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Afrashteh Nour M, Ghorbaninezhad F, Asadzadeh Z, Baghbanzadeh A, Hassanian H, Leone P, Jafarlou M, Alizadeh N, Racanelli V, Baradaran B. The emerging role of noncoding RNAs in systemic lupus erythematosus: new insights into the master regulators of disease pathogenesis. Ther Adv Chronic Dis 2023; 14:20406223231153572. [PMID: 37035097 PMCID: PMC10074641 DOI: 10.1177/20406223231153572] [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: 06/18/2022] [Accepted: 01/11/2023] [Indexed: 04/11/2023] Open
Abstract
Auto-immune diseases are a form of chronic disorders in which the immune system destroys the body's cells due to a loss of tolerance to self-antigens. Systemic lupus erythematosus (SLE), identified by the production of autoantibodies in different body parts, is one of the most well-known examples of these diseases. Although the etiology of SLE is unclear, the disease's progression may be affected by genetic and environmental factors. As studies in twins provide adequate evidence for genetic involvement in the SLE, other phenomena such as metallization, histone modifications, and alterations in the expression of noncoding RNAs (ncRNAs) also indicate the involvement of epigenetic factors in this disease. Among all the epigenetic alterations, ncRNAs appear to have the most crucial contribution to the pathogenesis of SLE. The ncRNAs' length and size are divided into three main classes: micro RNAs, long noncoding RNAs (LncRNA), and circular RNAs (circRNAs). Accumulating evidence suggests that dysregulations in these ncRNAs contributed to the pathogenesis of SLE. Hence, clarifying the function of these groups of ncRNAs in the pathophysiology of SLE provides a deeper understanding of the disease. It also opens up new opportunities to develop targeted therapies for this disease.
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Affiliation(s)
- Mina Afrashteh Nour
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
| | - Farid Ghorbaninezhad
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine,
Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
| | - Hamidreza Hassanian
- Student Research Committee, Tabriz University
of Medical Sciences, Tabriz, Iran
| | - Patrizia Leone
- Department of Interdisciplinary Medicine,
University of Bari ‘Aldo Moro’, Bari, Italy
| | - Mahdi Jafarlou
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
| | - Nazila Alizadeh
- Immunology Research Center, Tabriz University
of Medical Sciences, Tabriz, Iran
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102
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Lee SJ, Kim JM, Lee ES, Park KY, Kim HR. Relationship Between MicroRNA Signature and Arterial Stiffness in Patients With Ischemic Stroke. J Clin Neurol 2023; 19:28-35. [PMID: 36606643 PMCID: PMC9833874 DOI: 10.3988/jcn.2023.19.1.28] [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: 11/02/2021] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND AND PURPOSE We investigated whether circulating microRNAs (miRNAs) is associated with arterial stiffness in patients with acute ischemic stroke. METHODS We recruited patients with acute ischemic stroke who were admitted to a university hospital stroke center and underwent carotid-femoral pulse wave velocity (cfPWV) measurement using SphygmoCor (AtCor Medical, Sydney, Australia) and brachial-ankle PWV using a volume-plethysmography device (VP-1000, Omron Colin, Komaki, Japan). Circulating miRNAs were measured in venous blood samples stored in EDTA. We selected five miRNAs (miR-17, miR-93, miR-450, miR-629, and let-7i) related to atherosclerosis based on a literature review. Pearson's correlation analysis was applied to the correlations between miRNAs and arterial stiffness parameters. Finally, multivariable linear regression analysis was performed to identify the independent factors for cfPWV. RESULTS This study included 70 patients (age=71.1±10.3 years [mean±SD], 29 females). The expression levels of miR-93 (r=-0.27, p=0.049) and let-7i (r=-0.27, p=0.039) were inversely correlated with cfPWV. Multivariable linear regression analysis including age, hypertension, and estimated glomerular filtration rate showed that let-7i was independently related with cfPWV (standardized coefficient=-0.262, p=0.036). Correlation analysis indicated that let-7i was positively associated with visceral muscle Hounsfield units on computed tomography (r=0.264, p=0.043). CONCLUSIONS The expression level of let-7i was independently related to arterial stiffness in patients with cerebral infarction, suggesting that it plays a pathophysiological role in atherosclerosis.
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Affiliation(s)
- Sang-Jin Lee
- Department of Neurology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeong-Min Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Sun Lee
- Department of Laboratory Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Kwang-Yeol Park
- Department of Neurology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Hye Ryoun Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Sarangi R, Mishra S, Das S, Mishra A. Nonalcoholic Fatty Liver Disease and MicroRNAs: A Weighty Consideration. BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL (BBRJ) 2023. [DOI: 10.4103/bbrj.bbrj_319_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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104
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Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
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Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
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105
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MicroRNA-155 is a main part of proinflammatory puzzle during severe coronavirus disease 2019 (COVID-19). Allergol Immunopathol (Madr) 2023; 51:115-119. [PMID: 36916095 DOI: 10.15586/aei.v51i2.698] [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: 06/12/2022] [Accepted: 08/28/2022] [Indexed: 03/08/2023]
Abstract
Genetic and epigenetic parameters play critical roles in determining the outcomes of the severe acute respiratory syndrome coronavirus type 19 (SARS-CoV-2) infection. MicroRNAs (miRNAs) are an important part of the epigenetic factors that regulate several functions of the immune cells and also viruses. Accordingly, the molecules can regulate expression of the immune cell proteins and virus in the host cells. Among the miRNAs, miRNA-155 (miR-155) is well-studied in patients suffering from severe coronavirus disease 2019 (COVID-19). It has been reported that the SARS-CoV-2 infected patients may be directed to induce a cytokine storm or severe proinflammatory responses. This review article discusses the pathological roles of miR-155 during COVID-19 infection.
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106
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Sun Y, Chen L, Xu T, Gou B, Mai JW, Luo DX, Xin WJ, Wu JY. MiR-672-5p-Mediated Upregulation of REEP6 in Spinal Dorsal Horn Participates in Bortezomib-Induced Neuropathic Pain in Rats. Neurochem Res 2023; 48:229-237. [PMID: 36064821 DOI: 10.1007/s11064-022-03741-7] [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: 04/25/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 01/07/2023]
Abstract
Evidence shows that miRNAs are deeply involved in nervous system diseases, but whether miRNAs contribute to the bortezomib (BTZ)-induced neuropathic pain remains unclear. We aimed to investigate whether miRNAs contribute to bortezomib (BTZ)-induced neuropathic pain and explore the related downstream cascades. The level of miRNAs in the spinal dorsal horn was explored using miRNA microarray and PCR. MiR-672-5p was significantly downregulated in dorsal horn neurons in the rats with BTZ treatment. Intrathecal injection of miR-672-5p agomir blunted the increase of the amplitude and frequency of sEPSCs in dorsal horn neurons and mechanical allodynia induced by BTZ. In addition, the knockdown of miR-672-5p by intrathecal injection of antagomir increased the amplitude and frequency of sEPSCs in dorsal horn neurons and decreased the mechanical withdrawal threshold in naïve rats. Furthermore, silico analysis and the data from subsequent assays indicated that REEP6, a potential miR-672-5p-regulating molecule, was increased in the spinal dorsal horn of rats with BTZ-induced neuropathic pain. Blocking REEP6 alleviated the mechanical pain behavior induced by BTZ, whereas overexpressing REEP6 induced pain hypersensitivity in naïve rats. Importantly, we further found that miR-672-5p was expressed in the REEP6-positive cells, and overexpression or knockdown of miR-672-5p reversely regulated the REEP6 expression. Bioinformatics analysis and double-luciferase reporter assay showed the existence of interaction sites between REEP6 mRNA and miR-672-5p. Overall, our study demonstrated that miR-672-5p directly regulated the expression of REEP6, which participated in the neuronal hyperexcitability in the spinal dorsal horn and neuropathic pain following BTZ treatment. This signaling pathway may potentially serve as a novel therapeutic avenue for chemotherapeutic-induced mechanical hypersensitivity.
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Affiliation(s)
- Yang Sun
- Graduate Department, Department of Sport Medicine, Xi'an Physical Education University, Xi'an, 710068, Shanxi, China.,Department of Rehabilitation Medicine, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shanxi, China
| | - Li Chen
- Zhongshan School of Medicine and Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, 74 Zhongshan Rd. 2, Guangzhou, 510080, China
| | - Ting Xu
- Zhongshan School of Medicine and Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, 74 Zhongshan Rd. 2, Guangzhou, 510080, China
| | - Bo Gou
- Graduate Department, Department of Sport Medicine, Xi'an Physical Education University, Xi'an, 710068, Shanxi, China
| | - Jing-Wen Mai
- Department of Anesthesiology, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - De-Xing Luo
- Department of Anesthesiology, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Wen-Jun Xin
- Zhongshan School of Medicine and Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, 74 Zhongshan Rd. 2, Guangzhou, 510080, China
| | - Jia-Yan Wu
- Zhongshan School of Medicine and Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-Sen University, 74 Zhongshan Rd. 2, Guangzhou, 510080, China.
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107
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Sato K, Takayama KI, Inoue S. Role of piRNA biogenesis and its neuronal function in the development of neurodegenerative diseases. Front Aging Neurosci 2023; 15:1157818. [PMID: 37207075 PMCID: PMC10191213 DOI: 10.3389/fnagi.2023.1157818] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/21/2023] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are caused by neuronal loss and dysfunction. Despite remarkable improvements in our understanding of these pathogeneses, serious worldwide problems with significant public health burdens are remained. Therefore, new efficient diagnostic and therapeutic strategies are urgently required. PIWI-interacting RNAs (piRNAs) are a major class of small non-coding RNAs that silence gene expression through transcriptional and post-transcriptional processes. Recent studies have demonstrated that piRNAs, originally found in the germ line, are also produced in non-gonadal somatic cells, including neurons, and further revealed the emerging roles of piRNAs, including their roles in neurodevelopment, aging, and neurodegenerative diseases. In this review, we aimed to summarize the current knowledge regarding the piRNA roles in the pathophysiology of neurodegenerative diseases. In this context, we first reviewed on recent updates on neuronal piRNA functions, including biogenesis, axon regeneration, behavior, and memory formation, in humans and mice. We also discuss the aberrant expression and dysregulation of neuronal piRNAs in neurodegenerative diseases, such as AD, PD, and ALS. Moreover, we review pioneering preclinical studies on piRNAs as biomarkers and therapeutic targets. Elucidation of the mechanisms underlying piRNA biogenesis and their functions in the brain would provide new perspectives for the clinical diagnosis and treatment of AD and various neurodegenerative diseases.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia (IRIDE), Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
| | - Ken-ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
- *Correspondence: Satoshi Inoue,
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Naringenin Prevents Oxidative Stress and Inflammation in LPS-Induced Liver Injury through the Regulation of LncRNA-mRNA in Male Mice. Molecules 2022; 28:molecules28010198. [PMID: 36615393 PMCID: PMC9821796 DOI: 10.3390/molecules28010198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Inflammation accompanies hepatic dysfunction resulting from tissue oxidative damage. Naringenin (Nar), a natural flavanone, has known antioxidant and anti-inflammatory activities, but its mechanism of action in the regulation of liver dysfunction requires further investigation. In this study, the role of naringenin in lipopolysaccharide (LPS)-induced hepatic oxidative stress and inflammation was explored, as well as its mechanism by transcriptome sequencing. The results indicated that compared with the LPS group, Nar treatment caused a significant increase in the mRNA levels of antioxidant factors glutamate-cysteine ligase catalytic subunit (GCLC) and glutamate-cysteine ligase modifier subunit (GCLM), yet the expression of related inflammatory factors (MCP1, TNFα, IL-1β and IL-6) showed less of an increase. RNA sequencing identified 36 differentially expressed lncRNAs and 603 differentially expressed mRNAs. KEGG enrichment analysis indicated that oxidative stress and inflammation pathways are meticulously linked with naringenin treatment. The Co-lncRNA-mRNA network was also constructed. Tissue expression profiles showed that lncRNA played a higher role in the liver. Subsequently, expression levels of inflammatory factors indicated that lncRNAs and target mRNAs were significantly reduced after naringenin treatment in mouse liver AML12 cells and obese mouse. These results suggest that naringenin helps to prevent liver dysfunction through the regulation of lncRNA-mRNA axis to reduce oxidative stress and inflammatory factors.
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109
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MDM4: What do we know about the association between its polymorphisms and cancer? MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 40:61. [PMID: 36566308 DOI: 10.1007/s12032-022-01929-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
MDM4 is an important p53-negative regulator, consequently, it is involved in cell proliferation, DNA repair, and apoptosis regulation. MDM4 overexpression and amplification are described to lead to cancer formation, metastasis, and poor disease prognosis. Several MDM4 SNPs are in non-coding regions, and some affect the MDM4 regulation by disrupting the micro RNA binding site in 3'UTR (untranslated region). Here, we gathered several association studies with different MDM4 SNPs and populations to understand the relationship between its SNPs and solid tumor risk. Many studies failed to replicate their results regarding different populations, cancer types, and risk genotypes, leading to conflicting conclusions. We suggested that distinct haplotype patterns in different populations might affect the association between MDM4 SNPs and cancer risk. Thus, we propose to investigate some linkage SNPs in specific haplotypes to provide informative MDM4 markers for association studies with cancer.
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110
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Wang L, Shui X, Zhang M, Mei Y, Xia Y, Lan G, Hu L, Gan CL, Tian Y, Li R, Gu X, Zhang T, Chen D, Lee TH. MiR-191-5p Attenuates Tau Phosphorylation, Aβ Generation, and Neuronal Cell Death by Regulating Death-Associated Protein Kinase 1. ACS Chem Neurosci 2022; 13:3554-3566. [PMID: 36454178 DOI: 10.1021/acschemneuro.2c00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Dysregulation of microRNAs has been implicated in diverse diseases, including Alzheimer's disease (AD). MiR-191-5p in plasma/serum has been identified as a novel and promising noninvasive diagnostic biomarker for AD. However, whether miR-191-5p is involved in AD pathogenesis is largely unknown, and its levels in human AD brains are undetermined. Herein, we demonstrated that miR-191-5p downregulated tau phosphorylation at multiple AD-related sites and promoted neurite outgrowth using immunoblotting, immunofluorescence, and neurite outgrowth assays. Moreover, immunoblotting and enzyme-linked immunosorbent assays indicated that miR-191-5p decreased amyloid precursor protein phosphorylation levels and beta-amyloid (Aβ) generation. Furthermore, miR-191-5p reduced ceramide-induced neuronal cell death analyzed by trypan blue staining, the in situ cell death detection kit, and Annexin V-FITC/PI flow cytometry. Next, we verified that death-associated protein kinase 1 (DAPK1) was a direct target of miR-191-5p through the dual luciferase reporter assay and confirmed that the effects of miR-191-5p were antagonized by restoration of DAPK1 expression. Finally, the hippocampal miR-191-5p level was found to be decreased in humans with AD compared with controls and was inversely correlated with the DAPK1 expression level. Collectively, these findings suggest that miR-191-5p might exert inhibitory effects on tau phosphorylation, Aβ secretion, and neuronal cell death by directly targeting DAPK1, providing an attractive therapeutic option for AD.
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Affiliation(s)
- Long Wang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Xindong Shui
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Mi Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Yingxue Mei
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Yongfang Xia
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Guihua Lan
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Li Hu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Chen-Ling Gan
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Yuan Tian
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Ruomeng Li
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Xi Gu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Dongmei Chen
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute of Basic Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian350122, China
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Serum microRNAs as new criteria for referral to early palliative care services in treatment-naïve advanced cancer patients. Oncotarget 2022; 13:1341-1349. [PMID: 36528878 PMCID: PMC9760266 DOI: 10.18632/oncotarget.28327] [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] [Indexed: 12/23/2022] Open
Abstract
A major obstacle to the implementation of early palliative care (EPC) is the lack of objective criteria for referral to EPC. Circulating microRNAs (miRNAs) have been recognized as promising biomarkers. The present study investigated objective definitions for referral to EPC using microRNA. A total of 178 serum samples were obtained from patients with lung, gastrointestinal, colorectal, bile duct, pancreas and bladder cancers who were treatment-naïve and received chemotherapy between January 2011 and December 2013 at National Cancer Center Hospital East. We investigated expression levels of miRNAs using microarrays. The primary outcome was prediction of admission to a palliative care unit ≤6 months after first visit. Diagnostic models using clinical characteristics, miRNAs and combinations of both were constructed. The miRNA models were constructed using 6 miRNA levels. The best areas under the receiver operating characteristic curve (AUCs) of the clinical model was 0.741, while the average AUCs of miRNA-based models and combination models were 0.769 and 0.806, respectively. Combination models showed higher AUCs than the clinical model (p < 0.023). The present combination models might offer new objective definitions for referral to EPC and thus contribute to real-world implementation of EPC.
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112
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Symeonidis A, Chatzilygeroudi T, Chondrou V, Sgourou A. Contingent Synergistic Interactions between Non-Coding RNAs and DNA-Modifying Enzymes in Myelodysplastic Syndromes. Int J Mol Sci 2022; 23:ijms232416069. [PMID: 36555712 PMCID: PMC9785516 DOI: 10.3390/ijms232416069] [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: 11/21/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell disorders with maturation and differentiation defects exhibiting morphological dysplasia in one or more hematopoietic cell lineages. They are associated with peripheral blood cytopenias and by increased risk for progression into acute myelogenous leukemia. Among their multifactorial pathogenesis, age-related epigenetic instability and the error-rate DNA methylation maintenance have been recognized as critical factors for both the initial steps of their pathogenesis and for disease progression. Although lower-risk MDS is associated with an inflammatory bone marrow microenvironment, higher-risk disease is delineated by immunosuppression and clonal expansion. "Epigenetics" is a multidimensional level of gene regulation that determines the specific gene networks expressed in tissues under physiological conditions and guides appropriate chromatin rearrangements upon influence of environmental stimulation. Regulation of this level consists of biochemical modifications in amino acid residues of the histone proteins' N-terminal tails and their concomitant effects on chromatin structure, DNA methylation patterns in CpG dinucleotides and the tissue-specific non-coding RNAs repertoire, which are directed against various gene targets. The role of epigenetic modifications is widely recognized as pivotal both in gene expression control and differential molecular response to drug therapies in humans. Insights to the potential of synergistic cooperations of epigenetic mechanisms provide new avenues for treatment development to comfort human diseases with a known epigenetic shift, such as MDS. Hypomethylating agents (HMAs), such as epigenetic modulating drugs, have been widely used in the past years as first line treatment for elderly higher-risk MDS patients; however, just half of them respond to therapy and are benefited. Rational outcome predictors following epigenetic therapy in MDS and biomarkers associated with disease relapse are of high importance to improve our efforts in developing patient-tailored clinical approaches.
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Affiliation(s)
- Argiris Symeonidis
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
- Medical School University of Patras, University Campus, 26500 Patras, Greece
| | - Theodora Chatzilygeroudi
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Correspondence:
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Quévillon Huberdeau M, Shah VN, Nahar S, Neumeier J, Houle F, Bruckmann A, Gypas F, Nakanishi K, Großhans H, Meister G, Simard MJ. A specific type of Argonaute phosphorylation regulates binding to microRNAs during C. elegans development. Cell Rep 2022; 41:111822. [PMID: 36516777 PMCID: PMC10436268 DOI: 10.1016/j.celrep.2022.111822] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/22/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Argonaute proteins are at the core of the microRNA-mediated gene silencing pathway essential for animals. In C. elegans, the microRNA-specific Argonautes ALG-1 and ALG-2 regulate multiple processes required for proper animal developmental timing and viability. Here we identified a phosphorylation site on ALG-1 that modulates microRNA association. Mutating ALG-1 serine 642 into a phospho-mimicking residue impairs microRNA binding and causes embryonic lethality and post-embryonic phenotypes that are consistent with alteration of microRNA functions. Monitoring microRNA levels in alg-1 phosphorylation mutant animals shows that microRNA passenger strands increase in abundance but are not preferentially loaded into ALG-1, indicating that the miRNA binding defects could lead to microRNA duplex accumulation. Our genetic and biochemical experiments support protein kinase A (PKA) KIN-1 as the putative kinase that phosphorylates ALG-1 serine 642. Our data indicate that PKA triggers ALG-1 phosphorylation to regulate its microRNA association during C. elegans development.
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Affiliation(s)
- Miguel Quévillon Huberdeau
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Vivek Nilesh Shah
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Smita Nahar
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - François Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Foivos Gypas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, Columbus, OH 43210, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4056 Basel, Switzerland
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada.
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Pang XM, Peng ZY, Zheng X, Shi JJ, Zhou BC. Analysis of research hotspots in COVID-19 genomics based on citespace software: Bibliometric analysis. Front Cell Infect Microbiol 2022; 12:1060031. [PMID: 36579345 PMCID: PMC9791043 DOI: 10.3389/fcimb.2022.1060031] [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: 10/07/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction To analyze the current state, hotspots, and cutting-edge trends of genomics research on the outbreak of Corona Virus Disease 2019 (COVID-19) from 2019 to the present (March 2022). Methods Statistical and visual analysis of COVID-19 genomics results published in the 2019-2022 Web of Science Core Collection Database (WOSCC) was performed using CiteSpace software, including data on countries, institutions, authors, journals, co-citations, keywords, etc. Results A total of 9133 English literature were included. The number of publications has significantly increased in 2021, and it is expected that this upward trend will last into the future. The research hotspots of COVID-19 revolve around quarantine, biological management, angiotensin-converting enzyme-2, RNA-dependent RNA polymerase, etc. Research frontiers and trends focus on molecular docking, messenger RNA, functional receptor, etc. Conclusion The last two years have seen a significant increase in research interest in the field of novel coronavirus pneumonia genomics.
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Affiliation(s)
- Xue meng Pang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhao yun Peng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China,The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China,*Correspondence: Zhao yun Peng, ; Xin Zheng,
| | - Xin Zheng
- Qingdao Hospital of Traditional Chinese Medicine (Qingdao Hiser Hospital), Qingdao, Shandong, China,*Correspondence: Zhao yun Peng, ; Xin Zheng,
| | - Jing jing Shi
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Bao chen Zhou
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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Abstract
PURPOSE OF REVIEW The study of microRNA in asthma has revealed a vibrant new level of gene regulation underlying asthma pathology. Several miRNAs have been shown to be important in asthma, influencing various biological mechanisms which lead to asthma pathology and symptoms. In addition, miRNAs have been proposed as biomarkers of asthma affection status, asthma severity, and asthma treatment response. We review all recent asthma-miRNA work, while also presenting comprehensive tables of all miRNA results related to asthma. RECENT FINDINGS We here reviewed 63 recent studies published reporting asthma and miRNA research, and an additional 14 reviews of the same. We summarized the information for both adult and childhood asthma, as well as research on miRNAs in asthma-COPD overlap syndrome (ACOs), and virus-induced asthma exacerbations. We attempted to present a comprehensive collection of recently published asthma-associated miRNAs as well as tables of all published asthma-related miRNA results.
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Affiliation(s)
- Rinku Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Vitamin-D ameliorates sepsis-induced acute lung injury via augmenting miR-149-5p and downregulating ER stress. J Nutr Biochem 2022; 110:109130. [PMID: 35988833 DOI: 10.1016/j.jnutbio.2022.109130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/10/2022] [Accepted: 07/25/2022] [Indexed: 01/13/2023]
Abstract
Acute lung injury is a life-threatening medical problem induced by sepsis or endotoxins and may be associated with enhanced Endoplasmic reticulum stress (ER stress). Vitamin-D (Vit-D) possesses an anti-inflammatory effect; however, this specific mechanism on acute lung injury is still unknown. Here we scrutinize the mechanism of Vit-D on Acute lung injury (ALI) models and explored the Vit-D augmented miRNA's role in regulating the ER stress pathway in ALI. Sepsis was induced by CLP, and Endotoxemia was caused by lipopolysaccharide (LPS). We found that Vit-D alleviates pulmonary edema, improves lung histoarchitecture, infiltration of neutrophils, endothelial barrier in mice, and improves ER stress markers Activating Transcription Factor 6 (ATF6) and CHOP (C/EBP Homologous Protein) expression elevated by CLP/LPS induce ALI. Vit-D decreases the nitric oxide production and ATF6 in macrophages induced by LPS. Vit-D augments miR (miR-149-5p) in LPS-induce macrophages, CLP, and LPS-induced ALI models. Vit-D enhanced miRNA-149-5p when overexpressed, inhibited ER-specific ATF6 inflammatory pathway in LPS-stimulated macrophages, and improved histoarchitecture of the lung in LPS/CLP-induced mice models. This vitro and vivo studies demonstrate that Vit-D could improve ALI induced by CLP/LPS. In this regard, miR-149-5p may play a crucial role in vitamin-D inhibiting LPS/CLP induce ALI. The mechanism might be an association of increased miR-149-5p and its regulated gene target ATF6, and downstream CHOP proteins were suppressed. Thus, these findings demonstrate that the anti-inflammatory effect of Vit-D is achieved by augmentation of miRNA-149-5p expression, which may be a key physiologic mediator in the prevention and treatment of ALI.
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Modeling Movement Disorders via Generation of hiPSC-Derived Motor Neurons. Cells 2022; 11:cells11233796. [PMID: 36497056 PMCID: PMC9737271 DOI: 10.3390/cells11233796] [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: 10/30/2022] [Revised: 11/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Generation of motor neurons (MNs) from human-induced pluripotent stem cells (hiPSCs) overcomes the limited access to human brain tissues and provides an unprecedent approach for modeling MN-related diseases. In this review, we discuss the recent progression in understanding the regulatory mechanisms of MN differentiation and their applications in the generation of MNs from hiPSCs, with a particular focus on two approaches: induction by small molecules and induction by lentiviral delivery of transcription factors. At each induction stage, different culture media and supplements, typical growth conditions and cellular morphology, and specific markers for validation of cell identity and quality control are specifically discussed. Both approaches can generate functional MNs. Currently, the major challenges in modeling neurological diseases using iPSC-derived neurons are: obtaining neurons with high purity and yield; long-term neuron culture to reach full maturation; and how to culture neurons more physiologically to maximize relevance to in vivo conditions.
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Li TD, Murano K, Kitano T, Guo Y, Negishi L, Siomi H. TDP-43 safeguards the embryo genome from L1 retrotransposition. SCIENCE ADVANCES 2022; 8:eabq3806. [PMID: 36417507 PMCID: PMC9683724 DOI: 10.1126/sciadv.abq3806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Transposable elements (TEs) are genomic parasites that propagate within the host genome and introduce mutations. Long interspersed nuclear element-1 (LINE-1 or L1) is the major TE class, which occupies nearly 20% of the mouse genome. L1 is highly active in mammalian preimplantation embryos, posing a major threat to genome integrity, but the mechanism of stage-specific protection against L1 retrotransposition is unknown. Here, we show that TAR DNA-binding protein 43 (TDP-43), mutations in which constitute a major risk factor for amyotrophic lateral sclerosis, inhibits L1 retrotransposition in mouse embryonic stem cells (mESCs) and preimplantation embryos. Knockdown of TDP-43 resulted in massive genomic L1 expansion and impaired cell growth in preimplantation embryos and ESCs. Functional analysis demonstrated that TDP-43 interacts with L1 open reading frame 1 protein (L1 ORF1p) to mediate genomic protection, and loss of this interaction led to derepression of L1 retrotransposition. Our results identify TDP-43 as a guardian of the embryonic genome.
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Affiliation(s)
- Ten D. Li
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomohiro Kitano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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MicroRNA Changes Up to 24 h following Induced Hypoglycemia in Type 2 Diabetes. Int J Mol Sci 2022; 23:ijms232314696. [PMID: 36499023 PMCID: PMC9736413 DOI: 10.3390/ijms232314696] [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: 10/19/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Hypoglycemia, as a complication of type 2 diabetes (T2D), causes increased morbidity and mortality but the physiological response underlying hypoglycemia has not been fully elucidated. Small noncoding microRNA (miRNA) have multiple downstream biological effects. This pilot exploratory study was undertaken to determine if induced miRNA changes would persist and contribute to effects seen 24 h post-hypoglycemia. A parallel, prospective study design was employed, involving T2D (n = 23) and control (n = 23) subjects. The subjects underwent insulin-induced hypoglycemia (2 mmol/L; 36 mg/dL); blood samples were drawn at baseline, upon the induction of hypoglycemia, and 4 h and 24 h post-hypoglycemia, with a quantitative polymerase chain reaction analysis of miRNA undertaken. The baseline miRNAs did not differ. In the controls, 15 miRNAs were downregulated and one was upregulated (FDR < 0.05) from the induction of hypoglycemia to 4 h later while, in T2D, only four miRNAs were altered (downregulated), and these were common to both cohorts (miR-191-5p; miR-143-3p; let-7b-5p; let-7g-5p), correlated with elevated glucagon levels, and all were associated with energy balance. From the induction of hypoglycemia to 24 h, 14 miRNAs were downregulated and 5 were upregulated (FDR < 0.05) in the controls; 7 miRNAs were downregulated and 7 upregulated (FDR < 0.05) in T2D; a total of 6 miRNAs were common between cohorts, 5 were downregulated (miR-93-5p, let-7b-5p, miR-191-5p, miR-185-5p, and miR-652-3p), and 1 was upregulated (miR-369-3p). An ingenuity pathway analysis indicated that many of the altered miRNAs were associated with metabolic and coagulation pathways; however, of the inflammatory proteins expressed, only miR-143-3p at 24 h correlated positively with tumor necrosis factor-α (TNFa; p < 0.05 and r = 0.46) and negatively with toll-like receptor-4 (TLR4; p < 0.05 and r = 0.43). The MiRNA levels altered by hypoglycemia reflected changes in counter-regulatory glucagon and differed between cohorts, and their expression at 24 h suggests miRNAs may potentiate and prolong the physiological response. Trial registration: ClinicalTrials.gov NCT03102801.
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Zytnicki M, Gaspin C. srnaMapper: an optimal mapping tool for sRNA-Seq reads. BMC Bioinformatics 2022; 23:495. [DOI: 10.1186/s12859-022-05048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Sequencing is the key method to study the impact of short RNAs, which include micro RNAs, tRNA-derived RNAs, and piwi-interacting RNA, among others. The first step to make use of these reads is to map them to a genome. Existing mapping tools have been developed for long RNAs in mind, and, so far, no tool has been conceived for short RNAs. However, short RNAs have several distinctive features which make them different from messenger RNAs: they are shorter, they are often redundant, they can be produced by duplicated loci, and they may be edited at their ends.
Results
In this work, we present a new tool, srnaMapper, that exhaustively maps these reads with all these features in mind, and is most efficient when applied to reads no longer than 50 base pairs. We show, on several datasets, that srnaMapper is very efficient considering computation time and edition error handling: it retrieves all the hits, with arbitrary number of errors, in time comparable with non-exhaustive tools.
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121
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Xu T, Li LX, Jia Y, Wu Q, Zhu W, Xu Z, Zheng B, Lu X. One microRNA has the potential to target whole viral mRNAs in a given human coronavirus. Front Microbiol 2022; 13:1035044. [PMID: 36439806 PMCID: PMC9686371 DOI: 10.3389/fmicb.2022.1035044] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/24/2022] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNAs) can repress viral replication by targeting viral messenger RNA (mRNA), which makes them potential antiviral agents. The antiviral effects of miRNAs on infectious viruses have been explored extensively; however, recent studies mainly considered the action modes of miRNAs, neglecting another key factor, the molecular biology of viruses, which may be particularly important in the study of miRNA actions against a given virus. In this paper, the action modes of miRNAs and the molecular biology of viruses are jointly considered for the first time and based on the reported roles of miRNAs on viruses and human coronaviruses (HCoVs) molecular biology, the general and specific interaction modes of miRNAs-HCoVs are systematically reviewed. It was found that HCoVs transcriptome is a nested set of subgenomic mRNAs, sharing the same 5' leader, 3' untranslated region (UTR) and open reading frame (ORF). For a given HCoV, one certain miRNA with a target site in the 5' leader or 3' UTR has the potential to target all viral mRNAs, indicating tremendous antiviral effects against HCoVs. However, for the shared ORFs, some parts are untranslatable attributed to the translation pattern of HCoVs mRNA, and it is unknown whether the base pairing between the untranslated ORFs and miRNAs plays a regulatory effect on the local mRNAs where the untranslated ORFs are located; therefore, the regulatory effects of miRNAs with targets within the shared ORFs are complicated and need to be confirmed. Collectively, miRNAs may bepromising antiviral agents against HCoVs due to their intrinsically nested set of mRNAs, and some gaps are waiting to be filled. In this review, insight is provided into the exploration of miRNAs that can interrupt HCoVs infection.
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Affiliation(s)
- Tielong Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Long-xue Li
- Laboratory Animal Science and Technology Center, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yao Jia
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Qingni Wu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Weifeng Zhu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zhou Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Bin Zheng
- National Institute of Parasitic Diseases Chinese Center for Disease Control and Prevention, and WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Xuexin Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Gargiulo P, Marzano F, Salvatore M, Basile C, Buonocore D, Parlati ALM, Nardi E, Asile G, Abbate V, Colella A, Chirico A, Marciano C, Paolillo S, Perrone‐Filardi P. MicroRNAs: diagnostic, prognostic and therapeutic role in heart failure—a review. ESC Heart Fail 2022; 10:753-761. [PMID: 36349485 PMCID: PMC10053166 DOI: 10.1002/ehf2.14153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022] Open
Abstract
Heart failure is a leading cause of morbidity and mortality, with relevant social and economic burden on global healthcare system. Although the development of novel diagnostic tools and the advance in therapies have deeply influenced the diagnosis and treatment of this disease, improving both prognosis and life expectancy of patients, hospitalization is still high, and mortality remains considerable. MicroRNAs are small endogenous RNA molecules that post-transcriptionally regulate gene expression in both physiological and pathological processes. In recent years, microRNA have arisen as attractive therapeutic targets in the treatment of a wide spectrum of pathologies, including heart failure. In cardiac pathology, deregulation of microRNAs expression and function is associated to adverse outcome and heart failure progression. Circulating levels of specific microRNAs have emerged as useful biomarkers for the diagnosis of heart failure or as prognostic indicators. In the present review, we summarize the state of current research on the role of miRNAs as biomarkers for diagnosis and prognosis in patients with heart failure and their use as potential therapeutic targets for this condition.
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Affiliation(s)
- Paola Gargiulo
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | | | | | - Christian Basile
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Davide Buonocore
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | | | - Ermanno Nardi
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Gaetano Asile
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Vincenza Abbate
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Angela Colella
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Alfonsina Chirico
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Caterina Marciano
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Stefania Paolillo
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
| | - Pasquale Perrone‐Filardi
- Department of Advanced Biomedical Sciences University of Naples Federico II Naples Italy
- Mediterranea Cardiocentro Naples Italy
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123
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Du J, Patel DJ. Cofactor-assisted dicing: insights from structural snapshots. Cell Res 2022; 32:965-966. [PMID: 36050374 PMCID: PMC9652320 DOI: 10.1038/s41422-022-00716-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jiamu Du
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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124
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Evolving understandings for the roles of non-coding RNAs in autoimmunity and autoimmune disease. J Autoimmun 2022:102948. [DOI: 10.1016/j.jaut.2022.102948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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Liu Y, Rao J, Mi Y, Chen L, Feng L, Li Q, Geng J, Yang X, Zhan X, Ren L, Chen J, Zhang X. SARS-CoV-2 RNAs are processed into 22-nt vsRNAs in Vero cells. Front Immunol 2022; 13:1008084. [DOI: 10.3389/fimmu.2022.1008084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global pandemic, resulting in great fatalities around the world. Although the antiviral roles of RNA interference (RNAi) have been well studied in plants, nematodes and insects, the antiviral roles of RNAi in mammalians are still debating as RNAi effect is suspected to be suppressed by interferon (IFN) signaling pathways in most cell types. To determine the role of RNAi in mammalian resistance to SARS-CoV-2, we studied the profiling of host small RNAs and SARS-CoV-2 virus-derived small RNAs (vsRNAs) in the early infection stages of Vero cells, an IFN-deficient cell line. We found that host microRNAs (miRNAs) were dysregulated upon SARS-CoV-2 infection, resulting in downregulation of microRNAs playing antiviral functions and upregulation of microRNAs facilitating viral proliferations. Moreover, vsRNA peaked at 22 nt at negative strand but not the positive strand of SARS-CoV-2 and formed successive Dicer-spliced pattern at both strands. Similar characteristics of vsRNAs were observed in IFN-deficient cell lines infected with Sindbis and Zika viruses. Together, these findings indicate that host cell may deploy RNAi pathway to combat SARS-CoV-2 infection in IFN-deficient cells, informing the alternative antiviral strategies to be developed for patients or tissues with IFN deficiency.
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126
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Tran TM, Rao DS. RNA binding proteins in MLL-rearranged leukemia. Exp Hematol Oncol 2022; 11:80. [PMID: 36307883 PMCID: PMC9615162 DOI: 10.1186/s40164-022-00343-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractRNA binding proteins (RBPs) have recently emerged as important post-transcriptional gene expression regulators in both normal development and disease. RBPs influence the fate of mRNAs through multiple mechanisms of action such as RNA modifications, alternative splicing, and miR-mediated regulation. This complex and, often, combinatorial regulation by RBPs critically impacts the expression of oncogenic transcripts and, thus, the activation of pathways that drive oncogenesis. Here, we focus on the major features of RBPs, their mechanisms of action, and discuss the current progress in investigating the function of important RBPs in MLL-rearranged leukemia.
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Qiao P, Wu W, Wu Y, Wang X. miR-328a-3p modulates the proliferative and migratory abilities of Schwann cells in peripheral nerves. Neurosci Lett 2022; 791:136893. [PMID: 36191794 DOI: 10.1016/j.neulet.2022.136893] [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: 06/16/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022]
Abstract
MicroRNAs (miRNAs) modulate Schwann cell phenotype. Here miR-328a-3p amounts after peripheral nerve damage were determined in injury stumps of the sciatic nerve in rats administered surgical crush. Quantitative real-time reverse transcription-polymerase chain reaction was performed to assess miR-328a-3p levels 0, 1, 4, 7 and 14 days post-sciatic nerve damage. The results showed miR-328a-3p was upregulated after nerve damage. CCK8 and EdU assays revealed elevated miR-328a-3p amounts suppressed Schwann cell viability and proliferation, respectively. Next, the migratory potential of cells was assessed by the Transwell chamber and wound healing assays. We found elevated miR-328a-3p amounts also suppressed Schwann cell migration. Conversely, low miR-328a-3p amounts promoted Schwann cell migration. The possible miR-328a-3p targets were predicted by bioinformatics. The 15 target genes retrieved provided insights into miR-328a-3p's effects on Schwann cells and expanded the understanding of miR-328a-3p's biological functions in the peripheral nervous system. Collectively, these findings revealed miR-328a-3p's effects on Schwann cells and provided further insights into the functions of miRNAs in peripheral nerves.
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Affiliation(s)
- Pingping Qiao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Wenshuang Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China
| | - Yumeng Wu
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226361, China
| | - Xinghui Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu 226001, China.
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128
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Amelkina O, da Silva AM, Silva AR, Comizzoli P. Feline microRNAome in ovary and testis: Exploration of in-silico miRNA-mRNA networks involved in gonadal function and cellular stress response. Front Genet 2022; 13:1009220. [PMID: 36226169 PMCID: PMC9548565 DOI: 10.3389/fgene.2022.1009220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to perform the first in-depth analysis of miRNAs in ovarian and testicular tissues of the domestic cat, a critical biomedical model. Specifically, potential miRNA involvement was explored in gonadal function, testis development, and cellular stress response to preservation protocols. We performed miRNA-sequencing on 20 ovarian and 20 testicular samples from 15 cats, including different ages and tissue treatments. Using fresh tissues (n = 15), we confirmed gonadal expression of 183 miRNA precursors and discovered additional 52 novel feline candidate precursors. We integrated the mRNA data from our previous study on the same age and treatment groups to create in-silico miRNA-mRNA networks and their functional enrichment, which allows comprehensive exploration into possible miRNA functions in cat gonads. Clusters of miRNAs united by shared differentially expressed mRNA targets are potentially involved in testicular development and spermatogenesis. MicroRNAs could play a significant role in ovarian tissue response to stress from microwave-assisted dehydration, with smaller roles in cellular response to vitrification in both ovary and testis. This new list of miRNAs with potential function in cat gonads is a major step towards understanding the gonadal biology, as well as optimizing fertility preservation protocols.
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Affiliation(s)
- Olga Amelkina
- Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Andreia M. da Silva
- Laboratory of Animal Germplasm Conservation, Federal Rural University of Semi-Arid—UFERSA, Mossoró, Brazil
| | - Alexandre R. Silva
- Laboratory of Animal Germplasm Conservation, Federal Rural University of Semi-Arid—UFERSA, Mossoró, Brazil
| | - Pierre Comizzoli
- Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
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129
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Yao J, Xie M, Ma X, Song J, Wang Y, Xue X. PIWI-interacting RNAs in cancer: Biogenesis, function, and clinical significance. Front Oncol 2022; 12:965684. [PMID: 36212439 PMCID: PMC9539321 DOI: 10.3389/fonc.2022.965684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a less-studied class of small non-coding RNAs approximately 24–31 nucleotides in length. They express in germline and somatic cells and form complexes with PIWI proteins to exert regulatory effects. New studies show that piRNAs are aberrantly expressed in various cancers. In this review, we focus on those piRNAs that are associated with cancer hallmarks such as proliferation, invasion, and chemoresistance and discuss their potential as biomarkers for cancer diagnosis and prognosis.
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Affiliation(s)
- Jie Yao
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mei Xie
- Department of Respiratory and Critical Care, The Chinese People's Liberation Army of China (PLA) General Hospital, Beijing, China
| | - Xidong Ma
- Department of Respiratory and Critical Care, The Chinese People's Liberation Army of China (PLA) General Hospital, Beijing, China
| | - Jialin Song
- Department of Respiratory and Critical Care, Weifang Medical College, Weifang, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Respiratory and Critical Care, Weifang Medical College, Weifang, China
- *Correspondence: Xinying Xue,
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130
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Matulić M, Gršković P, Petrović A, Begić V, Harabajsa S, Korać P. miRNA in Molecular Diagnostics. Bioengineering (Basel) 2022; 9:bioengineering9090459. [PMID: 36135005 PMCID: PMC9495386 DOI: 10.3390/bioengineering9090459] [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: 07/16/2022] [Revised: 08/05/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized.
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Affiliation(s)
- Maja Matulić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Paula Gršković
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Andreja Petrović
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Institute of Clinical Pathology and Cytology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Valerija Begić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Primary School “Sesvetski Kraljevec”, 10361 Sesvetski Kraljevec, Croatia
| | - Suzana Harabajsa
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Department of Pathology and Cytology, Division of Pulmonary Cytology Jordanovac, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4606-278
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131
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Cheong JK, Rajgor D, Lv Y, Chung KY, Tang YC, Cheng H. Noncoding RNome as Enabling Biomarkers for Precision Health. Int J Mol Sci 2022; 23:ijms231810390. [PMID: 36142304 PMCID: PMC9499633 DOI: 10.3390/ijms231810390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 12/06/2022] Open
Abstract
Noncoding RNAs (ncRNAs), in the form of structural, catalytic or regulatory RNAs, have emerged to be critical effectors of many biological processes. With the advent of new technologies, we have begun to appreciate how intracellular and circulatory ncRNAs elegantly choreograph the regulation of gene expression and protein function(s) in the cell. Armed with this knowledge, the clinical utility of ncRNAs as biomarkers has been recently tested in a wide range of human diseases. In this review, we examine how critical factors govern the success of interrogating ncRNA biomarker expression in liquid biopsies and tissues to enhance our current clinical management of human diseases, particularly in the context of cancer. We also discuss strategies to overcome key challenges that preclude ncRNAs from becoming standard-of-care clinical biomarkers, including sample pre-analytics standardization, data cross-validation with closer attention to discordant findings, as well as correlation with clinical outcomes. Although harnessing multi-modal information from disease-associated noncoding RNome (ncRNome) in biofluids or in tissues using artificial intelligence or machine learning is at the nascent stage, it will undoubtedly fuel the community adoption of precision population health.
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Affiliation(s)
- Jit Kong Cheong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
- NUS Centre for Cancer Research, Singapore 117599, Singapore
- Correspondence: (J.K.C.); (H.C.)
| | | | - Yang Lv
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | | | | | - He Cheng
- MiRXES Lab, Singapore 138667, Singapore
- Correspondence: (J.K.C.); (H.C.)
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132
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Exploring the Expression of Pro-Inflammatory and Hypoxia-Related MicroRNA-20a, MicroRNA-30e, and MicroRNA-93 in Periodontitis and Gingival Mesenchymal Stem Cells under Hypoxia. Int J Mol Sci 2022; 23:ijms231810310. [PMID: 36142220 PMCID: PMC9499533 DOI: 10.3390/ijms231810310] [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: 07/01/2022] [Revised: 08/21/2022] [Accepted: 08/28/2022] [Indexed: 11/22/2022] Open
Abstract
Hypoxia associated with inflammation are common hallmarks observed in several diseases, and it plays a major role in the expression of non-coding RNAs, including microRNAs (miRNAs). In addition, the miRNA target genes for hypoxia-inducible factor-1α (HIF-1α) and nuclear factor of activated T cells-5 (NFAT5) modulate the adaptation to hypoxia. The objective of the present study was to explore hypoxia-related miRNA target genes for HIF-1α and NFAT5, as well as miRNA-20a, miRNA-30e, and miRNA-93 expression in periodontitis versus healthy gingival tissues and gingival mesenchymal stem cells (GMSCs) cultured under hypoxic conditions. Thus, a case-control study was conducted, including healthy and periodontitis subjects. Clinical data and gingival tissue biopsies were collected to analyze the expression of miRNA-20a, miRNA-30e, miRNA-93, HIF-1α, and NFAT5 by qRT-PCR. Subsequently, GMSCs were isolated and cultured under hypoxic conditions (1% O2) to explore the expression of the HIF-1α, NFAT5, and miRNAs. The results showed a significant upregulation of miRNA-20a (p = 0.028), miRNA-30e (p = 0.035), and miRNA-93 (p = 0.026) in periodontitis tissues compared to healthy gingival biopsies. NFAT5 mRNA was downregulated in periodontitis tissues (p = 0.037), but HIF-1α was not affected (p = 0.60). Interestingly, hypoxic GMSCs upregulated the expression of miRNA-20a and HIF-1α, but they downregulated miRNA-93e. In addition, NFAT5 mRNA expression was not affected in hypoxic GMSCs. In conclusion, in periodontitis patients, the expression of miRNA-20a, miRNA-30e, and miRNA-93 increased, but a decreased expression of NFAT5 mRNA was detected. In addition, GMSCs under hypoxic conditions upregulate the HIF-1α and increase miRNA-20a (p = 0.049) expression. This study explores the role of inflammatory and hypoxia-related miRNAs and their target genes in periodontitis and GMSCs. It is crucial to determine the potential therapeutic target of these miRNAs and hypoxia during the periodontal immune–inflammatory response, which should be analyzed in greater depth in future studies.
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Mishra S, Bahinipati J, Sarangi R, Mohapatra SR, Das S, Mishra A. A comprehensive overview on Micro RNA signature in type 2 diabetes Mellitus and its complications. Indian J Clin Biochem 2022; 38:151-158. [PMID: 36090301 PMCID: PMC9441834 DOI: 10.1007/s12291-022-01069-1] [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: 05/24/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous, non-coding RNA molecules that can modulate the expression of their target genes. Since its discovery, an enormous breakthrough has been established regarding its biogenesis and pathophysiological action, which has revolutionized the field of molecular biology. In addition, recent studies have identified the existence of stable extracellular/circulating miRNAs tissues and in biological fluids like blood where they are safeguarded from endogenous ribonuclease activity. Type 2 diabetes mellitus (T2DM) has emerged as a prime health issue worldwide. Incidence has increased considerably over the past decade. There are various tests that have been employed to diagnose T2DM. But for early detection and development, the establishment of biomarkers are of paramount importance. Contemporary evidence also validates the signature of a set of this epigenetic factor miRNA in the development of various diseases, including T2DM. This article reviews the contemporary corroboration associating miRNAs and T2DM and emphasizes the potential role of miRNA as a circulatory biomarker that could alert the growing prevalence of T2DM. Also, it acknowledges the valuable compendium of information regarding biogenesis and functional role of circulating miRNA in insulin resistance which is intimately linked to T2DM.
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Affiliation(s)
- Sanjukta Mishra
- Department of Biochemistry, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Campus 5, 751024 Bhubaneswar, Odisha India
| | - Jyotirmayee Bahinipati
- Department of Biochemistry, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Campus 5, 751024 Bhubaneswar, Odisha India
| | - RajLaxmi Sarangi
- Department of Biochemistry, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Campus 5, 751024 Bhubaneswar, Odisha India
| | - Soumya Ranjan Mohapatra
- Department of Research & Development, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Campus 5, 751024 Bhubaneswar, Odisha India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Swarnalata Das
- Department of Paediatrics, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha India
| | - Amaresh Mishra
- Department of Surgery, Kalinga Institute of Medical Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha India
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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135
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Prajzlerová K, Šenolt L, Filková M. Is there a potential of circulating miRNAs as biomarkers in rheumatic diseases? Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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136
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Mutual regulation of noncoding RNAs and RNA modifications in psychopathology: Potential therapeutic targets for psychiatric disorders? Pharmacol Ther 2022; 237:108254. [DOI: 10.1016/j.pharmthera.2022.108254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022]
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137
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Sommerauer C, Kutter C. Noncoding RNAs in liver physiology and metabolic diseases. Am J Physiol Cell Physiol 2022; 323:C1003-C1017. [PMID: 35968891 DOI: 10.1152/ajpcell.00232.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The liver holds central roles in detoxification, energy metabolism and whole-body homeostasis but can develop malignant phenotypes when being chronically overwhelmed with fatty acids and glucose. The global rise of metabolic-associated fatty liver disease (MAFLD) is already affecting a quarter of the global population. Pharmaceutical treatment options against different stages of MAFLD do not yet exist and several clinical trials against hepatic transcription factors and other proteins have failed. However, emerging roles of noncoding RNAs, including long (lncRNA) and short noncoding RNAs (sRNA), in various cellular processes pose exciting new avenues for treatment interventions. Actions of noncoding RNAs mostly rely on interactions with proteins, whereby the noncoding RNA fine-tunes protein function in a process termed riboregulation. The developmental stage-, disease stage- and cell type-specific nature of noncoding RNAs harbors enormous potential to precisely target certain cellular pathways in a spatio-temporally defined manner. Proteins interacting with RNAs can be categorized into canonical or non-canonical RNA binding proteins (RBPs) depending on the existence of classical RNA binding domains. Both, RNA- and RBP-centric methods have generated new knowledge of the RNA-RBP interface and added an additional regulatory layer. In this review, we summarize recent advances of how of RBP-lncRNA interactions and various sRNAs shape cellular physiology and the development of liver diseases such as MAFLD and hepatocellular carcinoma.
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Affiliation(s)
- Christian Sommerauer
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
| | - Claudia Kutter
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
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138
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He X, Wu H, Ye Y, Gong X, Bao B. Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus. BMC Genomics 2022; 23:553. [PMID: 35922761 PMCID: PMC9347094 DOI: 10.1186/s12864-022-08787-z] [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: 09/30/2021] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism accumulation of TTX in ovary and testis, and the relationship between TTX accumulation with sex related genes expression remain largely unknown. The present study investigated the effects of exogenous TTX treatment on Takifugu flavidus. The results demonstrated that exogenous TTX administration significantly incresed level of TTX concentration in kidney, cholecyst, skin, liver, heart, muscle, ovary and testis of the treatment group (TG) than that of the control group (CG). Transcriptome sequencing and analysis were performed to study differential expression profiles of mRNA and piRNA after TTX administration of the ovary and testis. The results showed that compared with female control group (FCG) and male control group (MCG), TTX administration resulted in 80 and 23 piRNAs, 126 and 223 genes up and down regulated expression in female TTX-treated group (FTG), meanwhile, 286 and 223 piRNAs, 2 and 443 genes up and down regulated expression in male TTX-treated group (MTG). The female dominant genes cyp19a1, gdf9 and foxl2 were found to be up-regulated in MTG. The cyp19a1, whose corresponding target piRNA uniq_554482 was identified as down-regulated in the MTG, indicating the gene expression feminization in testis after exogenous TTX administration. The KEGG enrichment analysis revealed that differentially expressed genes (DEGs) and piRNAs (DEpiRNAs) in MTG vs MCG group were more enriched in metabolism pathways, indicating that the testis produced more metabolic pathways in response to exogenous TTX, which might be a reason for the sexual dimorphism of TTX distribution in gonads. In addition, TdT-mediated dUTP-biotin nick end labeling staining showed that significant apoptosis was detected in the MTG testis, and the role of the cell apoptotic pathways was further confirmed. Overall, our research revealed that the response of the ovary and testis to TTX administration was largely different, the ovary is more tolerant whereas the testis is more sensitive to TTX. These data will deepen our understanding on the accumulation of TTX sexual dimorphism in Takifugu.
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Affiliation(s)
- Xue He
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hexing Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yaping Ye
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaolin Gong
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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139
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Chronopoulou L, Falasca F, Di Fonzo F, Turriziani O, Palocci C. siRNA Transfection Mediated by Chitosan Microparticles for the Treatment of HIV-1 Infection of Human Cell Lines. MATERIALS 2022; 15:ma15155340. [PMID: 35955275 PMCID: PMC9369812 DOI: 10.3390/ma15155340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 02/01/2023]
Abstract
Gene delivery is the basis for developing gene therapies that, in the future, may be able to cure virtually any disease, including viral infections. The use of short interfering RNAs (siRNAs) targeting viral replication is a novel strategy for treating HIV-1 infection. In this study, we prepared chitosan particles containing siRNA tat/rev via ionotropic gelation. Chitosan-based particles were efficiently internalized by cells, as evidenced by fluorescence microscopy. The antiviral effect of chitosan-based particles was studied on the C8166 cell line infected with HIV-1 and compared with the use of commercial liposomes (ESCORT). A significant reduction in HIV replication was also observed in cells treated with empty chitosan particles, suggesting that chitosan may interfere with the early steps of the HIV life cycle and have a synergic effect with siRNA to reduce viral replication significantly.
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Affiliation(s)
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (F.F.); (O.T.)
| | - Federica Di Fonzo
- Department of Biochemical Sciences “Rossi Fanelli”, Sapienza University, 00185 Rome, Italy;
| | - Ombretta Turriziani
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (F.F.); (O.T.)
| | - Cleofe Palocci
- Department of Chemistry, Sapienza University, 00185 Rome, Italy;
- CIABC-Centro di Ricerca per le Scienze Applicate alla Protezione dell’Ambiente e dei Beni Culturali, Sapienza University, 00185 Rome, Italy
- Correspondence: ; Tel.: +39-0649913317
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140
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de Malmanche H, Hussain M, Marcellin E, Reid S, Asgari S. Knockout of Dicer-2 in the Sf9 cell line enhances the replication of Spodoptera frugiperda rhabdovirus and conditionally increases baculovirus replication. J Gen Virol 2022; 103. [PMID: 36018884 DOI: 10.1099/jgv.0.001779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Sf9 cell line, originally isolated from the ovarian tissue of Spodoptera frugiperda larvae, is widely used in academia and industry for the baculovirus-mediated production of recombinant proteins and virus-like particles. RNA interference (RNAi) is a conserved antiviral pathway present in eukaryotic organisms and is the primary antiviral defence mechanism in insects. Recent evidence has implicated RNAi as an antiviral response to baculovirus infection in Sf9 cells. To test this hypothesis, CRISPR/Cas9 technology was used to disable the RNAi pathway in Sf9 cells by knocking out Dicer-2, the protein responsible for cleaving viral double-stranded RNA precursors into short interfering RNAs. Infection of Dicer-2 knockout Sf9 cells with either the wild-type baculovirus Autographa californica nucleopolyhedrovirus (AcMNPV), recombinant AcMNPV (rAcMNPV) expressing β-galactosidase (β-gal), or rAcMNPV expressing a wasp venom protein (Vn50) at a multiplicity of infection (m.o.i.) of 1 resulted in a modest increase in virus replication compared to control Sf9 cells under adherent culture conditions. In contrast, Dicer-2 knockout Sf9 monolayer or suspension cultures infected by the rAcMNPV expressing β-gal at higher m.o.i.s (3.5 and 20) did not exhibit increases in either viral DNA replication or β-gal production. Intriguingly, during long-term passaging in suspension, Dicer-2 knockout Sf9 cultures underwent transient crashes in cell proliferation and viability. It was discovered that these periods of low growth and viability coincided with a dramatic increase in the RNA levels of S. frugiperda rhabdovirus, a recently identified adventitious virus that persistently infects the Sf9 cell line, suggesting a role for Dicer-2 in managing chronic viral infections in this industrially relevant insect cell line.
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Affiliation(s)
- Henry de Malmanche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mazhar Hussain
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Steve Reid
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
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141
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Abstract
Small RNAs are ubiquitous regulators of gene expression that participate in nearly all aspects of physiology in a wide range of organisms. There are many different classes of eukaryotic small RNAs that play regulatory roles at every level of gene expression, including transcription, RNA stability, and translation. While eukaryotic small RNAs display diverse functions across and within classes, they are generally grouped functionally based on the machinery required for their biogenesis, the effector proteins they associate with, and their molecular characteristics. The development of techniques to clone and sequence small RNAs has been critical for their identification, yet the ligation-dependent addition of RNA adapters and the use of reverse transcriptase to generate cDNA in traditional library preparation protocols can be unsuitable to detect certain small RNA subtypes. In particular, 3' or 5' chemical modifications that are characteristic of specific types of small RNAs can impede the ligation-dependent addition of RNA adapters, while internal RNA modifications can interfere with accurate reverse transcription. The inability to clone certain small RNA subtypes with traditional protocols results in an inaccurate assessment of small RNA abundance and diversity, where some RNAs appear over-represented and others are not detected. This overview aims to guide users on how to design small RNA cloning workflows in eukaryotes to more accurately capture specific small RNAs of interest. Hence, we discuss the molecular biology underlying the identification and quantitation of small RNAs, explore the limitations of commonly used protocols, and detail the alternative approaches that can be used to enrich specific small RNA classes. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Olivia J Crocker
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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142
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Vujovic F, Hunter N, Farahani RM. Cellular self-organization: An overdrive in Cambrian diversity? Bioessays 2022; 44:e2200033. [PMID: 35900058 DOI: 10.1002/bies.202200033] [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: 02/05/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022]
Abstract
During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. A variety of explanations have been proposed to address this major evolutionary phenomenon termed the "Cambrian explosion." While most hypotheses address environmental, developmental, and ecological factors that facilitated evolutionary innovations, the biological basis for accelerated emergence of species diversity in the Cambrian period remains largely conjectural. Herein, we posit that morphogenesis by self-organization enables the uncoupling of genomic mutational landscape from phenotypic diversification. Evidence is provided for a two-tiered interpretation of genomic changes in metazoan animals wherein mutations not only impact upon function of individual cells, but also alter the self-organization outcome during developmental morphogenesis. We provide evidence that the morphological impacts of mutations on self-organization could remain repressed if associated with an unmet negative energetic cost. We posit that accelerated morphological diversification in transition to the Cambrian period has occurred by emergence of dormant (i.e., reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period.
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Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ramin M Farahani
- IDR/Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
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143
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Sato K, Takayama KI, Hashimoto M, Inoue S. Transcriptional and Post-Transcriptional Regulations of Amyloid-β Precursor Protein (APP ) mRNA. FRONTIERS IN AGING 2022; 2:721579. [PMID: 35822056 PMCID: PMC9261399 DOI: 10.3389/fragi.2021.721579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/28/2021] [Indexed: 01/01/2023]
Abstract
Alzheimer’s disease (AD) is an age-associated neurodegenerative disorder characterized by progressive impairment of memory, thinking, behavior, and dementia. Based on ample evidence showing neurotoxicity of amyloid-β (Aβ) aggregates in AD, proteolytically derived from amyloid precursor protein (APP), it has been assumed that misfolding of Aβ plays a crucial role in the AD pathogenesis. Additionally, extra copies of the APP gene caused by chromosomal duplication in patients with Down syndrome can promote AD pathogenesis, indicating the pathological involvement of the APP gene dose in AD. Furthermore, increased APP expression due to locus duplication and promoter mutation of APP has been found in familial AD. Given this background, we aimed to summarize the mechanism underlying the upregulation of APP expression levels from a cutting-edge perspective. We first reviewed the literature relevant to this issue, specifically focusing on the transcriptional regulation of APP by transcription factors that bind to the promoter/enhancer regions. APP expression is also regulated by growth factors, cytokines, and hormone, such as androgen. We further evaluated the possible involvement of post-transcriptional regulators of APP in AD pathogenesis, such as RNA splicing factors. Indeed, alternative splicing isoforms of APP are proposed to be involved in the increased production of Aβ. Moreover, non-coding RNAs, including microRNAs, post-transcriptionally regulate the APP expression. Collectively, elucidation of the novel mechanisms underlying the upregulation of APP would lead to the development of clinical diagnosis and treatment of AD.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Makoto Hashimoto
- Department of Basic Technology, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
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144
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Saburi A, Kahrizi MS, Naghsh N, Etemadi H, İlhan A, Adili A, Ghoreishizadeh S, Tamjidifar R, Akbari M, Ercan G. A comprehensive survey into the role of microRNAs in ovarian cancer chemoresistance; an updated overview. J Ovarian Res 2022; 15:81. [PMID: 35799305 PMCID: PMC9264529 DOI: 10.1186/s13048-022-01012-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Ovarian cancer (OC), a frequent malignant tumor that affects women, is one of the leading causes of cancer-related death in this group of individuals. For the treatment of ovarian cancer, systemic chemotherapy with platinum-based drugs or taxanes is the first-line option. However, drug resistance developed over time during chemotherapy medications worsens the situation. Since uncertainty exists for the mechanism of chemotherapy resistance in ovarian cancer, there is a need to investigate and overcome this problem. miRNAs are engaged in various signaling pathways that contribute to the chemotherapeutic resistance of ovarian cancer. In the current study, we have tried to shed light on the mechanisms by which microRNAs contribute to the drug resistance of ovarian cancer and the use of some microRNAs to combat this chemoresistance, leading to the worse outcome of ovarian cancer patients treated with systemic chemotherapeutics.
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Affiliation(s)
- Ahmad Saburi
- Department of Biology, Faculty of Basic Sciences, Gonbad Kavous University, Gonbad Kavous, Iran
| | | | - Navid Naghsh
- Department of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hasti Etemadi
- Department of Biotechnology, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth University, Pune, India
| | - Ahmet İlhan
- Department of Medical Biochemistry, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Ali Adili
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South Florida, Tampa, Florida USA
- Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Rozita Tamjidifar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, 35100 Turkey
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gülinnaz Ercan
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, 35100 Turkey
- Department of Stem Cell, Institute of Health Sciences, Ege University, Izmir, 35100 Turkey
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145
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Comprehensive analysis of ncRNA involvement in brain microglia immunology. Clin Immunol 2022; 241:109075. [PMID: 35809855 DOI: 10.1016/j.clim.2022.109075] [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: 04/11/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/23/2022]
Abstract
Microglia is a major class of brain-resident myeloid cells and non-coding RNAs (ncRNAs) serves as key regulators in microglia homeostasis and inflammatory process. Here, we constructed the systematical association between microglia and ncRNAs including miRNAs, lncRNAs and circRNAs from two aspects, manual retrieval and computational detection. A total of 648 experimental verified ncRNA-microglia associations were obtained from published studies, including ncRNA regulatory patterns within different experimental models. Furthermore, we extracted 9 miRNA and 1 lncRNA expression profiles from the GEO database. Also, we obtained 31 sample-match miRNA and mRNA expression profiles, containing a total of 2335 normal or disordered brain samples. Finally, we developed a platform named MG-ncRexplorer (http://bio-bigdata.hrbmu.edu.cn/MG-ncRexplorer/), exploring the associations between ncRNAs and microglia among experimental validated and computational detection. To demonstrate the usage of MG-ncRexplorer, we constructed regulatory target networks based on manual retrieval associations and identified risk glioma miRNAs among multiple high-throughput expression profiles.
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146
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miR-106b as an emerging therapeutic target in cancer. Genes Dis 2022; 9:889-899. [PMID: 35685464 PMCID: PMC9170583 DOI: 10.1016/j.gendis.2021.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/24/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) comprise short non-coding RNAs that function in regulating the expression of tumor suppressors or oncogenes and modulate oncogenic signaling pathways in cancer. miRNAs expression alters significantly in several tumor tissues and cancer cell lines. For example, miR-106b functions as an oncogene and increases in multiple cancers. The miR-106b directly targets genes involved in tumorigenesis, proliferation, invasion, migration, and metastases. This review has focused on the miR-106b function and its downstream target in different cancers and provide perspective into how miR-106 regulates cancer cell proliferation, migration, invasion, and metastases by regulating the tumor suppressor genes. Since miRNAs-based therapies are currently being developed to enhance cancer therapy outcomes, miR-106b could be an attractive and prospective candidate in different cancer types for detection, diagnosis, and prognosis assessment in the tumor.
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147
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Domingo‐Rodriguez L, Cabana‐Domínguez J, Fernàndez‐Castillo N, Cormand B, Martín‐García E, Maldonado R. Differential expression of miR‐1249‐3p and miR‐34b‐5p between vulnerable and resilient phenotypes of cocaine addiction. Addict Biol 2022; 27:e13201. [PMID: 36001423 PMCID: PMC9286869 DOI: 10.1111/adb.13201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 05/13/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Domingo‐Rodriguez
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - Judit Cabana‐Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Noèlia Fernàndez‐Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Elena Martín‐García
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM) Barcelona Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM) Barcelona Spain
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148
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Eshkoor SA, Ghodsian N, Akhtari-Zavare M. MicroRNAs influence and longevity. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00316-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
MiRNAs play critical roles in the regulation of cellular function, life span, and the aging process. They can affect longevity positively and negatively through different aging pathways.
Main text
MiRNAs are a group of short non-coding RNAs that regulate gene expressions at post-transcriptional levels. The different types of alterations in miRNAs biogenesis, mRNA expressions, and activities of miRNA-protein complexes can affect the regulation of normal post-transcriptional gene process, which may lead to aging, age-related diseases, and an earlier death. It seems that the influence of deregulation of miRNAs on senescence and age-related diseases occurring by targeting aging molecular pathways can be used for diagnosis and prognosis of them. Therefore, the expression and function of miRNAs should be studied more accurately with new applicable and validated experimental tools. However, the current review wishes to highlight simply a connection among miRNAs, senescence and some age-related diseases.
Conclusion
Despite several research indicating the key roles of miRNAs in aging and longevity, further investigations are still needed to elucidate the essential roles of miRNAs in controlling mRNA regulation, cell proliferation, death and/or protection during stress and health problems. Besides, more research on miRNAs will help to identify new targets for alternative strategies regarding effectively screen, treat, and prevent diseases as well as make slow the aging process.
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149
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Suleiman M, Kounosu A, Murcott B, Dayi M, Pawluk R, Yoshida A, Viney M, Kikuchi T, Hunt VL. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 2022; 12:10156. [PMID: 35710810 PMCID: PMC9203780 DOI: 10.1038/s41598-022-14247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5' uridine (21-22Us) and a 5' monophosphate, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and a 5' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
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Affiliation(s)
- Mona Suleiman
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Asuka Kounosu
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Ben Murcott
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Mehmet Dayi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Rebecca Pawluk
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Akemi Yoshida
- Laboratory of Genomics, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Taisei Kikuchi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Vicky L Hunt
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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150
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Examples of Inverse Comorbidity between Cancer and Neurodegenerative Diseases: A Possible Role for Noncoding RNA. Cells 2022; 11:cells11121930. [PMID: 35741059 PMCID: PMC9221903 DOI: 10.3390/cells11121930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the most common causes of death; in parallel, the incidence and prevalence of central nervous system diseases are equally high. Among neurodegenerative diseases, Alzheimer’s dementia is the most common, while Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. There is a significant amount of evidence on the complex biological connection between cancer and neurodegeneration. Noncoding RNAs (ncRNAs) are defined as transcribed nucleotides that perform a variety of regulatory functions. The mechanisms by which ncRNAs exert their functions are numerous and involve every aspect of cellular life. The same ncRNA can act in multiple ways, leading to different outcomes; in fact, a single ncRNA can participate in the pathogenesis of more than one disease—even if these seem very different, as cancer and neurodegenerative disorders are. The ncRNA activates specific pathways leading to one or the other clinical phenotype, sometimes with obvious mechanisms of inverse comorbidity. We aimed to collect from the existing literature examples of inverse comorbidity in which ncRNAs seem to play a key role. We also investigated the example of mir-519a-3p, and one of its target genes Poly (ADP-ribose) polymerase 1, for the inverse comorbidity mechanism between some cancers and PD. We believe it is very important to study the inverse comorbidity relationship between cancer and neurodegenerative diseases because it will help us to better assess these two major areas of human disease.
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