
- Department of Pharmacy, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Jingwen Chen
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Chaochen Wang
- ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Zhejiang, China
| | - Wenwen Guo
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaping Wang
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
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27
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Li S, Qiu N, Ni A, Hamblin MH, Yin KJ. Role of regulatory non-coding RNAs in traumatic brain injury. Neurochem Int 2024; 172:105643. [PMID: 38007071 PMCID: PMC10872636 DOI: 10.1016/j.neuint.2023.105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
Traumatic brain injury (TBI) is a potentially fatal health event that cannot be predicted in advance. After TBI occurs, it can have enduring consequences within both familial and social spheres. Yet, despite extensive efforts to improve medical interventions and tailor healthcare services, TBI still remains a major contributor to global disability and mortality rates. The prompt and accurate diagnosis of TBI in clinical contexts, coupled with the implementation of effective therapeutic strategies, remains an arduous challenge. However, a deeper understanding of changes in gene expression and the underlying molecular regulatory processes may alleviate this pressing issue. In recent years, the study of regulatory non-coding RNAs (ncRNAs), a diverse class of RNA molecules with regulatory functions, has been a potential game changer in TBI research. Notably, the identification of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and other ncRNAs has revealed their potential as novel diagnostic biomarkers and therapeutic targets for TBI, owing to their ability to regulate the expression of numerous genes. In this review, we seek to provide a comprehensive overview of the functions of regulatory ncRNAs in TBI. We also summarize regulatory ncRNAs used for treatment in animal models, as well as miRNAs, lncRNAs, and circRNAs that served as biomarkers for TBI diagnosis and prognosis. Finally, we discuss future challenges and prospects in diagnosing and treating TBI patients in the clinical settings.
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Affiliation(s)
- Shun Li
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA
| | - Na Qiu
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA
| | - Andrew Ni
- Warren Alpert Medical School, Brown University, 222 Richmond Street, Providence, RI, 02903, USA
| | - Milton H Hamblin
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 1212 Webber Hall, 900 University Avenue, Riverside, CA, 92521, USA
| | - Ke-Jie Yin
- Department of Neurology, School of Medicine, University of Pittsburgh, S514 BST, 200 Lothrop Street, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15261, USA.
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28
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Mohan S, Hakami MA, Dailah HG, Khalid A, Najmi A, Zoghebi K, Halawi MA. The emerging role of noncoding RNAs in the EGFR signaling pathway in lung cancer. Pathol Res Pract 2024; 253:155016. [PMID: 38070221 DOI: 10.1016/j.prp.2023.155016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/24/2024]
Abstract
Noncoding ribonucleic acids (ncRNAs) have surfaced as essential orchestrators within the intricate system of neoplastic biology. Specifically, the epidermal growth factor receptor (EGFR) signalling cascade shows a central role in the etiological underpinnings of pulmonary carcinoma. Pulmonary malignancy persists as a preeminent contributor to worldwide mortality attributable to malignant neoplasms, with non-small cell lung carcinoma (NSCLC) emerging as the most predominant histopathological subcategory. EGFR is a key driver of NSCLC, and its dysregulation is frequently associated with tumorigenesis, metastasis, and resistance to therapy. Over the past decade, researchers have unveiled a complex network of ncRNAs, encompassing microRNAs, long noncoding RNAs, and circular RNAs, which intricately regulate EGFR signalling. MicroRNAs, as versatile post-transcriptional regulators, have been shown to target various components of the EGFR pathway, influencing cancer cell proliferation, migration, and apoptosis. Additionally, ncRNAs have emerged as critical modulators of EGFR signalling, with their potential to act as scaffolds, decoys, or guides for EGFR-related proteins. Circular RNAs, a relatively recent addition to the ncRNA family, have also been implicated in EGFR signalling regulation. The clinical implications of ncRNAs in EGFR-driven lung cancer are substantial. These molecules exhibit diagnostic potential as robust biomarkers for early cancer detection and personalized treatment. Furthermore, their predictive value extends to predicting disease progression and therapeutic outcomes. Targeting ncRNAs in the EGFR pathway represents a novel therapeutic approach with promising results in preclinical and early clinical studies. This review explores the increasing evidence supporting the significant role of ncRNAs in modulating EGFR signalling in lung cancer, shedding light on their potential diagnostic, prognostic, and therapeutic implications.
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Affiliation(s)
- Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; School of Health Sciences, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India; Center for Global health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India.
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Hamad Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | - Maryam A Halawi
- Department of Clinical Pharmacy, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
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29
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Subaiea GM, Syed RU, Afsar S, Alhaidan TMS, Alzammay SA, Alrashidi AA, Alrowaili SF, Alshelaly DA, Alenezi AMSRA. Non-coding RNAs (ncRNAs) and multidrug resistance in glioblastoma: Therapeutic challenges and opportunities. Pathol Res Pract 2024; 253:155022. [PMID: 38086292 DOI: 10.1016/j.prp.2023.155022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024]
Abstract
Non-coding RNAs (ncRNAs) have been recognized as pivotal regulators of transcriptional and post-transcriptional gene modulation, exerting a profound influence on a diverse array of biological and pathological cascades, including the intricate mechanisms underlying tumorigenesis and the acquisition of drug resistance in neoplastic cells. Glioblastoma (GBM), recognized as the foremost and most aggressive neoplasm originating in the brain, is distinguished by its formidable resistance to the cytotoxic effects of chemotherapeutic agents and ionizing radiation. Recent years have witnessed an escalating interest in comprehending the involvement of ncRNAs, particularly lncRNAs, in GBM chemoresistance. LncRNAs, a subclass of ncRNAs, have been demonstrated as dynamic modulators of gene expression at the epigenetic, transcriptional, and post-transcriptional levels. Disruption in the regulation of lncRNAs has been observed across various human malignancies, including GBM, and has been linked with developing multidrug resistance (MDR) against standard chemotherapeutic agents. The potential of targeting specific ncRNAs or their downstream effectors to surmount chemoresistance is also critically evaluated, specifically focusing on ongoing preclinical and clinical investigations exploring ncRNA-based therapeutic strategies for glioblastoma. Nonetheless, targeting lncRNAs for therapeutic objectives presents hurdles, including overcoming the blood-brain barrier and the brief lifespan of oligonucleotide RNA molecules. Understanding the complex relationship between ncRNAs and the chemoresistance characteristic in glioblastoma provides valuable insights into the fundamental molecular mechanisms. It opens the path for the progression of innovative and effective therapeutic approaches to counter the therapeutic challenges posed by this aggressive brain tumor. This comprehensive review highlights the complex functions of diverse ncRNAs, including miRNAs, circRNAs, and lncRNAs, in mediating glioblastoma's chemoresistance.
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Affiliation(s)
- Gehad Mohammed Subaiea
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia.
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | | | - Seham Ahmed Alzammay
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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30
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Shi Q, Chu Q, Zeng Y, Yuan X, Wang J, Zhang Y, Xue C, Li L. Non-coding RNA methylation modifications in hepatocellular carcinoma: interactions and potential implications. Cell Commun Signal 2023; 21:359. [PMID: 38111040 PMCID: PMC10726651 DOI: 10.1186/s12964-023-01357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/14/2023] [Indexed: 12/20/2023] Open
Abstract
RNA methylation modification plays a crucial role as an epigenetic regulator in the oncogenesis of hepatocellular carcinoma (HCC). Numerous studies have investigated the molecular mechanisms underlying the methylation of protein-coding RNAs in the progression of HCC. Beyond their impact on mRNA, methylation modifications also influence the biological functions of non-coding RNAs (ncRNAs). Here, we present an advanced and comprehensive overview of the interplay between methylation modifications and ncRNAs in HCC, with a specific focus on their potential implications for the tumor immune microenvironment. Moreover, we summarize promising therapeutic targets for HCC based on methylation-related proteins. In the future, a more profound investigation is warranted to elucidate the effects of ncRNA methylation modifications on HCC pathogenesis and devise valuable intervention strategies. Video Abstract.
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Affiliation(s)
- Qingmiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yifan Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Xin Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jinzhi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yaqi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250000, China.
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31
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Wang J, Wang W, Ma F, Qian H. A hidden translatome in tumors-the coding lncRNAs. Sci China Life Sci 2023; 66:2755-2772. [PMID: 37154857 DOI: 10.1007/s11427-022-2289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 05/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers. Through the application and development of ribosome analysis and sequencing technologies, advanced studies have discovered the translation of lncRNAs. Although lncRNAs were originally defined as noncoding RNAs, many lncRNAs actually contain small open reading frames that are translated into peptides. This opens a broad area for the functional investigation of lncRNAs. Here, we introduce prospective methods and databases for screening lncRNAs with functional polypeptides. We also summarize the specific lncRNA-encoded proteins and their molecular mechanisms that promote or inhibit cancerous. Importantly, the role of lncRNA-encoded peptides/proteins holds promise in cancer research, but some potential challenges remain unresolved. This review includes reports on lncRNA-encoded peptides or proteins in cancer, aiming to provide theoretical basis and related references to facilitate the discovery of more functional peptides encoded by lncRNA, and to further develop new anti-cancer therapeutic targets as well as clinical biomarkers of diagnosis and prognosis.
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Affiliation(s)
- Jinsong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenna Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Lin YH. The effects of intracellular and exosomal ncRNAs on cancer progression. Cancer Gene Ther 2023; 30:1587-1597. [PMID: 37884579 DOI: 10.1038/s41417-023-00679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Altered gene expression as well as mislocalization of a gene's encoded product (proteins or noncoding RNAs (ncRNAs)) can lead to disease and cancer formation. Multiple studies have indicated that exosomes and their contents act as cell-to-cell communicators and play a key role in cancer progression. Moreover, exosomes contain several functional molecules, including ncRNAs. NcRNAs function as master regulators to coordinate cell growth, cell motility and drug resistance. However, intracellular ncRNAs, which can be transferred to recipient cells via exosomes (exosomal ncRNAs), mediate common/distinct downstream molecules, signaling pathways and functions that are less emphasized concepts in cancer development research. In this study, by using exosomes as a model, we comprehensively discuss the current knowledge regarding (1) the functional role of ncRNAs, both their intracellular and exosomal forms, in cancer progression, (2) the possible mechanism of ncRNA incorporation into exosomes and (3) the therapeutic applications and limitations of exosomes based on current knowledge.
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Affiliation(s)
- Yang-Hsiang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Piao X, Ma L, Xu Q, Zhang X, Jin C. Noncoding RNAs: Versatile regulators of endothelial dysfunction. Life Sci 2023; 334:122246. [PMID: 37931743 DOI: 10.1016/j.lfs.2023.122246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Noncoding RNAs have recently emerged as versatile regulators of endothelial dysfunction in atherosclerosis, a chronic inflammatory disease characterized by the formation of plaques within the arterial walls. Through their ability to modulate gene expression, noncoding RNAs, including microRNAs, long noncoding RNAs, and circular RNAs, play crucial roles in various cellular processes involved in endothelial dysfunction (ECD), such as inflammation, pyroptosis, migration, proliferation, apoptosis, oxidative stress, and angiogenesis. This review provides an overview of the current understanding of the regulatory roles of noncoding RNAs in endothelial dysfunction during atherosclerosis. It highlights the specific noncoding RNAs that have been implicated in the pathogenesis of ECD, their target genes, and the mechanisms by which they contribute to ECD. Furthermore, we have reviewed the current therapeutics in atherosclerosis and explore their interaction with noncoding RNAs. Understanding the intricate regulatory network of noncoding RNAs in ECD may open up new opportunities for the development of novel therapeutic strategies to combat ECD.
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Affiliation(s)
- Xiong Piao
- Cardiovascular Surgery, Yanbian University Hospital, Yanji 133000, China.
| | - Lie Ma
- Cardiovascular Surgery, Yanbian University Hospital, Yanji 133000, China
| | - Qinqi Xu
- Cardiovascular Surgery, Yanbian University Hospital, Yanji 133000, China
| | - Xiaomin Zhang
- Cardiovascular Surgery, Yanbian University Hospital, Yanji 133000, China
| | - Chengzhu Jin
- Cardiovascular Surgery, Yanbian University Hospital, Yanji 133000, China
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Teragawa S, Wang L. ConF: A Deep Learning Model Based on BiLSTM, CNN, and Cross Multi-Head Attention Mechanism for Noncoding RNA Family Prediction. Biomolecules 2023; 13:1643. [PMID: 38002325 PMCID: PMC10669714 DOI: 10.3390/biom13111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
This paper presents ConF, a novel deep learning model designed for accurate and efficient prediction of noncoding RNA families. NcRNAs are essential functional RNA molecules involved in various cellular processes, including replication, transcription, and gene expression. Identifying ncRNA families is crucial for comprehensive RNA research, as ncRNAs within the same family often exhibit similar functionalities. Traditional experimental methods for identifying ncRNA families are time-consuming and labor-intensive. Computational approaches relying on annotated secondary structure data face limitations in handling complex structures like pseudoknots and have restricted applicability, resulting in suboptimal prediction performance. To overcome these challenges, ConF integrates mainstream techniques such as residual networks with dilated convolutions and cross multi-head attention mechanisms. By employing a combination of dual-layer convolutional networks and BiLSTM, ConF effectively captures intricate features embedded within RNA sequences. This feature extraction process leads to significantly improved prediction accuracy compared to existing methods. Experimental evaluations conducted using a single, publicly available dataset and applying ten-fold cross-validation demonstrate the superiority of ConF in terms of accuracy, sensitivity, and other performance metrics. Overall, ConF represents a promising solution for accurate and efficient ncRNA family prediction, addressing the limitations of traditional experimental and computational methods.
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Affiliation(s)
- Shoryu Teragawa
- School of Software, Dalian University of Technology, Dalian 116024, China;
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Zhang X, Sun S, Ren G, Liu W, Chen H. Advances in Intercellular Communication Mediated by Exosomal ncRNAs in Cardiovascular Disease. Int J Mol Sci 2023; 24:16197. [PMID: 38003385 PMCID: PMC10671547 DOI: 10.3390/ijms242216197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Cardiovascular diseases are a leading cause of worldwide mortality, and exosomes have recently gained attention as key mediators of intercellular communication in these diseases. Exosomes are double-layered lipid vesicles that can carry biomolecules such as miRNAs, lncRNAs, and circRNAs, and the content of exosomes is dependent on the cell they originated from. They can be involved in the pathophysiological processes of cardiovascular diseases and hold potential as diagnostic and monitoring tools. Exosomes mediate intercellular communication, stimulate or inhibit the activity of target cells, and affect myocardial hypertrophy, injury and infarction, ventricular remodeling, angiogenesis, and atherosclerosis. Exosomes can be released from various types of cells, including endothelial cells, smooth muscle cells, cardiomyocytes, fibroblasts, platelets, adipocytes, immune cells, and stem cells. In this review, we highlight the communication between different cell-derived exosomes and cardiovascular cells, with a focus on the roles of RNAs. This provides new insights for further exploring targeted therapies in the clinical management of cardiovascular diseases.
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Affiliation(s)
- Xiaoyan Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Shengjie Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Gang Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (S.S.); (G.R.)
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
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Morselli Gysi D, Barabási AL. Noncoding RNAs improve the predictive power of network medicine. Proc Natl Acad Sci U S A 2023; 120:e2301342120. [PMID: 37906646 PMCID: PMC10636370 DOI: 10.1073/pnas.2301342120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/09/2023] [Indexed: 11/02/2023] Open
Abstract
Network medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on a comprehensive map of protein-protein interactions (PPI), ignoring interactions mediated by noncoding RNAs (ncRNAs). Here, we systematically combine experimentally confirmed binding interactions mediated by ncRNA with PPI, constructing a comprehensive network of all physical interactions in the human cell. We find that the inclusion of ncRNA expands the number of genes in the interactome by 46% and the number of interactions by 107%, significantly enhancing our ability to identify disease modules. Indeed, we find that 132 diseases lacked a statistically significant disease module in the protein-based interactome but have a statistically significant disease module after inclusion of ncRNA-mediated interactions, making these diseases accessible to the tools of network medicine. We show that the inclusion of ncRNAs helps unveil disease-disease relationships that were not detectable before and expands our ability to predict comorbidity patterns between diseases. Taken together, we find that including noncoding interactions improves both the breath and the predictive accuracy of network medicine.
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Affiliation(s)
- Deisy Morselli Gysi
- Network Science Institute, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- US Department of Veteran Affairs, Boston, MA02130
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- US Department of Veteran Affairs, Boston, MA02130
- Department of Network and Data Science, Central European University, Budapest1051, Hungary
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37
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Waseem A, Khan AQ, Khan MA, Khan R, Uddin S, Boltze J, Raza SS. Unveiling the Therapeutic Potential of Non-Coding RNAs in Stroke-Induced Tissue Regeneration. Stem Cells 2023; 41:987-1005. [PMID: 37591309 DOI: 10.1093/stmcls/sxad062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023]
Abstract
Stroke is a major contributor to mortality and impairment on a global scale, with few effective treatments available. Aberrant expression of various non-coding RNAs (ncRNAs) has been identified after stroke onset, impacting neurogenesis, angiogenesis, apoptosis, and autophagy. The roles and mechanisms of ncRNAs hold great promise for future ischemic stroke treatments, as they could modify stroke impact and course on a well-controllable molecular level. Exploring the functions and underlying mechanisms of ncRNAs after stroke has the potential to unveil novel therapeutic targets for the treatment of stroke and may also pave the way toward novel and more precise diagnostic options for stroke and stroke outcomes. This review emphasizes the importance of ncRNAs in the treatment of stroke and their potential as therapeutic targets.
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Affiliation(s)
- Arshi Waseem
- Laboratory for Stem Cell & Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College Hospital, Era University, Sarfarazganj, Lucknow, India
| | - Abdul Quaiyoom Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Mohsin Ali Khan
- Metabolic Unit, Department of Biotechnology, Era's Lucknow Medical College Hospital, Era University, Sarfarazganj, Lucknow, India
| | - Rehan Khan
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, Punjab, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Johannes Boltze
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Department of Biotechnology, Era's Lucknow Medical College Hospital, Era University, Sarfarazganj, Lucknow, India
- Department of Stem Cell Biology and Regenerative Medicine, Era's Lucknow Medical College Hospital, Era University, Sarfarazganj, Lucknow, India
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Nguyen J, Le Q, Win PW, Hill KA, Singh SM, Castellani CA. Decoding mitochondrial-nuclear (epi)genome interactions: the emerging role of ncRNAs. Epigenomics 2023; 15:1121-1136. [PMID: 38031736 DOI: 10.2217/epi-2023-0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Bidirectional communication between the mitochondria and the nucleus is required for several physiological processes, and the nuclear epigenome is a key mediator of this relationship. ncRNAs are an emerging area of discussion for their roles in cellular function and regulation. In this review, we highlight the role of mitochondrial-encoded ncRNAs as mediators of communication between the mitochondria and the nuclear genome. We focus primarily on retrograde signaling, a process in which the mitochondrion relays ncRNAs to translate environmental stress signals to changes in nuclear gene expression, with implications on stress responses that may include disease(s). Other biological roles of mitochondrial-encoded ncRNAs, such as mitochondrial import of proteins and regulation of cell signaling, will also be discussed.
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Affiliation(s)
- Julia Nguyen
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Quinn Le
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Phyo W Win
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Kathleen A Hill
- Department of Biology, Western University, London, ON, N6A 3K7, Canada
| | - Shiva M Singh
- Department of Biology, Western University, London, ON, N6A 3K7, Canada
- Children's Health Research Institute, Lawson Research Institute, London, ON, N6C 2R5, Canada
| | - Christina A Castellani
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
- Department of Epidemiology & Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
- Children's Health Research Institute, Lawson Research Institute, London, ON, N6C 2R5, Canada
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Zhang M, Chen Y, Niu F, Luo X, Li J, Hu W. MicroRNA-30a-3p: a potential noncoding RNA target for the treatment of arteriosclerosis obliterans. Aging (Albany NY) 2023; 15:11875-11890. [PMID: 37899171 PMCID: PMC10683622 DOI: 10.18632/aging.205154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
An increasing number of studies have shown that noncoding RNAs are involved in cardiovascular diseases. Our study shows that the expression of microRNA-30a-3p (miR-30a-3p) in patients with arteriosclerosis obliterans (ASO) of the lower extremities is significantly decreased after endovascular treatment, but its role is unclear. This study aims to explore the role of microRNA-30a-3p in ASO and its related mechanisms. Immunofluorescence and in situ hybridization costaining indicated that microRNA-30a-3p mostly exists in vascular smooth muscle cells (VSMCs). Furthermore, after transfection into VSMCs, microRNA-30a-3p inhibited VSMC proliferation, migration and phenotype switching. In addition, luciferase reporter and western blot analyses indicated that ROCK2 (Rho-related spiral coil 2 containing protein kinase) is a microRNA-30a-3p target gene, and participates in the microRNA-30a-3p mediated cell inhibitory effect. At last, the rat carotid artery was infected by lentivirus after balloon injury, which increased microRNA-30a-3p levels and apparently suppressed the formation of neointima in vivo. Overall, exogenous introduction of microRNA-30a-3p, a noncoding RNA with unlimited potential, may be a new approach to treat ASO.
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Affiliation(s)
- Mao Zhang
- Department of Vascular Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Chen
- Department of Cardiology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fang Niu
- Department of Vascular Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaohui Luo
- Department of Gynaecology and Obstetrics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiangping Li
- Department of Oncological Radiotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Hu
- Department of Vascular Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
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Abstract
Maintenance of skeletal muscle quantity and quality is essential to ensure various vital functions of the body. Muscle homeostasis is regulated by multiple cytoskeletal proteins and myogenic transcriptional programs responding to endogenous and exogenous signals influencing cell structure and function. Since actin is an essential component in cytoskeleton dynamics, actin-binding proteins (ABPs) have been recognized as crucial players in skeletal muscle health and diseases. Hence, dysregulation of ABPs leads to muscle atrophy characterized by loss of mass, strength, quality, and capacity for regeneration. This comprehensive review summarizes the recent studies that have unveiled the role of ABPs in actin cytoskeletal dynamics, with a particular focus on skeletal myogenesis and diseases. This provides insight into the molecular mechanisms that regulate skeletal myogenesis via ABPs as well as research avenues to identify potential therapeutic targets. Moreover, this review explores the implications of non-coding RNAs (ncRNAs) targeting ABPs in skeletal myogenesis and disorders based on recent achievements in ncRNA research. The studies presented here will enhance our understanding of the functional significance of ABPs and mechanotransduction-derived myogenic regulatory mechanisms. Furthermore, revealing how ncRNAs regulate ABPs will allow diverse therapeutic approaches for skeletal muscle disorders to be developed.
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Affiliation(s)
- Mai Thi Nguyen
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea;
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Republic of Korea
| | - Kyuho Jeong
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Wan Lee
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
- Channelopathy Research Center, Dongguk University College of Medicine, 32 Dongguk-ro, Ilsan Dong-gu, Goyang 10326, Republic of Korea
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Contreras X, Depierre D, Akkawi C, Srbic M, Helsmoortel M, Nogaret M, LeHars M, Salifou K, Heurteau A, Cuvier O, Kiernan R. PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. Nat Commun 2023; 14:6745. [PMID: 37875486 PMCID: PMC10598014 DOI: 10.1038/s41467-023-42620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
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Affiliation(s)
- Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - David Depierre
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Charbel Akkawi
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marina Srbic
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Maguelone Nogaret
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Matthieu LeHars
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Alexandre Heurteau
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France.
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Marino M, D’Auria R, Mele E, Pastorino GMG, Di Pietro P, D’Angelo S, Della Rocca N, Operto FF, Vecchione C, Fasano S, Pierantoni R, Viggiano A, Meccariello R, Santoro A. The interplay between kisspeptin and endocannabinoid systems modulates male hypothalamic and gonadic control of reproduction in vivo. Front Endocrinol (Lausanne) 2023; 14:1269334. [PMID: 37900144 PMCID: PMC10602894 DOI: 10.3389/fendo.2023.1269334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/07/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Male reproduction is under the control of the hypothalamus-pituitary-gonadal (HPG) axis. The endocannabinoid system (ECS) and the kisspeptin system (KS) are two major signaling systems in the central and peripheral control of reproduction, but their possible interaction has been poorly investigated in mammals. This manuscript analyzes their possible reciprocal modulation in the control of the HPG axis. Materials and methods Adolescent male rats were treated with kisspeptin-10 (Kp10) and endocannabinoid anandamide (AEA), the latter alone or in combination with the type 1 cannabinoid receptor (CB1) antagonist rimonabant (SR141716A). The hypothalamic KS system and GnRH expression, circulating sex steroids and kisspeptin (Kiss1) levels, and intratesticular KS and ECS were evaluated by immunohistochemical and molecular methods. Non-coding RNAs (i.e., miR145-5p, miR-132-3p, let7a-5p, let7b-5p) were also considered. Results Circulating hormonal values were not significantly affected by Kp10 or AEA; in the hypothalamus, Kp10 significantly increased GnRH mRNA and aromatase Cyp19, Kiss1, and Kiss1 receptor (Kiss1R) proteins. By contrast, AEA treatment affected the hypothalamic KS at the protein levels, with opposite effects on the ligand and receptor, and SR141716A was capable of attenuating the AEA effects. Among the considered non-coding RNA, only the expression of miR145-5p was positively affected by AEA but not by Kp10 treatment. Localization of Kiss1+/Kiss1R+ neurons in the arcuate nucleus revealed an increase of Kiss1R-expressing neurons in Kp10- and AEA-treated animals associated with enlargement of the lateral ventricles in Kp10-treated animals. In the brain and testis, the selected non-coding RNA was differently modulated by Kp10 or AEA. Lastly, in the testis, AEA treatment affected the KS at the protein levels, whereas Kp10 affected the intragonadal levels of CB1 and FAAH, the main modulator of the AEA tone. Changes in pubertal transition-related miRNAs and the intratesticular distribution of Kiss1, Kiss1R, CB1, and CB2 following KP and AEA treatment corroborate the KS-ECS crosstalk also showing that the CB1 receptor is involved in this interplay. Conclusion For the first time in mammals, we report the modulation of the KS in both the hypothalamus and testis by AEA and revealed the KP-dependent modulation of CB1 and FAAH in the testis. KP involvement in the progression of spermatogenesis is also suggested.
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Affiliation(s)
- Marianna Marino
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | - Raffaella D’Auria
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | - Elena Mele
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, Napoli, Italy
| | - Grazia Maria Giovanna Pastorino
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
- Unità Operativa Complessa (U.O.C.) Neuropsichiatria Infantile, Azienda Ospedaliero Universitaria San Giovanni di Dio Ruggi d’Aragona, “Scuola Medica Salernitana”, Salerno, Italy
| | - Paola Di Pietro
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | - Stefania D’Angelo
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, Napoli, Italy
| | - Natalia Della Rocca
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | | | - Carmine Vecchione
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | - Silvia Fasano
- Dipartimento di Medicina Sperimentale, Università della Campania L. Vanvitelli, Napoli, Italy
| | - Riccardo Pierantoni
- Dipartimento di Medicina Sperimentale, Università della Campania L. Vanvitelli, Napoli, Italy
| | - Andrea Viggiano
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
| | - Rosaria Meccariello
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, Napoli, Italy
| | - Antonietta Santoro
- Dipartimento di Medicina, Chirurgia e Odontoiatria “Scuola Medica Salernitana” Università di Salerno, Baronissi, Italy
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Wu C, Xu Q, Li J, Qin C, Tulafu H, Liu W, Lu Q, Zheng W, Fu X. Regulation of cashmere fineness traits by noncoding RNA in Jiangnan cashmere goats. BMC Genomics 2023; 24:604. [PMID: 37821834 PMCID: PMC10566132 DOI: 10.1186/s12864-023-09531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/24/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Cashmere has long been used as the raw material for wool textiles. The diameter of the cashmere fibre determines its quality and economic value. However, the regulatory role of noncoding RNAs (ncRNAs) in cashmere fineness remains unclear, especially regarding the interaction between ncRNAs and coding RNAs. RESULTS Transcriptome sequencing was used to identify the expression profiles of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in the skin tissues of Jiangnan cashmere goats with different cashmere fineness levels. Integration analysis of ncRNA and coding RNA was performed in combination with previous research results. The results showed that 16,437 lncRNAs, 2234 circRNAs, and 1322 miRNAs were identified in 8 skin samples of cashmere goats. A total of 403 differentially expressed (DE) lncRNAs, 62 DE circRNAs and 30 DE miRNAs were identified in the skin tissues of the fine groups (Fe) and coarse groups (Ce). We predicted the target gene of DE lncRNA, the target gene of DE miRNA and the host gene of DE circRNA. Based on functional annotation and enrichment analysis of target genes, we found that DE lncRNAs could be involved in regulating the fineness traits of cashmere. The most potential lncRNAs were MSTRG.42054.1, MSTRG.18602.3, and MSTRG.2199.13. CONCLUSIONS The data from this study enriched the cashmere goat noncoding RNA database and helped to supplement the annotation of the goat genome. The results provided a new direction for the breeding of cashmere characters.
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Affiliation(s)
- Cuiling Wu
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Qin Xu
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Jianying Li
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Chongkai Qin
- Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, China
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Wenna Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Qingwei Lu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wenxin Zheng
- Xinjiang Uygur Autonomous Region Breeding sheep and wool Cashmere Quality Safety Supervision and Inspection Center, Institute of Animal Husbandry Quality Standard, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.
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Theisen B, Holtz A, Rajagopalan V. Noncoding RNAs and Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes in Cardiac Arrhythmic Brugada Syndrome. Cells 2023; 12:2398. [PMID: 37830612 PMCID: PMC10571919 DOI: 10.3390/cells12192398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023] Open
Abstract
Hundreds of thousands of people die each year as a result of sudden cardiac death, and many are due to heart rhythm disorders. One of the major causes of these arrhythmic events is Brugada syndrome, a cardiac channelopathy that results in abnormal cardiac conduction, severe life-threatening arrhythmias, and, on many occasions, death. This disorder has been associated with mutations and dysfunction of about two dozen genes; however, the majority of the patients do not have a definite cause for the diagnosis of Brugada Syndrome. The protein-coding genes represent only a very small fraction of the mammalian genome, and the majority of the noncoding regions of the genome are actively transcribed. Studies have shown that most of the loci associated with electrophysiological traits are located in noncoding regulatory regions and are expected to affect gene expression dosage and cardiac ion channel function. Noncoding RNAs serve an expanding number of regulatory and other functional roles within the cells, including but not limited to transcriptional, post-transcriptional, and epigenetic regulation. The major noncoding RNAs found in Brugada Syndrome include microRNAs; however, others such as long noncoding RNAs are also identified. They contribute to pathogenesis by interacting with ion channels and/or are detectable as clinical biomarkers. Stem cells have received significant attention in the recent past, and can be differentiated into many different cell types including those in the heart. In addition to contractile and relaxational properties, BrS-relevant electrophysiological phenotypes are also demonstrated in cardiomyocytes differentiated from stem cells induced from adult human cells. In this review, we discuss the current understanding of noncoding regions of the genome and their RNA biology in Brugada Syndrome. We also delve into the role of stem cells, especially human induced pluripotent stem cell-derived cardiac differentiated cells, in the investigation of Brugada syndrome in preclinical and clinical studies.
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Affiliation(s)
- Benjamin Theisen
- Department of Biomedical and Anatomical Sciences, New York Institute of Technology College of Osteopathic Medicine at Arkansas State University, Jonesboro, AR 72401, USA
| | - Austin Holtz
- Department of Biomedical and Anatomical Sciences, New York Institute of Technology College of Osteopathic Medicine at Arkansas State University, Jonesboro, AR 72401, USA
| | - Viswanathan Rajagopalan
- Department of Biomedical and Anatomical Sciences, New York Institute of Technology College of Osteopathic Medicine at Arkansas State University, Jonesboro, AR 72401, USA
- Arkansas Biosciences Institute, Jonesboro, AR 72401, USA
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45
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Wiegard JC, Damm K, Lechner M, Thölken C, Ngo S, Putzer H, Hartmann RK. Processing and decay of 6S-1 and 6S-2 RNAs in Bacillus subtilis. RNA 2023; 29:1481-1499. [PMID: 37369528 PMCID: PMC10578484 DOI: 10.1261/rna.079666.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
Noncoding 6S RNAs regulate transcription by binding to the active site of bacterial RNA polymerase holoenzymes. Processing and decay of 6S-1 and 6S-2 RNA were investigated in Bacillus subtilis by northern blot and RNA-seq analyses using different RNase knockout strains, as well as by in vitro processing assays. For both 6S RNA paralogs, we identified a key-but mechanistically different-role of RNase J1. RNase J1 catalyzes 5'-end maturation of 6S-1 RNA, yet relatively inefficient and possibly via the enzyme's "sliding endonuclease" activity. 5'-end maturation has no detectable effect on 6S-1 RNA function, but rather regulates its decay: The generated 5'-monophosphate on matured 6S-1 RNA propels endonucleolytic cleavage in its apical loop region. The major 6S-2 RNA degradation pathway is initiated by endonucleolytic cleavage in the 5'-central bubble to trigger 5'-to-3'-exoribonucleolytic degradation of the downstream fragment by RNase J1. The four 3'-exonucleases of B. subtilis-RNase R, PNPase, YhaM, and particularly RNase PH-are involved in 3'-end trimming of both 6S RNAs, degradation of 6S-1 RNA fragments, and decay of abortive transcripts (so-called product RNAs, ∼14 nt in length) synthesized on 6S-1 RNA during outgrowth from stationary phase. In the case of the growth-retarded RNase Y deletion strain, we were unable to infer a specific role of RNase Y in 6S RNA decay. Yet, a participation of RNase Y in 6S RNA decay still remains possible, as evidence for such a function may have been obscured by overlapping substrate specificities of RNase Y, RNase J1, and RNase J2.
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Affiliation(s)
- Jana Christin Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Katrin Damm
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Marcus Lechner
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Clemens Thölken
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Harald Putzer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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46
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Kansara S, Singh A, Badal AK, Rani R, Baligar P, Garg M, Pandey AK. The emerging regulatory roles of non-coding RNAs associated with glucose metabolism in breast cancer. Semin Cancer Biol 2023; 95:1-12. [PMID: 37364663 DOI: 10.1016/j.semcancer.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/20/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Altered energy metabolism is one of the hallmarks of tumorigenesis and essential for fulfilling the high demand for metabolic energy in a tumor through accelerating glycolysis and reprogramming the glycolysis metabolism through the Warburg effect. The dysregulated glucose metabolic pathways are coordinated not only by proteins coding genes but also by non-coding RNAs (ncRNAs) during the initiation and cancer progression. The ncRNAs are responsible for regulating numerous cellular processes under developmental and pathological conditions. Recent studies have shown that various ncRNAs such as microRNAs, circular RNAs, and long noncoding RNAs are extensively involved in rewriting glucose metabolism in human cancers. In this review, we demonstrated the role of ncRNAs in the progression of breast cancer with a focus on outlining the aberrant expression of glucose metabolic pathways. Moreover, we have discussed the existing and probable future applications of ncRNAs to regulate energy pathways along with their importance in the prognosis, diagnosis, and future therapeutics for human breast carcinoma.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Agrata Singh
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Abhishesh Kumar Badal
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Reshma Rani
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida 201313, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida 201313, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India; National Institute of Pharmaceutical Education and Research, Ahmedabad, Palaj, Gandhinagar 382355, Gujarat, India.
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47
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Szatkowska R, Furmanek E, Kierzek AM, Ludwig C, Adamczyk M. Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis. Int J Mol Sci 2023; 24:14763. [PMID: 37834211 PMCID: PMC10572830 DOI: 10.3390/ijms241914763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.
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Affiliation(s)
- Roza Szatkowska
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Emil Furmanek
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Andrzej M. Kierzek
- Certara UK Limited, Sheffield S1 2BJ, UK;
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
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48
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Limouse C, Smith OK, Jukam D, Fryer KA, Greenleaf WJ, Straight AF. Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions. Nat Commun 2023; 14:6073. [PMID: 37770513 PMCID: PMC10539311 DOI: 10.1038/s41467-023-41848-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
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Affiliation(s)
- Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Owen K Smith
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - David Jukam
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California, USA.
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Su Q, Long Y, Wang J, Gou D. CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation. Brief Bioinform 2023; 24:bbad374. [PMID: 37874949 DOI: 10.1093/bib/bbad374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/07/2023] [Accepted: 09/30/2023] [Indexed: 10/26/2023] Open
Abstract
Dynamic tuning of the poly(A) tail is a crucial mechanism for controlling translation and stability of eukaryotic mRNA. Achieving a comprehensive understanding of how this regulation occurs requires unbiased abundance quantification of poly(A)-tail transcripts and simple poly(A)-length measurement using high-throughput sequencing platforms. Current methods have limitations due to complicated setups and elaborate library preparation plans. To address this, we introduce central limit theorem (CLT)-managed RNA-seq (CLT-seq), a simple and straightforward homopolymer-sequencing method. In CLT-seq, an anchor-free oligo(dT) primer rapidly binds to and unbinds from anywhere along the poly(A) tail string, leading to position-directed reverse transcription with equal probability. The CLT mechanism enables the synthesized poly(T) lengths, which correspond to the templated segment of the poly(A) tail, to distribute normally. Based on a well-fitted pseudogaussian-derived poly(A)-poly(T) conversion model, the actual poly(A)-tail profile is reconstructed from the acquired poly(T)-length profile through matrix operations. CLT-seq follows a simple procedure without requiring RNA-related pre-treatment, enrichment or selection, and the CLT-shortened poly(T) stretches are more compatible with existing sequencing platforms. This proof-of-concept approach facilitates direct homopolymer base-calling and features unbiased RNA-seq. Therefore, CLT-seq provides unbiased, robust and cost-efficient transcriptome-wide poly(A)-tail profiling. We demonstrate that CLT-seq on the most common Illumina platform delivers reliable poly(A)-tail profiling at a transcriptome-wide scale in human cellular contexts. We find that the poly(A)-tail-tuned ncRNA regulation undergoes a dynamic, complex process similar to mRNA regulation. Overall, CLT-seq offers a simplified, effective and economical approach to investigate poly(A)-tail regulation, with potential implications for understanding gene expression and identifying therapeutic targets.
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Affiliation(s)
- Qiang Su
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China
| | - Yi Long
- The School of Medicine, Life and Health Sciences (MED | LHS), Chinese University of Hong Kong, Shenzhen, No. 2001 Longxiang Blvd., Longgang District, Shenzhen 518172, Guangdong, China
| | - Jun Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China
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50
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Shan C, Liang Y, Wang K, Li P. Noncoding RNAs in cancer ferroptosis: From biology to clinical opportunity. Biomed Pharmacother 2023; 165:115053. [PMID: 37379641 DOI: 10.1016/j.biopha.2023.115053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Ferroptosis is a recently discovered pattern of programmed cell death that is nonapoptotic and irondependent. It is involved in lipid peroxidation dependent on reactive oxygen species. Ferroptosis has been verified to play a crucial regulatory role in a variety of pathological courses of disease, in particularly cancer. Emerging research has highlighted the potential of ferroptosis in tumorigenesis, cancer development and resistance to chemotherapy. However, the regulatory mechanism of ferroptosis remains unclear, which limits the application of ferroptosis in cancer treatment. Noncoding RNAs (ncRNAs) are noncoding transcripts that regulate gene expression in various ways to affect the malignant phenotypes of cancer cells. At present, the biological function and underlying regulatory mechanism of ncRNAs in cancer ferroptosis have been partially elucidated. Herein, we summarize the current knowledge of the central regulatory network of ferroptosis, with a focus on the regulatory functions of ncRNAs in cancer ferroptosis. The clinical application and prospects of ferroptosis-related ncRNAs in cancer diagnosis, prognosis and anticancer therapies are also discussed. Elucidating the function and mechanism of ncRNAs in ferroptosis, along with assessing the clinical significance of ferroptosis-related ncRNAs, provides new perspectives for understanding cancer biology and treatment approaches, which may benefit numerous cancer patients in the future.
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Affiliation(s)
- Chan Shan
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Yan Liang
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Peifeng Li
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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