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Bu L, Lu L, Laidemitt MR, Zhang SM, Mutuku M, Mkoji G, Steinauer M, Loker ES. A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni. PLoS Negl Trop Dis 2023; 17:e0011208. [PMID: 36961841 PMCID: PMC10075465 DOI: 10.1371/journal.pntd.0011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/05/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Biomphalaria pfeifferi is the world's most widely distributed and commonly implicated vector snail species for the causative agent of human intestinal schistosomiasis, Schistosoma mansoni. In efforts to control S. mansoni transmission, chemotherapy alone has proven insufficient. New approaches to snail control offer a way forward, and possible genetic manipulations of snail vectors will require new tools. Towards this end, we here offer a diverse set of genomic resources for the important African schistosome vector, B. pfeifferi. METHODOLOGY/PRINCIPAL FINDINGS Based largely on PacBio High-Fidelity long reads, we report a genome assembly size of 772 Mb for B. pfeifferi (Kenya), smaller in size than known genomes of other planorbid schistosome vectors. In a total of 505 scaffolds (N50 = 3.2Mb), 430 were assigned to 18 large linkage groups inferred to represent the 18 known chromosomes, based on whole genome comparisons with Biomphalaria glabrata. The annotated B. pfeifferi genome reveals a divergence time of 3.01 million years with B. glabrata, a South American species believed to be similar to the progenitors of B. pfeifferi which undertook a trans-Atlantic colonization < five million years ago. CONCLUSIONS/SIGNIFICANCE The genome for this preferentially self-crossing species is less heterozygous than related species known to be preferential out-crossers; its smaller genome relative to congeners may similarly reflect its preference for selfing. Expansions of gene families with immune relevance are noted, including the FReD gene family which is far more similar in its composition to B. glabrata than to Bulinus truncatus, a vector for Schistosoma haematobium. Provision of this annotated genome will help better understand the dependencies of trematodes on snails, enable broader comparative insights regarding factors contributing to susceptibility/ resistance of snails to schistosome infections, and provide an invaluable resource with respect to identifying and manipulating snail genes as potential targets for more specific snail control programs.
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Affiliation(s)
- Lijing Bu
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Lijun Lu
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Martina R Laidemitt
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Si-Ming Zhang
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Martin Mutuku
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gerald Mkoji
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Michelle Steinauer
- College of Osteopathic Medicine of the Pacific-Northwest, Western University of Health Sciences, Lebanon, Oregon, United States of America
| | - Eric S Loker
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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152
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Bai Y, Ren H, Bian L, Zhou Y, Wang X, Xiong Z, Liu Z, Han B, Yao H. Regulation of Glial Function by Noncoding RNA in Central Nervous System Disease. Neurosci Bull 2023; 39:440-452. [PMID: 36161582 PMCID: PMC10043107 DOI: 10.1007/s12264-022-00950-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a class of functional RNAs that play critical roles in different diseases. NcRNAs include microRNAs, long ncRNAs, and circular RNAs. They are highly expressed in the brain and are involved in the regulation of physiological and pathophysiological processes of central nervous system (CNS) diseases. Mounting evidence indicates that ncRNAs play key roles in CNS diseases. Further elucidating the mechanisms of ncRNA underlying the process of regulating glial function that may lead to the identification of novel therapeutic targets for CNS diseases.
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Affiliation(s)
- Ying Bai
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Hui Ren
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Liang Bian
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - You Zhou
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xinping Wang
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Zhongli Xiong
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Ziqi Liu
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Bing Han
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Honghong Yao
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210009, China.
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153
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Crosstalk between Oxidative Stress and Aging in Neurodegeneration Disorders. Cells 2023; 12:cells12050753. [PMID: 36899889 PMCID: PMC10001353 DOI: 10.3390/cells12050753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
The world population is aging rapidly, and increasing lifespan exacerbates the burden of age-related health issues. On the other hand, premature aging has begun to be a problem, with increasing numbers of younger people suffering aging-related symptoms. Advanced aging is caused by a combination of factors: lifestyle, diet, external and internal factors, as well as oxidative stress (OS). Although OS is the most researched aging factor, it is also the least understood. OS is important not only in relation to aging but also due to its strong impact on neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Parkinson's disease (PD). In this review, we will discuss the aging process in relation to OS, the function of OS in neurodegenerative disorders, and prospective therapeutics capable of relieving neurodegenerative symptoms associated with the pro-oxidative condition.
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154
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de Klerk JA, Beulens JWJ, Mei H, Bijkerk R, van Zonneveld AJ, Koivula RW, Elders PJM, 't Hart LM, Slieker RC. Altered blood gene expression in the obesity-related type 2 diabetes cluster may be causally involved in lipid metabolism: a Mendelian randomisation study. Diabetologia 2023; 66:1057-1070. [PMID: 36826505 PMCID: PMC10163084 DOI: 10.1007/s00125-023-05886-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
AIMS/HYPOTHESIS The aim of this study was to identify differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in whole blood of people with type 2 diabetes across five different clusters: severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD), mild diabetes (MD) and mild diabetes with high HDL-cholesterol (MDH). This was to increase our understanding of different molecular mechanisms underlying the five putative clusters of type 2 diabetes. METHODS Participants in the Hoorn Diabetes Care System (DCS) cohort were clustered based on age, BMI, HbA1c, C-peptide and HDL-cholesterol. Whole blood RNA-seq was used to identify differentially expressed lncRNAs and mRNAs in a cluster compared with all others. Differentially expressed genes were validated in the Innovative Medicines Initiative DIabetes REsearCh on patient straTification (IMI DIRECT) study. Expression quantitative trait loci (eQTLs) for differentially expressed RNAs were obtained from a publicly available dataset. To estimate the causal effects of RNAs on traits, a two-sample Mendelian randomisation analysis was performed using public genome-wide association study (GWAS) data. RESULTS Eleven lncRNAs and 175 mRNAs were differentially expressed in the MOD cluster, the lncRNA AL354696.2 was upregulated in the SIDD cluster and GPR15 mRNA was downregulated in the MDH cluster. mRNAs and lncRNAs that were differentially expressed in the MOD cluster were correlated among each other. Six lncRNAs and 120 mRNAs validated in the IMI DIRECT study. Using two-sample Mendelian randomisation, we found 52 mRNAs to have a causal effect on anthropometric traits (n=23) and lipid metabolism traits (n=10). GPR146 showed a causal effect on plasma HDL-cholesterol levels (p = 2×10-15), without evidence for reverse causality. CONCLUSIONS/INTERPRETATION Multiple lncRNAs and mRNAs were found to be differentially expressed among clusters and particularly in the MOD cluster. mRNAs in the MOD cluster showed a possible causal effect on anthropometric traits, lipid metabolism traits and blood cell fractions. Together, our results show that individuals in the MOD cluster show aberrant RNA expression of genes that have a suggested causal role on multiple diabetes-relevant traits.
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Affiliation(s)
- Juliette A de Klerk
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Joline W J Beulens
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Robert W Koivula
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Malmö, Sweden
| | - Petra J M Elders
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Leen M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands.
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands.
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155
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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156
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Chen MJ, Gatignol A, Scarborough RJ. The discovery and development of RNA-based therapies for treatment of HIV-1 infection. Expert Opin Drug Discov 2023; 18:163-179. [PMID: 36004505 DOI: 10.1080/17460441.2022.2117296] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Long-term control of HIV-1 infection can potentially be achieved using autologous stem cell transplants with gene-modified cells. Non-coding RNAs represent a diverse class of therapeutic agents including ribozymes, RNA aptamers and decoys, small interfering RNAs, short hairpin RNAs, and U1 interference RNAs that can be designed to inhibit HIV-1 replication. They have been engineered for delivery as drugs to complement current HIV-1 therapies and as gene therapies for a potential HIV-1 functional cure. AREAS COVERED This review surveys the past three decades of development of these RNA technologies with a focus on their efficacy and safety for treating HIV-1 infections. We describe the mechanisms of each RNA-based agent, targets they have been developed against, efforts to enhance their stability and efficacy, and we evaluate their performance in past and ongoing preclinical and clinical trials. EXPERT OPINION RNA-based technologies are among the top candidates for gene therapies where they can be stably expressed for long-term suppression of HIV-1. Advances in both gene and drug delivery strategies and improvements to non-coding RNA stability and antiviral properties will cooperatively drive forward progress in improving drug therapy and engineering HIV-1 resistant cells.
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Affiliation(s)
- Michelle J Chen
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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157
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Bernardo VS, Torres FF, da Silva DGH. FoxO3 and oxidative stress: a multifaceted role in cellular adaptation. J Mol Med (Berl) 2023; 101:83-99. [PMID: 36598531 DOI: 10.1007/s00109-022-02281-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
Abstract
Oxidative stress is a major cause of morbidity and mortality in human health and disease. In this review, we focus on the Forkhead Box (Fox) subclass O3 (FoxO3), an extensively studied transcription factor that plays a pleiotropic role in a wide range of physiological and pathological processes by regulating multiple gene regulatory networks involved in the modulation of numerous aspects of cellular metabolism, including fuel metabolism, cell death, and stress resistance. This review will also focus on regulatory mechanisms of FoxO3 expression and activity, such as crucial post-translational modifications and non-coding RNAs. Moreover, this work discusses and evidences some pathways to how this transcription factor and reactive oxygen species regulate each other, which may lead to the pathogenesis of various types of diseases. Therefore, in addition to being a promising therapeutic target, the FoxO3-regulated signaling pathways can also be used as reliable diagnostic and prognostic biomarkers and indicators for drug responsiveness.
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Affiliation(s)
| | | | - Danilo Grünig Humberto da Silva
- Department of Biology, Universidade Estadual Paulista (UNESP), São Paulo, Brazil.
- Campus de Três Lagoas, Universidade Federal de Mato Grosso Do Sul (CPTL/UFMS), Avenida Ranulpho Marques Leal, 3484, Três Lagoas, Mato Grosso Do Sul, Distrito Industrial-Post code 79613-000, Brazil.
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158
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Mozammel N, Amini M, Baradaran B, Mahdavi SZB, Hosseini SS, Mokhtarzadeh A. The function of miR-145 in colorectal cancer progression; an updated review on related signaling pathways. Pathol Res Pract 2023; 242:154290. [PMID: 36621158 DOI: 10.1016/j.prp.2022.154290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNA) are a broad class of small, highly conserved non-coding RNAs that largely influence gene expression after transcription through binding to various target mRNAs. miRNAs are frequently dysregulated in a wide array of human cancers, possessing great value as diagnostic and therapeutic targets. miR-145, as promising tumor suppressor miRNA, also exhibits deregulated expression levels in human malignancies and participates in various processes, including cell proliferation, apoptosis, migration and differentiation. In particular, miR-145 has been shown to be downregulated in colorectal cancer (CRC), which in turn leads to cell growth, invasion, metastasis and drug resistance. Furthermore, miR-145 is involved in the regulation of multiple tumor specific signaling pathways, such as KRAS and P53 signaling by targeting various genes through colorectal tumorigenesis. Therefore, considering its diagnostic and therapeutic potential, it was aimed to present the recent finding focusing on miR-145 functions to better understand its involvement in CRC incidence and progression through interplay with various signaling pathways. This study is based on articles indexed in PubMed and Google scholar until 2021.
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Affiliation(s)
- Nazila Mozammel
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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159
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Peña-Flores JA, Enríquez-Espinoza D, Muela-Campos D, Álvarez-Ramírez A, Sáenz A, Barraza-Gómez AA, Bravo K, Estrada-Macías ME, González-Alvarado K. Functional Relevance of the Long Intergenic Non-Coding RNA Regulator of Reprogramming (Linc-ROR) in Cancer Proliferation, Metastasis, and Drug Resistance. Noncoding RNA 2023; 9:ncrna9010012. [PMID: 36827545 PMCID: PMC9965135 DOI: 10.3390/ncrna9010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Cancer is responsible for more than 10 million deaths every year. Metastasis and drug resistance lead to a poor survival rate and are a major therapeutic challenge. Substantial evidence demonstrates that an increasing number of long non-coding RNAs are dysregulated in cancer, including the long intergenic non-coding RNA, regulator of reprogramming (linc-ROR), which mostly exerts its role as an onco-lncRNA acting as a competing endogenous RNA that sequesters micro RNAs. Although the properties of linc-ROR in relation to some cancers have been reviewed in the past, active research appends evidence constantly to a better comprehension of the role of linc-ROR in different stages of cancer. Moreover, the molecular details and some recent papers have been omitted or partially reported, thus the importance of this review aimed to contribute to the up-to-date understanding of linc-ROR and its implication in cancer tumorigenesis, progression, metastasis, and chemoresistance. As the involvement of linc-ROR in cancer is elucidated, an improvement in diagnostic and prognostic tools could promote and advance in targeted and specific therapies in precision oncology.
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160
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Yu D, Xin L, Qing X, Hao Z, Yong W, Jiangjiang Z, Yaqiu L. Key circRNAs from goat: discovery, integrated regulatory network and their putative roles in the differentiation of intramuscular adipocytes. BMC Genomics 2023; 24:51. [PMID: 36707755 PMCID: PMC9883971 DOI: 10.1186/s12864-023-09141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The procession of preadipocytes differentiation into mature adipocytes involves multiple cellular and signal transduction pathways. Recently. a seirces of noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) were proved to play important roles in regulating differentiation of adipocytes. RESULT In this study, we aimed to identificate the potential circRNAs in the early and late stages of goat intramuscular adipocytes differentiation. Using bioinformatics methods to predict their biological functions and map the circRNA-miRNA interaction network. Over 104 million clean reads in goat intramuscular preadipocytes and adipocytes were mapped, of which16 circRNAs were differentially expressed (DE-circRNAs). Furthermore, we used real-time fluorescent quantitative PCR (qRT-PCR) technology to randomly detect the expression levels of 8 circRNAs among the DE-circRNAs, and our result verifies the accuracy of the RNA-seq data. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the DE-circRNAs, two circRNAs, circ_0005870 and circ_0000946, were found in Focal adhesion and PI3K-Akt signaling pathway. Then we draw the circRNA-miRNA interaction network and obtained the miRNAs that possibly interact with circ_0005870 and circ_0000946. Using TargetScan, miRTarBase and miR-TCDS online databases, we further obtained the mRNAs that may interact with the miRNAs, and generated the final circRNA-miRNA-mRNA interaction network. Combined with the following GO (Gene Ontology) and KEGG enrichment analysis, we obtained 5 key mRNAs related to adipocyte differentiation in our interaction network, which are FOXO3(forkhead box O3), PPP2CA (protein phosphatase 2 catalytic subunit alpha), EEIF4E (eukaryotic translation initiation factor 4), CDK6 (cyclin dependent kinase 6) and ACVR1 (activin A receptor type 1). CONCLUSIONS By using Illumina HiSeq and online databases, we generated the final circRNA-miRNA-mRNA interaction network that have valuable functions in adipocyte differentiation. Our work serves as a valuable genomic resource for in-depth exploration of the molecular mechanism of ncRNAs interaction network regulating adipocyte differentiation.
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Affiliation(s)
- Du Yu
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Li Xin
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Xu Qing
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Zhang Hao
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Wang Yong
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Zhu Jiangjiang
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Lin Yaqiu
- grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XKey Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China ,grid.412723.10000 0004 0604 889XCollege of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Liu W, An S, Cheng P, Zhang K, Gong M, Zhang Z, Zhang R. Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks. Parasit Vectors 2023; 16:33. [PMID: 36703236 PMCID: PMC9878986 DOI: 10.1186/s13071-022-05648-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/29/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The Asian tiger mosquito, Aedes albopictus, is one of the most invasive species and a vector of numerous arboviruses. The deleterious effects of long-term and inappropriate use of chemical pesticides have stimulated the exploration of new, environmentally friendly control strategies. Non-coding RNAs (ncRNAs) have been proven to participate in almost all biological processes of insects. METHODS In this study, circular RNAs (circRNAs) and microRNAs (miRNAs) covering five developmental stages [egg, early larvae, late larvae, pupae, adult (female and male)] of A. albopictus were obtained using whole-transcriptome sequencing technology. Combined with long non-coding RNAs (lncRNAs) from previous research, circRNA/lncRNA‒miRNA‒mitochondrial RNA (mRNA) networks were constructed. RESULTS A total of 1434 circRNAs and 208 miRNAs were identified. More differentially expressed circRNAs (DE circRNAs) and miRNAs (DE miRNAs) were found in the egg versus early larvae comparison group. Functional enrichment analysis demonstrated that most of the circRNA/lncRNA‒miRNA‒mRNA networks were involved in chitin metabolism. Hub genes of each circRNA/lncRNA‒miRNA‒mRNA network were screened out, which can be used as novel targets to disturb the molting process of A. albopictus. CONCLUSIONS Regulatory relationships obtained from competing endogenous RNA (ceRNA) networks provide more information to manipulate the metamorphosis process and are helpful for developing effective and sustainable methods to control mosquitoes.
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Affiliation(s)
- Wenjuan Liu
- grid.410587.fSchool of Clinical and Basic Medical Sciences, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China
| | - Sha An
- grid.410587.fSchool of Clinical and Basic Medical Sciences, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China
| | - Peng Cheng
- grid.410638.80000 0000 8910 6733Shandong Institute of Parasitic Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Jining, 272033 China
| | - Kexin Zhang
- grid.410587.fSchool of Clinical and Basic Medical Sciences, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China
| | - Maoqing Gong
- grid.410638.80000 0000 8910 6733Shandong Institute of Parasitic Diseases, Shandong First Medical University (Shandong Academy of Medical Sciences), Jining, 272033 China
| | - Zhong Zhang
- grid.410587.fSchool of Clinical and Basic Medical Sciences, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China ,grid.410587.fSchool of Laboratory Animal (Shandong Laboratory Animal Center), Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China
| | - Ruiling Zhang
- grid.410587.fSchool of Clinical and Basic Medical Sciences, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China ,grid.410587.fSchool of Laboratory Animal (Shandong Laboratory Animal Center), Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, 250117 China
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Non-Coding RNAs in Pulmonary Diseases: Comparison of Different Airway-Derived Biosamples. Int J Mol Sci 2023; 24:ijms24032006. [PMID: 36768329 PMCID: PMC9916756 DOI: 10.3390/ijms24032006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These molecules have been investigated both in a cellular and an extracellular context. Sources of ncRNAs may include organ-specific body fluids. Therefore, studies on ncRNAs in respiratory diseases include those on sputum, bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC). It is worth identifying the limitations of these biosamples in terms of ncRNA abundance, processing and diagnostic potential. This review describes the progress in the literature on the role of ncRNAs in the pathogenesis and progression of severe respiratory diseases, including cystic fibrosis, asthma and interstitial lung disease. We showed that there is a deficit of information on lncRNAs and circRNAs in selected diseases, despite attempts to functionally bind them to miRNAs. miRNAs remain the most well-studied, but only a few investigations have been conducted on the least invasive biosample material, i.e., EBC. To summarise the studies conducted to date, we also performed a preliminary in silico analysis of the reported miRNAs, demonstrating the complexity of their role and interactions in selected respiratory diseases.
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163
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Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
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Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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164
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Ziętara KJ, Lejman J, Wojciechowska K, Lejman M. The Importance of Selected Dysregulated microRNAs in Diagnosis and Prognosis of Childhood B-Cell Precursor Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020428. [PMID: 36672378 PMCID: PMC9856444 DOI: 10.3390/cancers15020428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a frequent type of childhood hematological malignancy. The disease is classified into several subtypes according to genetic abnormalities. MicroRNAs (miRNAs) are involved in pathological processes (e.g., proliferation, apoptosis, differentiation). A miRNA is a group of short non-coding RNAs with relevant regulatory effects on gene expression achieved by suppression of the translation or degradation of messenger RNA (mRNA). These molecules act as tumor suppressors and/or oncogenes in the pathogenesis of pediatric leukemias. The characteristic features of miRNAs are their stable form and the possibility of secretion to the circulatory system. The role of miRNA in BCP-ALL pathogenesis is still emerging, but several studies have suggested using miRNA expression profiles as biomarkers for diagnosis, prognosis, and response to therapy in leukemia. The dysregulation of some miRNAs involved in childhood acute lymphoid leukemia, such as miR-155, miR-200c, miR-100, miR-181a, miR125b, and miR146a is discussed, showing their possible employment as therapeutic targets. In the current review, the capabilities of miRNAs in non-invasive diagnostics and their prognostic potential as biomarkers are presented.
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Affiliation(s)
- Karolina Joanna Ziętara
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Jan Lejman
- Independent Public Health Care Facility of The Ministry of Internal Affairs and Administration in Lublin, 20-331 Lublin, Poland
| | - Katarzyna Wojciechowska
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-059 Lublin, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-059 Lublin, Poland
- Correspondence:
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165
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Tantray I, Ojha R, Sharma AP. Non-coding RNA and autophagy: Finding novel ways to improve the diagnostic management of bladder cancer. Front Genet 2023; 13:1051762. [PMID: 36685879 PMCID: PMC9845264 DOI: 10.3389/fgene.2022.1051762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Major fraction of the human genome is transcribed in to the RNA but is not translated in to any specific functional protein. These transcribed but not translated RNA molecules are called as non-coding RNA (ncRNA). There are thousands of different non-coding RNAs present inside the cells, each regulating different cellular pathway/pathways. Over the last few decades non-coding RNAs have been found to be involved in various diseases including cancer. Non-coding RNAs are reported to function both as tumor enhancer and/or tumor suppressor in almost each type of cancer. Urothelial carcinoma of the urinary bladder is the second most common urogenital malignancy in the world. Over the last few decades, non-coding RNAs were demonstrated to be linked with bladder cancer progression by modulating different signalling pathways and cellular processes such as autophagy, metastasis, drug resistance and tumor proliferation. Due to the heterogeneity of bladder cancer cells more in-depth molecular characterization is needed to identify new diagnostic and treatment options. This review emphasizes the current findings on non-coding RNAs and their relationship with various oncological processes such as autophagy, and their applicability to the pathophysiology of bladder cancer. This may offer an understanding of evolving non-coding RNA-targeted diagnostic tools and new therapeutic approaches for bladder cancer management in the future.
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Affiliation(s)
- Ishaq Tantray
- School of Medicine, Department of Pathology, Stanford University, Stanford, CA, United States
| | - Rani Ojha
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
| | - Aditya P. Sharma
- Department of Urology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India,*Correspondence: Rani Ojha, ; Aditya P. Sharma,
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166
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Hasi G, Sodnompil T, Na H, Liu H, Ji M, Xie W, Nasenochir N. Whole transcriptome sequencing reveals core genes related to spermatogenesis in Bactrian camels. J Anim Sci 2023; 101:skad115. [PMID: 37083698 PMCID: PMC10718809 DOI: 10.1093/jas/skad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/19/2023] [Indexed: 04/22/2023] Open
Abstract
Bactrian camels survive and reproduce better in extreme climatic conditions than other domestic animals can. However, the reproductive efficiency of camels under their natural pastoral conditions is low. Several factors affect mammalian reproductive performance, including testicular development, semen quality, libido, and mating ability. Testis is a main reproductive organ of the male and is responsible for producing spermatozoa and hormones. However, our understanding of the expression patterns of the genes in camel testis is minimal. Thus, we performed total RNA-sequencing to investigate the gene expression pattern. As a result, 1,538 differential expressed mRNAs (DEmRNAs), 702 differential expressed long non-coding RNAs (DElncRNAs), and 61 differential expressed microRNAs (DEmiRNAs) were identified between pubertal and adult Bactrian camel testes. Then the genomic features, length distribution, and other characteristics of the lncRNAs and mRNAs in the Bactrian camel testis were investigated. Target genes of the DEmiRNAs and DEmRNAs were further subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Genes, such as AMHR2, FGF1, ACTL7A, GATA4, WNT4, ID2, LAMA1, IGF1, INHBB, and TLR2, were mainly involved in the TGF-β, PI3K-AKT, Wnt, GnRH, and Hippo signaling pathways which relate to spermatogenesis. Some of the DEmiRNAs were predicted to be associated with numerous DElncRNAs and DEmRNAs through competing endogenous RNA (ceRNA) regulatory network. At last, the candidate genes were validated by RT-qPCR, dual fluorescent reporter gene, and a fluorescence in situ hybridization (FISH) assay. This research provides high-throughput RNA sequencing data of the testes of Bactrian camels across different developmental stages. It lays the foundation for further investigations on lncRNAs, miRNAs, and mRNAs that involved in Bactrian camel spermatogenesis.
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Affiliation(s)
- Gaowa Hasi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Tserennadmid Sodnompil
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Haya Na
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Hejie Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Musi Ji
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Wangwei Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
| | - Narenhua Nasenochir
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot 010018, Inner Mongolia, China
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167
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Ghazimoradi MH, Karimpour-Fard N, Babashah S. The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia. Genes (Basel) 2023; 14:131. [PMID: 36672872 PMCID: PMC9859176 DOI: 10.3390/genes14010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.
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Affiliation(s)
- Mohammad H. Ghazimoradi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Naeim Karimpour-Fard
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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Tumolo MR, Scoditti E, Guarino R, Grassi T, Bagordo F, Sabina S. MIR-29A-3P, MIR-29C-3P, MIR-146B-5P AND MIR-150-5P, Their Target Genes and lncrnas in HIV Infection: A Bioinformatic Study. Curr HIV Res 2023; 21:128-139. [PMID: 37226785 DOI: 10.2174/1570162x21666230524151328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
INTRODUCTION Increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have emerged as attractive targets in viral infections, including Human immunodeficiency virus (HIV). OBJECTIVE To deepen the understanding of the molecular mechanisms that lead to HIV and provide potential targets for the future development of molecular therapies for its treatment. METHODS Four miRNAs were selected as candidates based on a previous systematic review. A combination of bioinformatic analyses was performed to identify their target genes, lncRNAs and biological processes that regulate them. RESULTS In the constructed miRNA-mRNA network, 193 gene targets are identified. These miRNAs potentially control genes from several important processes, including signal transduction and cancer. LncRNA-XIST, lncRNA-NEAT1 and lncRNA-HCG18 interact with all four miRNAs. CONCLUSION This preliminary result forms the basis for improving reliability in future studies to fully understand the role these molecules and their interactions play in HIV.
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Affiliation(s)
- Maria Rosaria Tumolo
- Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Egeria Scoditti
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
| | - Roberto Guarino
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
| | - Tiziana Grassi
- Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Francesco Bagordo
- Department of Pharmacy- Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Saverio Sabina
- Institute of Clinical Physiology, National Research Council, Branch of Lecce, Lecce, Italy
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169
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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170
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Wang JQ, Liu YR, Xia QR, Liang J, Wang JL, Li J. Functional roles, regulatory mechanisms and theranostics applications of ncRNAs in alcohol use disorder. Int J Biol Sci 2023; 19:1316-1335. [PMID: 36923934 PMCID: PMC10008696 DOI: 10.7150/ijbs.81518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/02/2023] [Indexed: 03/14/2023] Open
Abstract
Alcohol use disorder (AUD) is one of the most prevalent neuropsychological disorders worldwide, and its pathogenesis is convoluted and poorly understood. There is considerable evidence demonstrating significant associations between multiple heritable factors and the onset and progression of AUD. In recent years, a substantial body of research conducted by emerging biotechnologies has increasingly highlighted the crucial roles of noncoding RNAs (ncRNAs) in the pathophysiology of mental diseases. As in-depth understanding of ncRNAs and their mechanisms of action, they have emerged as prospective diagnostic indicators and preclinical therapeutic targets for a variety of psychiatric illness, including AUD. Of note, dysregulated expression of ncRNAs such as circRNAs, lncRNAs and miRNAs was routinely found in AUD individuals, and besides, exogenous regulation of partial ncRNAs has also been shown to be effective in ameliorating alcohol preference and excessive alcohol consumption. However, the exact molecular mechanism still remains elusive. Herein, we systematically summarized current knowledge regarding alterations in the expression of certain ncRNAs as well as their-mediated regulatory mechanisms in individuals with AUD. And finally, we detailedly reviewed the potential theranostics applications of gene therapy agents targeting ncRNAs in AUD mice. Overall, a deeper comprehension of functional roles and biological mechanisms of ncRNAs may make significant contributions to the accurate diagnosis and effective treatment of AUD.
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Affiliation(s)
- Jie-Quan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Ya-Ru Liu
- Department of Pharmacy, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.,The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, 230022, China
| | - Qing-Rong Xia
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jun Liang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jin-Liang Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, 230000, China.,Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, 230000, China.,Psychopharmacology Research Laboratory, Anhui Mental Health Center, Hefei, 230000, China.,Anhui Clinical Research Center for Mental Disorders, Hefei,230000, China
| | - Jun Li
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
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Zhang JS, Pan RS, Tian XB. Identification and validation of an anoikis-related lncRNA signature to predict prognosis and immune landscape in osteosarcoma. Front Oncol 2023; 13:1156663. [PMID: 37035149 PMCID: PMC10076677 DOI: 10.3389/fonc.2023.1156663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Background Anoikis is a specialized form of programmed apoptosis that occurs in two model epithelial cell lines and plays an important role in tumors. However, the prognostic value of anoikis-related lncRNA (ARLncs) in osteosarcoma (OS) has not been reported. Methods Based on GTEx and TARGET RNA sequencing data, we carried out a thorough bioinformatics analysis. The 27 anoikis-related genes were obtained from the Gene Set Enrichment Analysis (GSEA). Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analysis were successively used to screen for prognostic-related ARLncs. To create the prognostic signature of ARLncs, we performed multivariate Cox regression analysis. We calculated the risk score based on the risk coefficient, dividing OS patients into high- and low-risk subgroups. Additionally, the relationship between the OS immune microenvironment and risk prognostic models was investigated using function enrichment, including Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), single-sample gene set enrichment analysis (ssGSEA), and GSEA analysis. Finally, the potential effective drugs in OS were found by immune checkpoint and drug sensitivity screening. Results A prognostic signature consisting of four ARLncs (AC079612.1, MEF2C-AS1, SNHG6, and TBX2-AS1) was constructed. To assess the regulation patterns of anoikis-related lncRNA genes, we created a risk score model. According to a survival analysis, high-risk patients have a poor prognosis as they progress. By using immune functional analysis, the lower-risk group demonstrated the opposite effects compared with the higher-risk group. GO and KEGG analysis showed that the ARLncs pathways and immune-related pathways were enriched. Immune checkpoints and drug sensitivity analysis might be used to determine the better effects of the higher group. Conclusion We identified a novel prognostic model based on a four-ARLncs signature that might serve as potential prognostic indicators that can be used to predict the prognosis of OS patients, and immunotherapy and drugs that may contribute to improving the overall survival of OS patients and advance our understanding of OS.
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Affiliation(s)
- Jun-Song Zhang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Run-Sang Pan
- School of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiao-Bin Tian
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Orthopedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- *Correspondence: Xiao-Bin Tian,
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Limkul S, Phiwthong T, Massu A, Boonanuntanasarn S, Teaumroong N, Somboonwiwat K, Boonchuen P. Transcriptome-based insights into the regulatory role of immune-responsive circular RNAs in Litopanaeus vannamei upon WSSV infection. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108499. [PMID: 36549581 DOI: 10.1016/j.fsi.2022.108499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) originating from a post-transcriptional modification process called back-splicing. Despite circRNAs being traditionally considered by-products rather than independently functional, circRNAs play many vital roles, such as in host immunity during viral infection. However, in shrimp, these remain largely unexplored. Therefore, this study aims to identify circRNAs in Litopenaeus vannamei in the context of WSSV infection, one of the most eradicative pathogens threatening shrimp populations worldwide. We identified 290 differentially expressed circRNAs (DECs) in L. vannamei upon WSSV infection. Eight DECs were expressed from their parental genes, including alpha-1-inhibitor-3, calpain-B, integrin-V, hemicentin-2, hemocytin, mucin-17, proPO2, and rab11-FIP4. These were examined quantitatively by qRT-PCR, which revealed the relevant expression profiles to those obtained from circRNA-Seq. Furthermore, the structural and chemical validation of the DECs conformed to the characteristics of circRNAs. One of the functional properties of circRNAs as a miRNA sponge was examined via the interaction network between DECs and WSSV-responsive miRNAs, which highlighted the targets of miRNA sponges. Our discovery could provide insight into the participation of these ncRNAs in shrimp antiviral responses.
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Affiliation(s)
- Sirawich Limkul
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Tannatorn Phiwthong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Amarin Massu
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Surintorn Boonanuntanasarn
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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Sangeeth A, Malleswarapu M, Mishra A, Gutti RK. Long Non-Coding RNAs as Cellular Metabolism and Haematopoiesis Regulators. J Pharmacol Exp Ther 2023; 384:79-91. [PMID: 35667690 DOI: 10.1124/jpet.121.001120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a category of non-coding RNAs (ncRNAs) that are more than 200 bases long and play major regulatory roles in a wide range of biologic processes, including hematopoeisis and metabolism. Metabolism in cells is an immensely complex process that involves the interconnection and unification of numerous signaling pathways. A growing body of affirmation marks that lncRNAs do participate in metabolism, both directly and indirectly, via metabolic regulation of enzymes and signaling pathways, respectively. The complexities are disclosed by the latest studies demonstrating how lncRNAs could indeed alter tissue-specific metabolism. We have entered a new realm for discovery that is both intimidating and intriguing. Understanding the different functions of lncRNAs in various cellular pathways aids in the advancement of predictive and therapeutic capabilities for a wide variety of myelodysplastic and metabolic disorders. This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. We have focused on the pathway of action of several lncRNAs and have also delved into their prognostic value. Their use as biomarkers and possible therapeutic targets has also been discussed. SIGNIFICANCE STATEMENT: This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. The pathway of action of several lncRNAs and their prognostic value was discussed. Their use as biomarkers and possible therapeutic targets has also been elaborated.
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Affiliation(s)
- Anjali Sangeeth
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Mahesh Malleswarapu
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Amit Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
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174
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Jiang Y, Zhong S, He S, Weng J, Liu L, Ye Y, Chen H. Biomarkers (mRNAs and non-coding RNAs) for the diagnosis and prognosis of rheumatoid arthritis. Front Immunol 2023; 14:1087925. [PMID: 36817438 PMCID: PMC9929281 DOI: 10.3389/fimmu.2023.1087925] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
In recent years, diagnostic and therapeutic approaches for rheumatoid arthritis (RA) have continued to improve. However, in the advanced stages of the disease, patients are unable to achieve long-term clinical remission and often suffer from systemic multi-organ damage and severe complications. Patients with RA usually have no overt clinical manifestations in the early stages, and by the time a definitive diagnosis is made, the disease is already at an advanced stage. RA is diagnosed clinically and with laboratory tests, including the blood markers C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) and the autoantibodies rheumatoid factor (RF) and anticitrullinated protein antibodies (ACPA). However, the presence of RF and ACPA autoantibodies is associated with aggravated disease, joint damage, and increased mortality, and these autoantibodies have low specificity and sensitivity. The etiology of RA is unknown, with the pathogenesis involving multiple factors and clinical heterogeneity. The early diagnosis, subtype classification, and prognosis of RA remain challenging, and studies to develop minimally invasive or non-invasive biomarkers in the form of biofluid biopsies are becoming more common. Non-coding RNA (ncRNA) molecules are composed of long non-coding RNAs, small nucleolar RNAs, microRNAs, and circular RNAs, which play an essential role in disease onset and progression and can be used in the early diagnosis and prognosis of RA. In this review of the diagnostic and prognostic approaches to RA disease, we provide an overview of the current knowledge on the subject, focusing on recent advances in mRNA-ncRNA as diagnostic and prognostic biomarkers from the biofluid to the tissue level.
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Affiliation(s)
- Yong Jiang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuxin Zhong
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Shenghua He
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Juanling Weng
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Lijin Liu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yufeng Ye
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Hanwei Chen
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Department of Radiology, GuangzhouPanyu Health Management Center (Panyu Rehabilitation Hospital), Guangzhou, China
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175
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Varghese LN, Schwenke DO, Katare R. Role of noncoding RNAs in cardiac ageing. Front Cardiovasc Med 2023; 10:1142575. [PMID: 37034355 PMCID: PMC10073704 DOI: 10.3389/fcvm.2023.1142575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
The global population is estimated to reach 9.8 billion by 2050, of which 2.1 billion will comprise individuals above 60 years of age. As the number of elderly is estimated to double from 2017, it is a victory of the modern healthcare system but also worrisome as ageing, and the onset of chronic disease are correlated. Among other chronic conditions, cardiovascular diseases (CVDs) are the leading cause of death in the aged population. While the underlying cause of the age-associated development of CVDs is not fully understood, studies indicate the role of non-coding RNAs such as microRNAs (miRNAs) and long noncoding RNAs (lnc-RNAs) in the development of age-associated CVDs. miRNAs and lnc-RNAs are non-coding RNAs which control gene expression at the post-transcriptional level. The expression of specific miRNAs and lnc-RNAs are reportedly dysregulated with age, leading to cardiovascular system changes and ultimately causing CVDs. Since miRNAs and lnc-RNAs play several vital roles in maintaining the normal functioning of the cardiovascular system, they are also being explored for their therapeutic potential as a treatment for CVDs. This review will first explore the pathophysiological changes associated with ageing. Next, we will review the known mechanisms underlying the development of CVD in ageing with a specific focus on miRNA and lnc-RNAs. Finally, we will discuss the therapeutic options and future challenges towards healthy cardiac ageing. With the global ageing population on the rise, this review will provide a fundamental understanding of some of the underlying molecular mechanisms of cardiac ageing.
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176
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Decoding Roles of Exosomal lncRNAs in Tumor-Immune Regulation and Therapeutic Potential. Cancers (Basel) 2022; 15:cancers15010286. [PMID: 36612282 PMCID: PMC9818565 DOI: 10.3390/cancers15010286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/12/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Exosomes are nanovesicles secreted into biofluids by various cell types and have been implicated in different physiological and pathological processes. Interestingly, a plethora of studies emphasized the mediating role of exosomes in the bidirectional communication between donor and recipient cells. Among the various cargoes of exosomes, long non-coding RNAs (lncRNAs) have been identified as crucial regulators between cancer cells and immune cells in the tumor microenvironment (TME) that can interfere with innate and adaptive immune responses to affect the therapeutic efficiency. Recently, a few major studies have focused on the exosomal lncRNA-mediated interaction between cancer cells and immune cells infiltrated into TME. Nevertheless, a dearth of studies pertains to the immune regulating role of exosomal lncRNAs in cancer and is still in the early stages. Comprehensive mechanisms of exosomal lncRNAs in tumor immunity are not well understood. Herein, we provide an overview of the immunomodulatory function of exosomal lncRNAs in cancer and treatment resistance. In addition, we also summarize the potential therapeutic strategies toward exosomal lncRNAs in TME.
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177
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Szydełko J, Matyjaszek-Matuszek B. MicroRNAs as Biomarkers for Coronary Artery Disease Related to Type 2 Diabetes Mellitus-From Pathogenesis to Potential Clinical Application. Int J Mol Sci 2022; 24:ijms24010616. [PMID: 36614057 PMCID: PMC9820734 DOI: 10.3390/ijms24010616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease with still growing incidence among adults and young people worldwide. Patients with T2DM are more susceptible to developing coronary artery disease (CAD) than non-diabetic individuals. The currently used diagnostic methods do not ensure the detection of CAD at an early stage. Thus, extensive research on non-invasive, blood-based biomarkers is necessary to avoid life-threatening events. MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs that are stable in human body fluids and easily detectable. A number of reports have highlighted that the aberrant expression of miRNAs may impair the diversity of signaling pathways underlying the pathophysiology of atherosclerosis, which is a key player linking T2DM with CAD. The preclinical evidence suggests the atheroprotective and atherogenic influence of miRNAs on every step of T2DM-induced atherogenesis, including endothelial dysfunction, endothelial to mesenchymal transition, macrophage activation, vascular smooth muscle cells proliferation/migration, platelet hyperactivity, and calcification. Among the 122 analyzed miRNAs, 14 top miRNAs appear to be the most consistently dysregulated in T2DM and CAD, whereas 10 miRNAs are altered in T2DM, CAD, and T2DM-CAD patients. This up-to-date overview aims to discuss the role of miRNAs in the development of diabetic CAD, emphasizing their potential clinical usefulness as novel, non-invasive biomarkers and therapeutic targets for T2DM individuals with a predisposition to undergo CAD.
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178
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Li J, Xu J, Zheng S, Cheng S. LncRNA LINC02535 Induces Colorectal Adenocarcinoma Progression via Modulating miR-30d-5p/CHD1. Mol Biotechnol 2022:10.1007/s12033-022-00628-4. [PMID: 36577835 DOI: 10.1007/s12033-022-00628-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022]
Abstract
Growing evidence has suggested that lncRNAs play a significant role in the development of colorectal adenocarcinoma. LncRNA LINC02535 was a potential novel lncRNA marker of neoplastic processes of the colon. Nevertheless, the function and mechanisms of LINC02535 in colorectal adenocarcinoma remain unclear. Proteins levels were measured by western blotting. EdU, CCK-8, Transwell, and wound healing assays were performed to investigate the function of LINC02535 in colorectal adenocarcinoma. The distribution of LINC02535 in cells was evaluated by subcellular fractionation assay. The interaction among RNAs was identified by luciferase reporter and RIP assays. In this study, our findings revealed that LINC02535 was highly expressed in colorectal adenocarcinoma cells. Knockdown of LINC02535 inhibited colorectal adenocarcinoma cell proliferation, migration, and invasion. Mechanistically, LINC02535 bound with miR-30d-5p and worked as a competing endogenous RNA to facilitate the expression of messenger RNA chromodomain helicase DNA-binding protein 1 (CHD1). miR-30d-5p directly targeted the sequence of CHD1 3'-untranslated region. Notably, CHD1 upregulation abolished the suppressive influence of LINC02535 inhibition on the malignant phenotypes of colorectal adenocarcinoma cells. Overall, it was disclosed that LINC02535 played an oncogenic role in colorectal adenocarcinoma progression by sponging miR-30d-5p to upregulate CHD1 expression.
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Affiliation(s)
- Jiguang Li
- Department of Anorectal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437100, Hubei, China
| | - Jianhua Xu
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China
| | - Sen Zheng
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
| | - Si Cheng
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
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179
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Sheykhhasan M, Tanzadehpanah H, Ahmadieh Yazdi A, Mahaki H, Seyedebrahimi R, Akbari M, Manoochehri H, Kalhor N, Dama P. FLVCR1-AS1 and FBXL19-AS1: Two Putative lncRNA Candidates in Multiple Human Cancers. Noncoding RNA 2022; 9:ncrna9010001. [PMID: 36649030 PMCID: PMC9844485 DOI: 10.3390/ncrna9010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/03/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022] Open
Abstract
(1) Background: Mounting evidence supports the idea that one of the most critical agents in controlling gene expression could be long non-coding RNAs (lncRNAs). Upregulation of lncRNA is observed in the different processes related to pathologies, such as tumor occurrence and development. Among the crescent number of lncRNAs discovered, FLVCR1-AS1 and FBXL19-AS1 have been identified as oncogenes in many cancer progression and prognosis types, including cholangiocarcinoma, gastric cancer, glioma and glioblastoma, hepatocellular carcinoma, lung cancer, ovarian cancer, breast cancer, colorectal cancer, and osteosarcoma. Therefore, abnormal FBXL19-AS1 and FLVCR1-AS1 expression affect a variety of cellular activities, including metastasis, aggressiveness, and proliferation; (2) Methods: This study was searched via PubMed and Google Scholar databases until May 2022; (3) Results: FLVCR1-AS1 and FBXL19-AS1 participate in tumorigenesis and have an active role in impacting several signaling pathways that regulate cell proliferation, migration, invasion, metastasis, and EMT; (4) Conclusions: Our review focuses on the possible molecular mechanisms in a variety of cancers regulated by FLVCR1-AS1 and FBXL19-AS1. It is not surprising that there has been significant interest in the possibility that these lncRNAs might be used as biomarkers for diagnosis or as a target to improve a broader range of cancers in the future.
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Affiliation(s)
- Mohsen Sheykhhasan
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838636, Iran
- Department of Mesenchymal Stem Cells, Academic Center for Education, Culture and Research, Qom 3716986466, Iran
| | - Hamid Tanzadehpanah
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad 9177899191, Iran
| | - Amirhossein Ahmadieh Yazdi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838636, Iran
| | - Hanie Mahaki
- Vascular & Endovascular Surgery Research Center, Mashhad University of Medical Sciences, Mashhad 9177899191, Iran
| | - Reihaneh Seyedebrahimi
- Anatomy Department, Faculty of Medicine, Qom University of Medical Sciences, Qom 3715614566, Iran
| | - Mohammad Akbari
- General Physician, Department of Medical School, Faculty of Medical Sciences, Islamic Azad University, Tonekabon Branch, Mazandaran 4684161167, Iran
| | - Hamed Manoochehri
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838636, Iran
| | - Naser Kalhor
- Department of Mesenchymal Stem Cells, Academic Center for Education, Culture and Research, Qom 3716986466, Iran
| | - Paola Dama
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Correspondence: ; Tel.: +44-7366-835083
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180
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Tan Z, Li W, Cheng X, Zhu Q, Zhang X. Non-Coding RNAs in the Regulation of Hippocampal Neurogenesis and Potential Treatment Targets for Related Disorders. Biomolecules 2022; 13:biom13010018. [PMID: 36671403 PMCID: PMC9855933 DOI: 10.3390/biom13010018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, circRNAs, and piRNAs, do not encode proteins. Nonetheless, they have critical roles in a variety of cellular activities-such as development, neurogenesis, degeneration, and the response to injury to the nervous system-via protein translation, RNA splicing, gene activation, silencing, modifications, and editing; thus, they may serve as potential targets for disease treatment. The activity of adult neural stem cells (NSCs) in the subgranular zone of the hippocampal dentate gyrus critically influences hippocampal function, including learning, memory, and emotion. ncRNAs have been shown to be involved in the regulation of hippocampal neurogenesis, including proliferation, differentiation, and migration of NSCs and synapse formation. The interaction among ncRNAs is complex and diverse and has become a major topic within the life science. This review outlines advances in research on the roles of ncRNAs in modulating NSC bioactivity in the hippocampus and discusses their potential applications in the treatment of illnesses affecting the hippocampus.
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Affiliation(s)
- Zhengye Tan
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Wen Li
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Xiang Cheng
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qing Zhu
- School of Pharmacy, Nantong University, Nantong 226001, China
- Key Laboratory of Inflammation and Molecular Drug Target of Jiangsu Province, Nantong 226001, China
| | - Xinhua Zhang
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
- Central Lab, Yancheng Third People’s Hospital, The Sixth Affiliated Hospital of Nantong University, Yancheng 224001, China
- Correspondence:
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181
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Albano GD, Gagliardo R, Montalbano AM, Profita M. Non-Coding RNAs in Airway Diseases: A Brief Overview of Recent Data. Cancers (Basel) 2022; 15:cancers15010054. [PMID: 36612051 PMCID: PMC9817765 DOI: 10.3390/cancers15010054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Inflammation of the human lung is mediated in response to different stimuli (e.g., physical, radioactive, infective, pro-allergenic, or toxic) such as cigarette smoke and environmental pollutants. These stimuli often promote an increase in different inflammatory activities in the airways, manifesting themselves as chronic diseases (e.g., allergic airway diseases, asthma chronic bronchitis/chronic obstructive pulmonary disease, or even lung cancer). Non-coding RNA (ncRNAs) are single-stranded RNA molecules of few nucleotides that regulate the gene expression involved in many cellular processes. ncRNA are molecules typically involved in the reduction of translation and stability of the genes of mRNAs s. They regulate many biological aspects such as cellular growth, proliferation, differentiation, regulation of cell cycle, aging, apoptosis, metabolism, and neuronal patterning, and influence a wide range of biologic processes essential for the maintenance of cellular homeostasis. The relevance of ncRNAs in the pathogenetic mechanisms of respiratory diseases has been widely established and in the last decade many papers were published. However, once their importance is established in pathogenetic mechanisms, it becomes important to further deepen the research in this direction. In this review we describe several of most recent knowledge concerning ncRNA (overall miRNAs) expression and activities in the lung.
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182
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Plasil SL, Collins VJ, Baratta AM, Farris SP, Homanics GE. Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10831. [PMID: 36908580 PMCID: PMC10004261 DOI: 10.3389/adar.2022.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular mechanisms regulating the development and progression of alcohol use disorder (AUD) are largely unknown. While noncoding RNAs have previously been implicated as playing key roles in AUD, long-noncoding RNA (lncRNA) remains understudied in relation to AUD. In this study, we first identified ethanol-responsive lncRNAs in the mouse hippocampus that are transcriptional network hub genes. Microarray analysis of lncRNA, miRNA, circular RNA, and protein coding gene expression in the hippocampus from chronic intermittent ethanol vapor- or air- (control) exposed mice was used to identify ethanol-responsive competing endogenous RNA (ceRNA) networks. Highly interconnected lncRNAs (genes that had the strongest overall correlation to all other dysregulated genes identified) were ranked. The top four lncRNAs were novel, previously uncharacterized genes named Gm42575, 4930413E15Rik, Gm15767, and Gm33447, hereafter referred to as Pitt1, Pitt2, Pitt3, and Pitt4, respectively. We subsequently tested the hypothesis that CRISPR/Cas9 mutagenesis of the putative promoter and first exon of these lncRNAs in C57BL/6J mice would alter ethanol drinking behavior. The Drinking in the Dark (DID) assay was used to examine binge-like drinking behavior, and the Every-Other-Day Two-Bottle Choice (EOD-2BC) assay was used to examine intermittent ethanol consumption and preference. No significant differences between control and mutant mice were observed in the DID assay. Female-specific reductions in ethanol consumption were observed in the EOD-2BC assay for Pitt1, Pitt3, and Pitt4 mutant mice compared to controls. Male-specific alterations in ethanol preference were observed for Pitt1 and Pitt2. Female-specific increases in ethanol preference were observed for Pitt3 and Pitt4. Total fluid consumption was reduced in Pitt1 and Pitt2 mutants at 15% v/v ethanol and in Pitt3 and Pitt4 at 20% v/v ethanol in females only. We conclude that all lncRNAs targeted altered ethanol drinking behavior, and that lncRNAs Pitt1, Pitt3, and Pitt4 influenced ethanol consumption in a sex-specific manner. Further research is necessary to elucidate the biological mechanisms for these effects. These findings add to the literature implicating noncoding RNAs in AUD and suggest lncRNAs also play an important regulatory role in the disease.
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Affiliation(s)
- SL Plasil
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - VJ Collins
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - AM Baratta
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - SP Farris
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - GE Homanics
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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183
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Qi D, Li H, Wang S, Wang S, Zheng R, Liu N, Han B, Liu L. Construction of ceRNA network and key gene screening in cervical squamous intraepithelial lesions. Medicine (Baltimore) 2022; 101:e31928. [PMID: 36482542 PMCID: PMC9726336 DOI: 10.1097/md.0000000000031928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to construct an endogenous competition network for cervical squamous intraepithelial lesions using differential gene screening. METHODS GSE149763 was used to screen differentially expressed long non-coding RNAs (lncRNAs) and mRNAs to predict correlated microRNAs (miRNAs). The correlated miRNAs and GSE105409 were used to screen differentially expressed miRNAs for differential co-expression analysis, and the co-expressed differentially expressed miRNAs were used to predict correlated mRNAs. Differentially expressed mRNAs, miRNAs, and lncRNAs were visualized, and differential gene screening, enrichment, and pathway analysis were performed. RESULTS The ceRNA network of cervical squamous intraepithelial was successfully established and a potential differentially expressed network was identified. The key genes were VEGFA and FOS, and the key pathway was the MAPK signaling pathway. CONCLUSIONS The differential expression and potential effects of the lncRNA BACH1-IT1/miR-140-5p/VEGFA axis, key genes, VEGFA and FOS, and MAPK signaling in CIN were clarified, and the occurrence and potential effects of CIN were further clarified. The underlying molecular mechanism provides a certain degree of reference for subsequent treatments and experimental research.
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Affiliation(s)
- Ding Qi
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Hongmei Li
- The 2nd Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Shuoqi Wang
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Shimeng Wang
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Rui Zheng
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Ning Liu
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Buwei Han
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Li Liu
- The 1st Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
- * Correspondence: Li Liu, Department of Gynecology, The 1st Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang 150036, China (e-mail: )
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184
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Sangeeth A, Malleswarapu M, Mishra A, Gutti RK. Long Non-coding RNA Therapeutics: Recent Advances and Challenges. Curr Drug Targets 2022; 23:1457-1464. [PMID: 36121080 DOI: 10.2174/1389450123666220919122520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/06/2022] [Accepted: 08/01/2022] [Indexed: 01/25/2023]
Abstract
The discovery of the roles of RNA other than just as a messenger, such as a ribozyme, and regulatory RNAs, such as microRNA and long noncoding RNAs, is fascinating. RNA is now recognized as an important regulator involved in practically every biological process. Research in the field of non-coding RNAs, specifically microRNAs (miRNAs) and long non-coding RNAs (LncRNAs) have developed immensely over the years. Recent studies identified diverse RNAs, including non-coding RNAs such as LncRNA and their various modes of action in the cells. These RNAs are anticipated to be key targets for the treatment of various diseases since they control a broad array of biological pathways. LncRNA-targeted drug platform delivers the pharmaceutical industry a myriad of opportunities and has the potential to modulate diseases at the genetic level while also overcoming the limitations of inconsistent proteins. This article focuses on the recent advancement as well as the major challenges in the field and describes the various RNA-based therapeutics that alter the quality of healthcare for many diseases and bring personalized medicines to fruition. The article also summarizes RNA-based therapeutics that are undergoing testing in clinical trials or have been granted FDA approval.
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Affiliation(s)
- Anjali Sangeeth
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad 500046 (TS), India
| | - Mahesh Malleswarapu
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad 500046 (TS), India
| | - Amit Mishra
- Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037 (RJ), India
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad 500046 (TS), India
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185
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Pantazi P, Clements T, Venø M, Abrahams VM, Holder B. Distinct non-coding RNA cargo of extracellular vesicles from M1 and M2 human primary macrophages. J Extracell Vesicles 2022; 11:e12293. [PMID: 36544271 PMCID: PMC9772496 DOI: 10.1002/jev2.12293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/13/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Macrophages are important antigen presenting cells which can release extracellular vesicles (EVs) carrying functional cargo including non-coding RNAs. Macrophages can be broadly classified into M1 'classical' and M2 'alternatively-activated' macrophages. M1 macrophages have been linked with inflammation-associated pathologies, whereas a switch towards an M2 phenotype indicates resolution of inflammation and tissue regeneration. Here, we provide the first comprehensive analysis of the small RNA cargo of EVs from human M1 and M2 primary macrophages. Using small RNA sequencing, we identified several types of small non-coding RNAs in M1 and M2 macrophage EVs including miRNAs, isomiRs, tRNA fragments, piRNA, snRNA, snoRNA and Y-RNA fragments. Distinct differences were observed between M1 and M2 EVs, with higher relative abundance of miRNAs, and lower abundance of tRNA fragments in M1 compared to M2 EVs. MicroRNA-target enrichment analysis identified several gene targets involved in gene expression and inflammatory signalling pathways. EVs were also enriched in tRNA fragments, primarily originating from the 5' end or the internal region of the full length tRNAs, many of which were differentially abundant in M1 and M2 EVs. Similarly, several other small non-coding RNAs, namely snRNAs, snoRNAs and Y-RNA fragments, were differentially enriched in M1 and M2 EVs; we discuss their putative roles in macrophage EVs. In conclusion, we show that M1 and M2 macrophages release EVs with distinct RNA cargo, which has the potential to contribute to the unique effect of these cell subsets on their microenvironment.
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Affiliation(s)
- Paschalia Pantazi
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
| | - Toby Clements
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
| | | | - Vikki M. Abrahams
- Department of ObstetricsGynecology and Reproductive SciencesYale School of MedicineNew HavenConnecticutUSA
| | - Beth Holder
- Institute of Reproductive and Developmental BiologyDepartment of Metabolism, Digestion, and ReproductionImperial College LondonLondonUK
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186
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Muntyanu A, Le M, Ridha Z, O’Brien E, Litvinov IV, Lefrançois P, Netchiporouk E. Novel role of long non-coding RNAs in autoimmune cutaneous disease. J Cell Commun Signal 2022; 16:487-504. [PMID: 34346026 PMCID: PMC9733767 DOI: 10.1007/s12079-021-00639-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Systemic autoimmune rheumatic diseases (SARDs) are a heterogeneous group of chronic multisystem inflammatory disorders that are thought to have a complex pathophysiology, which is not yet fully understood. Recently, the role of non-coding RNAs, including long non-coding RNA (lncRNA), has been of particular interest in the pathogenesis of SARDs. We aimed to summarize the potential roles of lncRNA in SARDs affecting the skin including, systemic sclerosis (SSc), dermatomyositis (DM) and cutaneous lupus erythematosus (CLE). We conducted a narrative review summarizing original articles published until July 19, 2021, regarding lncRNA associated with SSc, DM, and CLE. Several lncRNAs were hypothesized to play an important role in disease pathogenesis of SSc, DM and CLE. In SSc, Negative Regulator of IFN Response (NRIR) was thought to modulate Interferon (IFN) response in monocytes, anti-sense gene to X-inactivation specific transcript (TSIX) to regulate increased collagen stability, HOX transcript antisense RNA (HOTAIR) to increase numbers of myofibroblasts, OTUD6B-Anti-Sense RNA 1 to decrease fibroblast apoptosis, ncRNA00201 to regulate pathways in SSc pathogenesis and carcinogenesis, H19X potentiating TGF-β-driven extracellular matrix production, and finally PSMB8-AS1 potentiates IFN response. In DM, linc-DGCR6-1 expression was hypothesized to target the USP18 protein, a type 1 IFN-inducible protein that is considered a key regulator of IFN signaling. Additionally, AL136018.1 is suggested to regulate the expression Cathepsin G, which increases the permeability of vascular endothelial cells and the chemotaxis of inflammatory cells in peripheral blood and muscle tissue in DM. Lastly, lnc-MIPOL1-6 and lnc-DDX47-3 in discoid CLE were thought to be associated with the expression of chemokines, which are significant in Th1 mediated disease. In this review, we summarize the key lncRNAs that may drive pathogenesis of these connective tissue diseases and could potentially serve as therapeutic targets in the future.
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Affiliation(s)
- Anastasiya Muntyanu
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
| | - Michelle Le
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
| | - Zainab Ridha
- Faculty of Medicine, Université de Laval, Québec, QC Canada
| | - Elizabeth O’Brien
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
| | - Ivan V. Litvinov
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
| | - Philippe Lefrançois
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
| | - Elena Netchiporouk
- Division Dermatology, McGill University Health Centre, 1650 Cedar Ave, Montreal, QC H3G 1A4 Canada
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187
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Salloum-Asfar S, Abdulla SA, Taha RZ, Thompson IR, Emara MM. Combined Noncoding RNA-mRNA Regulomics Signature in Reprogramming and Pluripotency in iPSCs. Cells 2022; 11:cells11233833. [PMID: 36497092 PMCID: PMC9737797 DOI: 10.3390/cells11233833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Somatic cells are reprogrammed with reprogramming factors to generate induced pluripotent stem cells (iPSCs), offering a promising future for disease modeling and treatment by overcoming the limitations of embryonic stem cells. However, this process remains inefficient since only a small percentage of transfected cells can undergo full reprogramming. Introducing miRNAs, such as miR-294 and miR302/3667, with reprogramming factors, has shown to increase iPSC colony formation. Previously, we identified five transcription factors, GBX2, NANOGP8, SP8, PEG3, and ZIC1, which may boost iPSC generation. In this study, we performed quantitative miRNAome and small RNA-seq sequencing and applied our previously identified transcriptome to identify the potential miRNA-mRNA regulomics and regulatory network of other ncRNAs. From each fibroblast (N = 4), three iPSC clones were examined (N = 12). iPSCs and original fibroblasts expressed miRNA clusters differently and miRNA clusters were compared to mRNA hits. Moreover, miRNA, piRNA, and snoRNAs expression profiles in iPSCs and original fibroblasts were assessed to identify the potential role of ncRNAs in enhancing iPSC generation, pluripotency, and differentiation. Decreased levels of let-7a-5p showed an increase of SP8 as described previously. Remarkably, the targets of identifier miRNAs were grouped into pluripotency canonical pathways, on stemness, cellular development, growth and proliferation, cellular assembly, and organization of iPSCs.
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Affiliation(s)
- Salam Salloum-Asfar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
- Correspondence: (S.S.-A.); (S.A.A.)
| | - Sara A. Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
- Correspondence: (S.S.-A.); (S.A.A.)
| | - Rowaida Z. Taha
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - I. Richard Thompson
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Mohamed M. Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
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188
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Huang H, Zhang S, Wen X, Sadee W, Wang D, Yang S, Li L. Transcription Factors and ncRNAs Associated with CYP3A Expression in Human Liver and Small Intestine Assessed with Weighted Gene Co-Expression Network Analysis. Biomedicines 2022; 10:biomedicines10123061. [PMID: 36551817 PMCID: PMC9775998 DOI: 10.3390/biomedicines10123061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
CYP3A4, CYP3A5, and CYP3A7, which are located in a multigene locus (CYP3A), play crucial roles in drug metabolism. To understand the highly variable hepatic expression of CYP3As, regulatory network analyses have focused on transcription factors (TFs). Since long non-coding RNAs (lncRNAs) likely contribute to such networks, we assessed the regulatory effects of both TFs and lncRNAs on CYP3A expression in the human liver and small intestine, main organs of CYP3A expression. Using weighted gene co-expression network analysis (WGCNA) of GTEx v8 RNA expression data and multiple stepwise regression analysis, we constructed TF-lncRNA-CYP3A co-expression networks. Multiple lncRNAs and TFs displayed robust associations with CYP3A expression that differed between liver and small intestines (LINC02499, HNF4A-AS1, AC027682.6, LOC102724153, and RP11-503C24.6), indicating that lncRNAs contribute to variance in CYP3A expression in both organs. Of these, HNF4A-AS1 had been experimentally demonstrated to affect CYP3A expression. Incorporating ncRNAs into CYP3A expression regulatory network revealed additional candidate TFs associated with CYP3A expression. These results serve as a guide for experimental studies on lncRNA-TF regulation of CYP3A expression in the liver and small intestines.
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Affiliation(s)
- Huina Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Siqi Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaozhen Wen
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Danxin Wang
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Siyao Yang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Liang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Experimental Education and Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Correspondence:
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189
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Pan X, Chen S, Shen R, Liu S, You Y. HOXA11-OS participates in lupus nephritis by targeting miR-124-3p mediating Cyr61 to regulate podocyte autophagy. Mol Med 2022; 28:138. [PMID: 36418932 PMCID: PMC9682779 DOI: 10.1186/s10020-022-00570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The long chain non-coding RNA HOXA11-OS was recently identified. Increasing studies have shown that HOXA11-OS has regulatory effects on genes in gastric cancer, prostate cancer, and various kidney diseases, but research on its role in systemic lupus erythematosus is still lacking. The present study aimed to investigate the role of HOXA11-OS in the regulation of podocyte autophagy in the development of lupus nephritis (LN) and its potential molecular mechanism. METHODS mRNA and protein expression of the target gene (i.e., Cyr61) was detected by quantitative real-time polymerase chain reaction, western blotting, and immunofluorescence. Mouse podocytes were induced using serum immunoglobulin G (IgG) from patients with lupus and their viability was detected using the cell counting kit-8 assay. The interaction of miR-124-3p with HOXA11-OS and Cyr61 was analyzed by double luciferase reporter gene assay. Serum autoantibody levels were detected by enzyme-linked immunosorbent assay. Pathological lesions in the kidney tissue were detected by hematoxylin-eosin and periodate-Schiff staining. The independent samples t-test was used for comparing two groups, and one-way analysis of variance for comparing multiple groups. RESULTS HOXA11-OS was highly expressed in LN tissues, serum, and cells, and the expression of some key autophagy factors and Cyr61 was significantly increased, while miR-124-3p expression was significantly decreased. In vitro, LN-IgG inhibited podocyte activity, increased autophagy and Cyr61 expression, and aggravated podocyte injury in a time- and dose-dependent manner. As a competitive endogenous RNA of miR-124-3p, HOXA11-OS promoted the expression of Cyr61, thus enhancing the autophagy increase induced by LN-IgG and aggravating podocyte injury. Knockdown of HOXA11-OS had the opposite effect. miR-124-3p mimic or Cyr61 knockdown restored the high expression of autophagy factors and Cyr61 induced by HOXA11-OS overexpression and alleviated podocyte injury. Further in vivo experiments showed that injection of sh-HOXA11-OS adeno-associated virus downregulated HOXA11-OS and significantly alleviated renal damage in lupus mice. CONCLUSIONS HOXA11-OS is involved in the occurrence and development of LN by regulating podocyte autophagy through miR-124-3p/Cyr61 sponging, which may provide a good potential therapeutic target for LN.
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Affiliation(s)
- Xiuhong Pan
- grid.460081.bDepartment of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan Road II, Baise, 533000 Guangxi Zhuang Autonomous Region China
| | - Shanshan Chen
- grid.460081.bDepartment of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan Road II, Baise, 533000 Guangxi Zhuang Autonomous Region China
| | - Ruiwen Shen
- grid.460081.bDepartment of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan Road II, Baise, 533000 Guangxi Zhuang Autonomous Region China
| | - Sen Liu
- grid.460081.bDepartment of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, No.18 Zhongshan Road II, Baise, 533000 Guangxi Zhuang Autonomous Region China
| | - Yanwu You
- grid.410652.40000 0004 6003 7358Department of Nephrology, People’s Hospital of Guangxi Zhuang Autonomous Region, No. 6 Taoyuan Road, Qingxiu District, Nanning, 530000 China
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190
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Identification of PAX6 and NFAT4 as the Transcriptional Regulators of the Long Noncoding RNA Mrhl in Neuronal Progenitors. Mol Cell Biol 2022; 42:e0003622. [PMID: 36317923 PMCID: PMC9670966 DOI: 10.1128/mcb.00036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The long noncoding RNA (lncRNA) Mrhl has been shown to be involved in coordinating meiotic commitment of mouse spermatogonial progenitors and differentiation events in mouse embryonic stem cells. Here, we characterized the interplay of Mrhl with lineage-specific transcription factors during mouse neuronal lineage development. Our results demonstrate that Mrhl is expressed in the neuronal progenitor populations in mouse embryonic brains and in retinoic acid-derived radial-glia-like neuronal progenitor cells. Depletion of Mrhl leads to early differentiation of neuronal progenitors to a more committed state. A master transcription factor, PAX6, directly binds to the Mrhl promoter at a major site in the distal promoter, located at 2.9 kb upstream of the transcription start site (TSS) of Mrhl. Furthermore, NFAT4 occupies the Mrhl-proximal promoter at two sites, at 437 base pairs (bp) and 143 bp upstream of the TSS. Independent knockdown studies for PAX6 and NFAT4 confirm that they regulate Mrhl expression in neuronal progenitors. We also show that PAX6 and NFAT4 associate with each other in the same chromatin complex. NFAT4 occupies the Mrhl promoter in PAX6-bound chromatin, implying possible coregulation of Mrhl. Our studies are crucial for understanding how lncRNAs are regulated by major lineage-specific transcription factors, in order to define specific development and differentiation events.
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191
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RNA-Mediated Regulation of Meiosis in Budding Yeast. Noncoding RNA 2022; 8:ncrna8060077. [PMID: 36412912 PMCID: PMC9680404 DOI: 10.3390/ncrna8060077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cells change their physiological state in response to environmental cues. In the absence of nutrients, unicellular fungi such as budding yeast exit mitotic proliferation and enter the meiotic cycle, leading to the production of haploid cells that are encased within spore walls. These cell state transitions are orchestrated in a developmentally coordinated manner. Execution of the meiotic cell cycle program in budding yeast, Saccharomyces cerevisiae, is regulated by the key transcription factor, Ime1. Recent developments have uncovered the role of non-coding RNA in the regulation of Ime1 and meiosis. In this review, we summarize the role of ncRNA-mediated and RNA homeostasis-based processes in the regulation of meiosis in Saccharomyces cerevisiae.
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192
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Cordeiro D, Canhoto J, Correia S. Regulatory non-coding RNAs: Emerging roles during plant cell reprogramming and in vitro regeneration. FRONTIERS IN PLANT SCIENCE 2022; 13:1049631. [PMID: 36438127 PMCID: PMC9684189 DOI: 10.3389/fpls.2022.1049631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Plant regeneration is a well-known capacity of plants occurring either in vivo or in vitro. This potential is the basis for plant micropropagation and genetic transformation as well as a useful system to analyse different aspects of plant development. Recent studies have proven that RNA species with no protein-coding capacity are key regulators of cellular function and essential for cell reprogramming. In this review, the current knowledge on the role of several ncRNAs in plant regeneration processes is summarized, with a focus on cell fate reprogramming. Moreover, the involvement/impact of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and small-interfering RNAs (siRNAs) in the regulatory networks of cell dedifferentiation, proliferation and differentiation is also analysed. A deeper understanding of plant ncRNAs in somatic cell reprogramming will allow a better modulation of in vitro regeneration processes such as organogenesis and somatic embryogenesis.
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193
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Elkommos-Zakhary M, Rajesh N, Beljanski V. Exosome RNA Sequencing as a Tool in the Search for Cancer Biomarkers. Noncoding RNA 2022; 8:ncrna8060075. [PMID: 36412910 PMCID: PMC9680254 DOI: 10.3390/ncrna8060075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
Numerous noninvasive methods are currently being used to determine biomarkers for diseases such as cancer. However, these methods are not always precise and reliable. Thus, there is an unmet need for better diagnostic and prognostic biomarkers that will be used to diagnose cancer in early, more treatable stages of the disease. Exosomes are extracellular vesicles of endocytic origin released by the majority of cells. Exosomes contain and transport nucleic acids, proteins, growth factors, and cytokines from their parent cells to surrounding or even distant cells via circulation in biofluids. Exosomes have attracted the interest of researchers, as recent data indicate that exosome content may be indicative of disease stages and may contribute to disease progression via exosome-mediated extracellular communication. Therefore, the contents of these vesicles are being investigated as possible biomarkers for disease diagnosis and prognosis. The functions of exosomes and their contents in disease development are becoming clearer as isolation and analytical methods, such as RNA sequencing, advance. In this review, we discuss current advances and challenges in exosomal content analyses with emphasis on information that can be generated using RNA sequencing. We also discuss how the RNA sequencing of exosomes may be used to discover novel biomarkers for the detection of different stages for various cancers using specific microRNAs that were found to be differentially expressed between healthy controls and cancer-diagnosed subjects.
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Affiliation(s)
- Marina Elkommos-Zakhary
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33314, USA
| | - Neeraja Rajesh
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33314, USA
| | - Vladimir Beljanski
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33314, USA
- Cell Therapy Institute, Nova Southeastern University, Davie, FL 33314, USA
- Correspondence:
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194
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Zhu M, Xiang H, Peng Z, Ma Z, Shen J, Wang T, Chen L, Cao D, Gu S, Wang M, Cao J. Silencing the expression of lncRNA SNHG15 may be a novel therapeutic approach in human breast cancer through regulating miR-345-5p. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1173. [PMID: 36467335 PMCID: PMC9708471 DOI: 10.21037/atm-22-5275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/07/2022] [Indexed: 12/01/2023]
Abstract
BACKGROUND Long noncoding RNA (lncRNA) short nucleolar RNA host gene 15 (SNHG15) has been found to have an oncogenic function in numerous malignancies. Nevertheless, the biological function and regulatory mechanisms of SNHG15 in breast cancer have not been fully elucidated. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of SNHG15 and in MDA-MB-231 breast cancer cells. The expression of SNHG15 was silenced using small interfering RNA (siRNA) technology. The proliferation and migration of the cells were examined by colony formation assays, cell counting kit 8 (CCK-8) assays, and transwell assays. For the zebrafish xenograft injection experiments, cultured cells labelled with the fluorescent dye CM-DiI were injected into the perivitelline space of the larvae. RESULTS This present study revealed that the expression of lncRNA SNHG15 (lnc-SNHG15) was significantly upregulated in breast cancer cells, and its overexpression was associated with the tumor. The relative expression of lnc-SNHG15 could be downregulated using siRNAs, and silencing lnc-SNHG15 inhibited the proliferation and the migration of MDA-MB-231 cells. In vivo experiments using the zebrafish xenograft model showed similar results. Mechanistically, the knockdown effect of lnc-SNHG15 could be restored by inhibiting the expression of the miR-345-5p, confirming the negative regulation between lnc-SNHG15 and miR-345-5p. Interestingly, cisplatin treatment combined with SNHG15 knockdown effectively inhibited MDA-MB-231 cell proliferation and migration in the zebrafish xenograft compared to negative controls. CONCLUSIONS In conclusion, lnc-SNHG15 knockdown increased miR-345-5p expression and negated cisplatin resistance in breast cancer cells, and thus, lnc-SNHG15 may be a potential novel target for breast cancer therapy.
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Affiliation(s)
- Minshu Zhu
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
| | - Haifei Xiang
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
| | - Zheng Peng
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Zhaosheng Ma
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
| | - Jianfei Shen
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Tingting Wang
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Lingyang Chen
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Donghang Cao
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Shanye Gu
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Mingcang Wang
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
| | - Jianbin Cao
- Department of Anesthesiology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Department of Surgical Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
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195
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Pan Z, Sun W, Chen Y, Tang H, Lin W, Chen J, Chen C. Extracellular Vesicles in Tissue Engineering: Biology and Engineered Strategy. Adv Healthc Mater 2022; 11:e2201384. [PMID: 36053562 DOI: 10.1002/adhm.202201384] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/07/2022] [Indexed: 01/28/2023]
Abstract
Extracellular vesicles (EVs), acting as an important ingredient of intercellular communication through paracrine actions, have gained tremendous attention in the field of tissue engineering (TE). Moreover, these nanosized extracellular particles (30-140 nm) can be incorporated into biomaterials according to different principles to facilitate signal delivery in various regenerative processes directly or indirectly. Bioactive biomaterials as the carrier will extend the retention time and realize the controlled release of EVs, which further enhance their therapeutic efficiency in tissue regeneration. Herein, the basic biological characteristics of EVs are first introduced, and then their outstanding performance in exerting direct impacts on target cells in tissue regeneration as well as indirect effects on promoting angiogenesis and regulating the immune environment, due to specific functional components of EVs (nucleic acid, protein, lipid, etc.), is emphasized. Furthermore, different design ideas for suitable EV-loaded biomaterials are also demonstrated. In the end, this review also highlights the engineered strategies, which aim at solving the problems related to natural EVs such as highly heterogeneous functions, inadequate tissue targeting capabilities, insufficient yield and scalability, etc., thus promoting the therapeutic pertinence and clinical potential of EV-based approaches in TE.
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Affiliation(s)
- Ziyin Pan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Weiyan Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Yi Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Hai Tang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Weikang Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School Of Medicine, Shanghai, 200092, China.,Shanghai Engineering Research Center of Lung Transplantation, Shanghai, 200433, China
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196
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Exploration of Tools for the Interpretation of Human Non-Coding Variants. Int J Mol Sci 2022; 23:ijms232112977. [PMID: 36361767 PMCID: PMC9654743 DOI: 10.3390/ijms232112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.
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197
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Identification of Differentially Expressed Intronic Transcripts in Osteosarcoma. Noncoding RNA 2022; 8:ncrna8060073. [PMID: 36412907 PMCID: PMC9680297 DOI: 10.3390/ncrna8060073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022] Open
Abstract
Over the past decade; the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed that they play a major role in the development of various diseases; including cancer. Intronic transcripts are one of the most fascinating lncRNAs that are located within intron regions of protein-coding genes, which have the advantage of encoding micropeptides. There have been several studies looking at intronic transcript expression profiles in cancer; but almost none in osteosarcoma. To overcome this problem; we have investigated differentially expressed intronic transcripts between osteosarcoma and normal bone tissues. The results highlighted that NRG1-IT1; FGF14-IT1; and HAO2-IT1 were downregulated; whereas ER3-IT1; SND1-IT1; ANKRD44-IT1; AGAP1-IT1; DIP2A-IT1; LMO7DN-IT1; SLIT2-IT1; RNF216-IT1; and TCF7L1-IT1 were upregulated in osteosarcoma tissues compared to normal bone tissues. Furthermore, we identified if the transcripts encode micropeptides and the transcripts' locations in a cell.
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198
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Wang K, Cheng Y, Guo T, Guo X, Zhang H, Ma X, Pan Y, Kebreab E, Wang D, Lyu L. Analyzing the interactions of mRNAs, miRNAs and lncRNAs to predict ceRNA networks in bovine cystic follicular granulosa cells. Front Vet Sci 2022; 9:1028867. [PMID: 36311668 PMCID: PMC9606814 DOI: 10.3389/fvets.2022.1028867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022] Open
Abstract
Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanism of bovine follicular cysts. Ovarian cyst has always been an intractable scientific problem and has led to considerable economic losses to bovine breeding industry. However, its pathogenesis and molecular mechanisms are still not well understood. Here, this study aimed to investigate the role of non-coding RNAs (ncRNAs) and the ceRNA networks in bovine follicular cyst. Whole transcriptome sequencing of bovine follicular granulosa cells (GCs) was conducted to obtain the expression profiles of mRNAs, lncRNAs and miRNAs. The results for the identified expressions of 8,003 mRNAs, 579 lncRNAs and 205 miRNAs were often altered between cystic and normal follicular GCs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed on these differentially expressed mRNAs. Furthermore, the ceRNA network combining mRNAs, miRNAs, and lncRNAs using several bioinformatics methods based on co-expression analysis between the differentially expressed RNAs was conducted. Finally, the lncRNA NONBTAT027373.1-miR-664b-HSD17B7 pathway was verified by dual-luciferase reporting assay and RNA binding protein immunoprecipitation (RIP) assay. LncRNA NONBTAT027373.1 sponged miR-664b in GCs and prevented miR-664b from binding to the HSD17B7 3′-UTR. These results indicated that genes and lncRNAs related to steroid hormone synthesis and energy metabolism could play important roles in the formation of bovine cystic follicles through the ceRNA mechanism and represent candidate targets for further research. This can be used as a practical guideline for promoting healthy and highly efficient development in the bovine industry.
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Affiliation(s)
- Kai Wang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Ying Cheng
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Tong Guo
- Department of Animal Husbandry and Veterinary Medicine, Beijing Vocational College of Agriculture, Beijing, China
| | - Xiangqian Guo
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Hongzhi Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Ma
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Ermias Kebreab
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Dong Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,Dong Wang
| | - Lihua Lyu
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China,*Correspondence: Lihua Lyu
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199
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Cheng Y, Wu X, Xia Y, Liu W, Wang P. The role of lncRNAs in regulation of DKD and diabetes-related cancer. Front Oncol 2022; 12:1035487. [PMID: 36313695 PMCID: PMC9606714 DOI: 10.3389/fonc.2022.1035487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
Diabetes mellitus often results in several complications, such as diabetic kidney disease (DKD) and end-stage renal diseases (ESRDs). Cancer patients often have the dysregulated glucose metabolism. Abnormal glucose metabolism can enhance the tumor malignant progression. Recently, lncRNAs have been reported to regulate the key proteins and signaling pathways in DKD development and progression and in cancer patients with diabetes. In this review article, we elaborate the evidence to support the function of lncRNAs in development of DKD and diabetes-associated cancer. Moreover, we envisage that lncRNAs could be diagnosis and prognosis biomarkers for DKD and cancer patients with diabetes. Furthermore, we delineated that targeting lncRNAs might be an alternative approach for treating DKD and cancer with dysregulated glucose metabolism.
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Affiliation(s)
- Yawei Cheng
- Department of Disease Prevention, Hainan Province Hospital of Traditional Chinese Medicine, Haikou, China
- Hainan Clinical Research Center for Preventive Treatment of Diseases, Haikou, China
- *Correspondence: Yawei Cheng, ; Peter Wang,
| | - Xiaowen Wu
- Department of Disease Prevention, Hainan Province Hospital of Traditional Chinese Medicine, Haikou, China
| | - Yujie Xia
- Department of Food Science and Technology Centers, National University of Singapore (Suzhou) Research Institute, Suzhou, China
| | - Wenjun Liu
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, China
| | - Peter Wang
- Department of Research and Development, Zhejiang Zhongwei Medical Research Center, Hangzhou, China
- *Correspondence: Yawei Cheng, ; Peter Wang,
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200
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Roles of Chromatin Remodelling and Molecular Heterogeneity in Therapy Resistance in Glioblastoma. Cancers (Basel) 2022; 14:cancers14194942. [PMID: 36230865 PMCID: PMC9563350 DOI: 10.3390/cancers14194942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary We review the role of chromatin and epigenetic dysregulation in therapy resistance in glioblastoma. We discuss how epigenetic and genetic forces may cooperate to programme functional cell states that are inherently resistant to therapy. Targeting epigenetic factors that are dysregulated in this malignancy could, therefore, improve clinical outcomes for patients. We highlight some preclinical and clinical compounds that were tested or are currently being explored for glioblastoma. Lastly, we present our thoughts on the requirements for the development of next-generation epigenetic therapies. Abstract Cancer stem cells (CSCs) represent a therapy-resistant reservoir in glioblastoma (GBM). It is now becoming clear that epigenetic and chromatin remodelling programs link the stemlike behaviour of CSCs to their treatment resistance. New evidence indicates that the epigenome of GBM cells is shaped by intrinsic and extrinsic factors, including their genetic makeup, their interactions and communication with other neoplastic and non-neoplastic cells, including immune cells, and their metabolic niche. In this review, we explore how all these factors contribute to epigenomic heterogeneity in a tumour and the selection of therapy-resistant cells. Lastly, we discuss current and emerging experimental platforms aimed at precisely understanding the epigenetic mechanisms of therapy resistance that ultimately lead to tumour relapse. Given the growing arsenal of drugs that target epigenetic enzymes, our review addresses promising preclinical and clinical applications of epidrugs to treat GBM, and possible mechanisms of resistance that need to be overcome.
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