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Mesarosova L, Scheper M, Iyer A, Anink JJ, Mills JD, Aronica E. miR-193b-3p/ PGC-1α pathway regulates an insulin dependent anti-inflammatory response in Parkinson's disease. Neurobiol Dis 2024; 199:106587. [PMID: 38950713 DOI: 10.1016/j.nbd.2024.106587] [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: 03/21/2024] [Revised: 06/18/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024] Open
Abstract
It has been shown that many miRNAs, including miR-193b-3p, are differentially expressed in Parkinson's disease (PD). Dysregulation of miR-193b-3p/PGC-1α axis may alter homeostasis in cells and can induce an inflammatory response commonly accompanied by metabolic disturbances. The aim of the present study is to investigate if dysregulation of the miR-193-3p/PGC-1α axis may contribute to the pathological changes observed in the PD brain. Brain tissue were obtained from middle frontal gyrus of non-demented controls and individuals with a PD diagnosis. RT-qPCR was used to determine the expression of miR-193b-3p and in situ hybridization (ISH) and immunological analysis were employed to establish the cellular distribution of miR-193b-3p. Functional assays were performed using SH-SY5Y cells, including transfection and knock-down of miR-193b-3p. We found significantly lower expression of miR-193b-3p in the early stages of PD (PD4) which increased throughout disease progression. Furthermore, altered expression of PGC-1α suggested a direct inhibitory effect of miR-193b-3p in the brain of individuals with PD. Moreover, we observed changes in expression of insulin after transfection of SH-SY5Y cells with miR-193b-3p, which led to dysregulation in the expression of several pro- or anti - inflammatory genes. Our findings indicate that the miR-193b-3p/PGC-1α axis is involved in the regulation of insulin signaling. This regulation is crucial, since insulin induced inflammatory response may serve as a protective mechanism during acute situations but potentially evolve into a pathological process in chronic conditions. This novel regulatory mechanism may represent an interesting therapeutic target with potential benefits for various neurodegenerative diseases.
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Affiliation(s)
- Lucia Mesarosova
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands.
| | - Mirte Scheper
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands
| | - Anand Iyer
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Jasper J Anink
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands.
| | - Eleonora Aronica
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, the Netherlands
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Mahmoudian Esfahani M, Mostashfi M, Vaheb Hosseinabadi S, Hashemi MS, Peymani M, Zohrabi D, Angaji SA, Nasr-Esfahani MH, Ghaedi K. Unveiling the regulatory of miR-101-3p on ZNF746 in a Parkinson's disease cell model: Implications for therapeutic targeting. Neurosci Res 2024; 203:18-27. [PMID: 38103579 DOI: 10.1016/j.neures.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/08/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
In this study, we explored the regulatory role of microRNA miR-101-3p on the zinc finger protein 746 (ZNF746), also known as PARIS, which is implicated in both sporadic and familial forms of Parkinson's disease. In a Parkinson's disease cell model, utilizing SH-SY5Y cells treated with 1-methyl-4-phenylpyridine (MPP+), we observed that miR-101-3p was downregulated, while ZNF746 was upregulated. To investigate the direct impact of miR-101-3p on ZNF746, our team conducted overexpression experiments, successfully reversing ZNF746's expression at both the mRNA and protein levels, as confirmed through quantitative PCR and western blotting. We also performed luciferase assays, providing compelling evidence that ZNF746 is a direct target of miR-101-3p. Additionally, we noted that miR-101-3p overexpression resulted in increased expression of PGC1α, a gene targeted by ZNF746. Functionally, we assessed the implications of miR-101-3p overexpression through MTS assays and flow cytometry, revealing significant promotion of cell viability, inhibition of ROS production, and reduced apoptosis in the Parkinson's disease cell model. In conclusion, this study highlights the role of miR-101-3p in regulating ZNF746 expression and suggests its potential as a therapeutic target for Parkinson's disease. These findings provide valuable molecular insights that could pave the way for innovative treatment strategies in combating this debilitating neurodegenerative disorder.
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Affiliation(s)
| | - Maryam Mostashfi
- Department of Cell and Molecular Biology, Faculty of Biosciences, Kharazmi University, Tehran, Iran
| | | | - Motahare-Sadat Hashemi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Dina Zohrabi
- Department of Biology, Faculty of Science, NourDanesh Institute of Higher Education, Isfahan, Iran
| | - Seyed Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biosciences, Kharazmi University, Tehran, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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Vahidi S, Agah S, Mirzajani E, Asghari Gharakhyli E, Norollahi SE, Rahbar Taramsari M, Babaei K, Samadani AA. microRNAs, oxidative stress, and genotoxicity as the main inducers in the pathobiology of cancer development. Horm Mol Biol Clin Investig 2024; 45:55-73. [PMID: 38507551 DOI: 10.1515/hmbci-2023-0012] [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: 02/05/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Cancer is one of the most serious leading causes of death in the world. Many eclectic factors are involved in cancer progression including genetic and epigenetic alongside environmental ones. In this account, the performance and fluctuations of microRNAs are significant in cancer diagnosis and treatment, particularly as diagnostic biomarkers in oncology. So, microRNAs manage and control the gene expression after transcription by mRNA degradation, or also they can inhibit their translation. Conspicuously, these molecular structures take part in controlling the cellular, physiological and pathological functions, which many of them can accomplish as tumor inhibitors or oncogenes. Relatively, Oxidative stress is defined as the inequality between the creation of reactive oxygen species (ROS) and the body's ability to detoxify the reactive mediators or repair the resulting injury. ROS and microRNAs have been recognized as main cancer promoters and possible treatment targets. Importantly, genotoxicity has been established as the primary reason for many diseases as well as several malignancies. The procedures have no obvious link with mutagenicity and influence the organization, accuracy of the information, or fragmentation of DNA. Conclusively, mutations in these patterns can lead to carcinogenesis. In this review article, we report the impressive and practical roles of microRNAs, oxidative stress, and genotoxicity in the pathobiology of cancer development in conjunction with their importance as reliable cancer biomarkers and their association with circulating miRNA, exosomes and exosomal miRNAs, RNA remodeling, DNA methylation, and other molecular elements in oncology.
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Affiliation(s)
- Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | | | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Morteza Rahbar Taramsari
- Department of Forensic Medicine, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | - Kosar Babaei
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran
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Zhang X, Zhao G, Yang F, Li C, Lin W, Dai H, Zhai L, Xi X, Yuan Q, Huo J. Transcriptional Regulation Analysis Provides Insight into the Function of GSK3β Gene in Diannan Small-Ear Pig Spermatogenesis. Genes (Basel) 2024; 15:655. [PMID: 38927591 PMCID: PMC11203124 DOI: 10.3390/genes15060655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Glycogen synthase kinase-3β (GSK3β) not only plays a crucial role in regulating sperm maturation but also is pivotal in orchestrating the acrosome reaction. Here, we integrated single-molecule long-read and short-read sequencing to comprehensively examine GSK3β expression patterns in adult Diannan small-ear pig (DSE) testes. We identified the most important transcript ENSSSCT00000039364 of GSK3β, obtaining its full-length coding sequence (CDS) spanning 1263 bp. Gene structure analysis located GSK3β on pig chromosome 13 with 12 exons. Protein structure analysis reflected that GSK3β consisted of 420 amino acids containing PKc-like conserved domains. Phylogenetic analysis underscored the evolutionary conservation and homology of GSK3β across different mammalian species. The evaluation of the protein interaction network, KEGG, and GO pathways implied that GSK3β interacted with 50 proteins, predominantly involved in the Wnt signaling pathway, papillomavirus infection, hippo signaling pathway, hepatocellular carcinoma, gastric cancer, colorectal cancer, breast cancer, endometrial cancer, basal cell carcinoma, and Alzheimer's disease. Functional annotation identified that GSK3β was involved in thirteen GOs, including six molecular functions and seven biological processes. ceRNA network analysis suggested that DSE GSK3β was regulated by 11 miRNA targets. Furthermore, qPCR expression analysis across 15 tissues highlighted that GSK3β was highly expressed in the testis. Subcellular localization analysis indicated that the majority of the GSK3β protein was located in the cytoplasm of ST (swine testis) cells, with a small amount detected in the nucleus. Overall, our findings shed new light on GSK3β's role in DSE reproduction, providing a foundation for further functional studies of GSK3β function.
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Affiliation(s)
- Xia Zhang
- Department of Biological and Food Engineering, Lyuliang University, Lvliang 033001, China;
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Fuhua Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Changyao Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Wan Lin
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Hongmei Dai
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Lan Zhai
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Xuemin Xi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Qingting Yuan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (G.Z.); (F.Y.); (C.L.); (W.L.); (H.D.); (L.Z.); (X.X.); (Q.Y.)
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Usha Satheesan S, Chowdhury S, Kolthur-Seetharam U. Metabolic and circadian inputs encode anticipatory biogenesis of hepatic fed microRNAs. Life Sci Alliance 2024; 7:e202302180. [PMID: 38408795 PMCID: PMC10897495 DOI: 10.26508/lsa.202302180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Starvation and refeeding are mostly unanticipated in the wild in terms of duration, frequency, and nutritional value of the refed state. Notwithstanding this, organisms mount efficient and reproducible responses to restore metabolic homeostasis. Hence, it is intuitive to invoke expectant molecular mechanisms that build anticipatory responses to enable physiological toggling during fed-fast cycles. In this regard, we report anticipatory biogenesis of oscillatory hepatic microRNAs that peak during a fed state and inhibit starvation-responsive genes. Our results clearly demonstrate that the levels of primary and precursor microRNA transcripts increase during a fasting state, in anticipation of a fed response. We delineate the importance of both metabolic and circadian cues in orchestrating hepatic fed microRNA homeostasis in a physiological setting. Besides illustrating metabo-endocrine control, our findings provide a mechanistic basis for the overarching influence of starvation on anticipatory biogenesis. Importantly, by using pharmacological agents that are widely used in clinics, we point out the high potential of interventions to restore homeostasis of hepatic microRNAs, whose deregulated expression is otherwise well established to cause metabolic diseases.
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Affiliation(s)
- Sandra Usha Satheesan
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shreyam Chowdhury
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ullas Kolthur-Seetharam
- https://ror.org/03ht1xw27 Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- https://ror.org/03ht1xw27 Tata Institute of Fundamental Research- Hyderabad (TIFR-H), Hyderabad, India
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Wu W, Ren J, Wang J, Wang J, Yu D, Zhang Y, Zeng F, Huang B. Metalloestrogens exposure and risk of gestational diabetes mellitus: Evidence emerging from the systematic review and meta-analysis. ENVIRONMENTAL RESEARCH 2024; 248:118321. [PMID: 38307186 DOI: 10.1016/j.envres.2024.118321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/04/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Metalloestrogens are metals and metalloid elements with estrogenic activity found everywhere. Their impact on human health is becoming more apparent as human activities increase. OBJECTIVE Our aim is to conduct a comprehensive systematic review and meta-analysis of observational studies exploring the correlation between metalloestrogens (specifically As, Sb, Cr, Cd, Cu, Se, Hg) and Gestational Diabetes Mellitus (GDM). METHODS PubMed, Web of Science, and Embase were searched to examine the link between metalloestrogens (As, Sb, Cr, Cd, Cu, Se, and Hg) and GDM until December 2023. Risk estimates were derived using random effects models. Subgroup analyses were conducted based on study countries, exposure sample, exposure assessment method, and detection methods. Sensitivity analyses and adjustments for publication bias were carried out to assess the strength of the findings. RESULTS Out of the 389 articles identified initially, 350 met our criteria and 33 were included in the meta-analysis, involving 141,175 subjects (9450 cases, 131,725 controls). Arsenic, antimony, and copper exposure exhibited a potential increase in GDM risk to some extent (As: OR = 1.28, 95 % CI [1.08, 1.52]; Sb: OR = 1.73, 95 % CI [1.13, 2.65]; Cu: OR = 1.29, 95 % CI [1.02, 1.63]), although there is a high degree of heterogeneity (As: Q = 52.93, p < 0.05, I2 = 64.1 %; Sb: Q = 31.40, p < 0.05, I2 = 80.9 %; Cu: Q = 21.14, p < 0.05, I2 = 71.6 %). Conversely, selenium, cadmium, chromium, and mercury exposure did not exhibit any association with the risk of GDM in our study. DISCUSSION Our research indicates that the existence of harmful metalloestrogens in the surroundings has a notable effect on the likelihood of GDM. Hence, we stress the significance of environmental elements in the development of GDM and the pressing need for relevant policies and measures.
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Affiliation(s)
- Wanxin Wu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Junjie Ren
- Department of Medical Psychology, School of Mental Health and Psychological Science, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Juan Wang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Jiamei Wang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Deshui Yu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yan Zhang
- School of Biology and Food Engineering, Hefei Normal University, Hefei, 230092, Anhui, China.
| | - Fa Zeng
- Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, Guangdong, China.
| | - Binbin Huang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, Anhui, China.
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Mennitti LV, de Souza EA, Santamarina AB, Sertorio MN, Jucá A, De Souza DV, Ribeiro DA, Pisani LP. Maternal dietary fatty acid composition and content prior to and during pregnancy and lactation influences serum profile, liver phenotype and hepatic miRNA expression in young male and female offspring. J Nutr Biochem 2024; 129:109639. [PMID: 38583498 DOI: 10.1016/j.jnutbio.2024.109639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024]
Abstract
This study aimed to investigate whether modifying the pre-gestational lipid content could mitigate metabolic damage in offspring from dams exposed to a high-fat (HF) diet before conception and during pregnancy and lactation, with a focus on sex-specific outcomes. Specific effects of maternal normolipidic diets on offspring were also assessed. Female Wistar rats received control (C) or HF diets before conception. During pregnancy and lactation, females were distributed in five groups: C-C, HF-HF, HF-C, HF-saturated (HF-S) or HF-polyunsaturated n-3 group (HF-P). Saturated and PUFA n-3 diets were normolipidic. In 21-day-old offspring, corporal parameters, adiposity, serum metabolites, OGTT, liver phenotype, and miR-34a-5p hepatic expression were determined. Pre-gestational HF diet impaired glycemic response in females, independent of any change in body weight. Female and male offspring from dams continuously exposed to HF diet exhibited hyperglycemia, increased adiposity, and disrupted serum lipid profiles. Male offspring showed increased hepatic fat accumulation and miR-34a-5p expression. Shifting maternal dietary lipid content to normolipidic diets restored offspring's phenotype; however, decreased SIRT1, IRβ and IRS1 expression in offspring from dams exposed to HF diet before conception suggested early indicators of glucose metabolism damage. Our findings indicated a pronounced metabolic impact on males. In conclusion, glucose tolerance impairment in females before conception disturbed intrauterine environment, influencing in offspring's phenotype. Modifying maternal dietary lipid content mitigated effects of pre-gestational HF diet exposure on young offspring. Nevertheless, decreased hepatic levels of critical insulin signaling proteins indicated that independently of the maternal diet, pre-existing HF diet-induced glucose intolerance before conception may adversely program the offspring's phenotype.
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Affiliation(s)
- Laís Vales Mennitti
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil; Metabolic Research Laboratories and MRC Metabolic Diseases Unit, University of Cambridge, Cambridge, United Kingdom
| | - Esther Alves de Souza
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Aline Boveto Santamarina
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Marcela Nascimento Sertorio
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Andrea Jucá
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Daniel Vitor De Souza
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Daniel Araki Ribeiro
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil
| | - Luciana Pellegrini Pisani
- Department of Bioscience, Institute of Health and Society, Laboratory of Nutrition and Endocrine Physiology, Federal University of São Paulo, Santos, Brazil.
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Roka Pun H, Karp X. An RNAi screen for conserved kinases that enhance microRNA activity after dauer in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkae007. [PMID: 38226857 PMCID: PMC10917497 DOI: 10.1093/g3journal/jkae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/17/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes posttranscriptionally through the activity of the microRNA-induced silencing complex. Argonaute is the core microRNA-induced silencing complex protein that binds to both the microRNA and to other microRNA-induced silencing complex proteins. The 2 major microRNA Argonautes in the Caenorhabditis elegans soma are ALG-1 and ALG-2, which function partially redundantly. Loss of alg-1 [alg-1(0)] causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent if alg-1(0) animals undergo a diapause stage called dauer. Levels of the relevant microRNAs are not higher during or after dauer, suggesting that activity of the microRNA-induced silencing complex may be enhanced in this context. To identify genes that are required for alg-1(0) mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating microRNA-induced silencing complex activity. We found RNAi knockdown of 4 kinase-encoding genes, air-2, bub-1, chk-1, and nekl-3, caused vulval defects and reiterative phenotypes in alg-1(0) mutants after dauer, and that these defects were more penetrant in an alg-1(0) background than in wild type. Our results implicate these kinases as potential regulators of microRNA-induced silencing complex activity during postdauer development in C. elegans.
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Affiliation(s)
- Himal Roka Pun
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Xantha Karp
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859, USA
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Su W, Ye Z, Wang G, Huang H, Fang Y. Circ_0008410 contributes to fibroblast-like synoviocytes dysfunction by regulating miR-149-5p/HIPK2 axis. Microbiol Immunol 2024; 68:100-110. [PMID: 38129937 DOI: 10.1111/1348-0421.13110] [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: 05/16/2023] [Revised: 11/14/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Circular RNAs (circRNAs) play functional roles in rheumatoid arthritis (RA) progression. Fibroblast-like synoviocytes (RASFs) are the main effectors in RA development. In this study, we explored the function and mechanism of circ_0008410 in RASFs. qRT-PCR was used to detect the expression of circ_0008410, microRNA-149-5p (miR-149-5p), and homeodomain-interacting protein kinase 2 (HIPK2). Cell counting kit-8, EdU assay, flow cytometry, and transwell assay were performed to evaluate cell proliferation, apoptosis, migration, and invasion. Western blot measured the protein levels of related markers and HIPK2. The levels of IL-1β, TNF-α, and IL-6 were tested by corresponding ELISA kits and Western blot. The combination between miR-149-5p and circ_0008410 or HIPK2 was detected by dual-luciferase reporter assay or RNA immunoprecipitation (RIP) assay. Our data showed that circ_0008410 and HIPK2 were elevated, while miR-149-5p was downregulated in RA synovial tissues and RASFs. Circ_0008410 promoted RASF proliferation, migration, invasion, and inflammation while inhibiting apoptosis. MiR-149-5p was a target of circ_0008410, and its overexpression could reverse the promoting effects of circ_0008410 on RASF dysfunction. Moreover, miR-149-5p could target HIPK2 to suppress RASF proliferation, migration, invasion, and inflammation. Collectively, circ_0008410 promoted RASF dysfunction via miR-149-5p/HIPK2, which might provide a potential target for RA therapy.
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Affiliation(s)
- Wensi Su
- Department of Geriatric Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, People's Republic of China
| | - Zhifang Ye
- Department of Sports Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, People's Republic of China
| | - Guangji Wang
- Department of Sports Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, People's Republic of China
| | - Hui Huang
- Department of Sports Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, People's Republic of China
| | - Yehan Fang
- Department of Sports Medicine, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, People's Republic of China
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10
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To KKW, Huang Z, Zhang H, Ashby CR, Fu L. Utilizing non-coding RNA-mediated regulation of ATP binding cassette (ABC) transporters to overcome multidrug resistance to cancer chemotherapy. Drug Resist Updat 2024; 73:101058. [PMID: 38277757 DOI: 10.1016/j.drup.2024.101058] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Multidrug resistance (MDR) is one of the primary factors that produces treatment failure in patients receiving cancer chemotherapy. MDR is a complex multifactorial phenomenon, characterized by a decrease or abrogation of the efficacy of a wide spectrum of anticancer drugs that are structurally and mechanistically distinct. The overexpression of the ATP-binding cassette (ABC) transporters, notably ABCG2 and ABCB1, are one of the primary mediators of MDR in cancer cells, which promotes the efflux of certain chemotherapeutic drugs from cancer cells, thereby decreasing or abolishing their therapeutic efficacy. A number of studies have suggested that non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play a pivotal role in mediating the upregulation of ABC transporters in certain MDR cancer cells. This review will provide updated information about the induction of ABC transporters due to the aberrant regulation of ncRNAs in cancer cells. We will also discuss the measurement and biological profile of circulating ncRNAs in various body fluids as potential biomarkers for predicting the response of cancer patients to chemotherapy. Sequence variations, such as alternative polyadenylation of mRNA and single nucleotide polymorphism (SNPs) at miRNA target sites, which may indicate the interaction of miRNA-mediated gene regulation with genetic variations to modulate the MDR phenotype, will be reviewed. Finally, we will highlight novel strategies that could be used to modulate ncRNAs and circumvent ABC transporter-mediated MDR.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Zoufang Huang
- Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Hang Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, United States
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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11
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Vaswani CM, Simone J, Pavelick JL, Wu X, Tan GW, Ektesabi AM, Gupta S, Tsoporis JN, Dos Santos CC. Tiny Guides, Big Impact: Focus on the Opportunities and Challenges of miR-Based Treatments for ARDS. Int J Mol Sci 2024; 25:2812. [PMID: 38474059 DOI: 10.3390/ijms25052812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Acute Respiratory Distress Syndrome (ARDS) is characterized by lung inflammation and increased membrane permeability, which represents the leading cause of mortality in ICUs. Mechanical ventilation strategies are at the forefront of supportive approaches for ARDS. Recently, an increasing understanding of RNA biology, function, and regulation, as well as the success of RNA vaccines, has spurred enthusiasm for the emergence of novel RNA-based therapeutics. The most common types of RNA seen in development are silencing (si)RNAs, antisense oligonucleotide therapy (ASO), and messenger (m)RNAs that collectively account for 80% of the RNA therapeutics pipeline. These three RNA platforms are the most mature, with approved products and demonstrated commercial success. Most recently, miRNAs have emerged as pivotal regulators of gene expression. Their dysregulation in various clinical conditions offers insights into ARDS pathogenesis and offers the innovative possibility of using microRNAs as targeted therapy. This review synthesizes the current state of the literature to contextualize the therapeutic potential of miRNA modulation. It considers the potential for miR-based therapeutics as a nuanced approach that incorporates the complexity of ARDS pathophysiology and the multifaceted nature of miRNA interactions.
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Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Julia Simone
- Department of Medicine, McMaster University, Hamilton, ON L8V 5C2, Canada
| | - Jacqueline L Pavelick
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xiao Wu
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Greaton W Tan
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sahil Gupta
- Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
- Institute of Medical Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Interdepartmental Division of Critical Care, St. Michael's Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada
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12
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Wu J, Duan C, Han C, Hou X. Identification of CXC Chemokine Receptor 2 (CXCR2) as a Novel Eosinophils-Independent Diagnostic Biomarker of Pediatric Eosinophilic Esophagitis by Integrated Bioinformatic and Machine-Learning Analysis. Immunotargets Ther 2024; 13:55-74. [PMID: 38328342 PMCID: PMC10849108 DOI: 10.2147/itt.s439289] [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: 09/08/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Background Eosinophilic esophagitis (EoE) is a complex allergic condition frequently accompanied by various atopic comorbidities in children, which significantly affects their life qualities. Therefore, this study aimed to evaluate pivotal molecular markers that may facilitate the diagnosis of EoE in pediatric patients. Methods Three available EoE-associated gene expression datasets in children: GSE184182, GSE 197702, GSE55794, along with GSE173895 were downloaded from the GEO database. Differentially expressed genes (DEGs) identified by "limma" were intersected with key module genes identified by weighted gene co-expression network analysis (WGCNA), and the shared genes went through functional enrichment analysis. The protein-protein interaction (PPI) network and the machine learning algorithms: least absolute shrinkage and selection operator (LASSO), random forest (RF), and XGBoost were used to reveal candidate diagnostic markers for EoE. The receiver operating characteristic (ROC) curve showed the efficacy of differential diagnosis of this marker, along with online databases predicting its molecular regulatory network. Finally, we performed gene set enrichment analysis (GSEA) and assessed immune cell infiltration of EoE/control samples by using the CIBERSORT algorithm. The correlations between the key diagnostic biomarker and immune cells were also investigated. Results The intersection of 936 DEGs and 1446 key module genes in EoE generated 567 genes, which were primarily enriched in immune regulation. Following the construction of the PPI network and filtration by machine learning, CXCR2 served as a potential diagnostic biomarker of pediatric EoE with a perfect diagnostic efficacy (AUC = ~1.00) in regional tissue/peripheral whole blood samples. Multiple infiltrated immune cells were observed to participate in disrupting the homeostasis of esophageal epithelium to varying degrees. Conclusion The immune-correlated CXCR2 gene was proved to be a promising diagnostic indicator for EoE, and dysregulated regulatory T cells (Tregs)/neutrophils might play a crucial role in the pathogenesis of EoE in children.
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Affiliation(s)
- Junhao Wu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Caihan Duan
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Chaoqun Han
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
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13
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Zhao Y, Qin J, Sun J, He J, Sun Y, Yuan R, Li Z. Motility-related microRNAs identified in pig seminal plasma exosomes by high-throughput small RNA sequencing. Theriogenology 2024; 215:351-360. [PMID: 38150851 DOI: 10.1016/j.theriogenology.2023.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Boar fertility is a key determinant of the production efficiency of the whole pig breeding industry and boar sperm motility is the seminal parameter with the greatest impact on the fecundity of a sow. Exosomes are small, extracellular vesicles found in many body fluids. Seminal plasma exosomes, which are secreted by the epididymis, prostate, seminal vesicles, and testes, contain a large number of miRNAs, the types and levels of which can reflect the physiological state of source cells. It has been shown that the expression profile of seminal plasma exosomal miRNA differs between low-motility semen and normal semen. The aim of this study was to investigate the relationship between semen motility and exosomal miRNA profiles to obtain information that would allow to predict boar fertility, as well as contribute to the understanding of the mechanisms by which exosomal miRNAs regulate semen motility. Three high-motility (semen motility >90 %) and three low-motility (semen motility <80 %) semen samples were collected from Landrace and Yorkshire boars, respectively, and seminal plasma exosomes were extracted by ultracentrifugation. Exosome characterization was performed using transmission electron microscopy, NTA, and Western blot. The expression profiles of exosomal miRNAs associated with semen motility in the two boar breeds were subsequently determined by small RNA sequencing. The results showed that 297 known miRNAs and 295 novel RNAs were co-expressed in the four groups. Notably, six miRNAs (ssc-miR-122-5p, ssc-miR-486, ssc-miR-451, ssc-miR-345-3p, ssc-miR-362, and ssc-miR-500-5p) were found to be differentially expressed in both boar breeds. Enrichment analysis of the target genes of the differentially expressed miRNAs showed that they were mainly involved in biological processes such as regulation of transcription from RNA polymerase II promoter, regulation of gene expression, and intracellular signal transduction and signaling pathways such as the PI3K-Akt, MAPK, and Ras signaling pathways. The six differentially expressed miRNAs identified in this study have significant potential as noninvasive markers of boar semen motility. Meanwhile, the results of the enrichment analysis provide novel insights into the mechanisms underlying the regulation of semen motility.
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Affiliation(s)
- Yunxiang Zhao
- College of Animal Science & Technology, Guangxi University, Nanning, 530004, Guangxi Autonomous Region, China; Guangxi Yangxiang Co., LTD, Guigang, 537000, Guangxi Autonomous Region, China
| | - Jiali Qin
- College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong province, China; Guangxi Yangxiang Co., LTD, Guigang, 537000, Guangxi Autonomous Region, China
| | - Jingshuai Sun
- College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong province, China
| | - Jian He
- College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong province, China
| | - Yanmei Sun
- College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong province, China
| | - Renqiang Yuan
- Guangxi Yangxiang Co., LTD, Guigang, 537000, Guangxi Autonomous Region, China
| | - Zhili Li
- College of Life Science and Engineering, Foshan University, Foshan, 528231, Guangdong province, China.
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14
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Guzman-Espinoza M, Kim M, Ow C, Hutchins EJ. "Beyond transcription: How post-transcriptional mechanisms drive neural crest EMT". Genesis 2024; 62:e23553. [PMID: 37735882 PMCID: PMC10954587 DOI: 10.1002/dvg.23553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The neural crest is a stem cell population that originates from the ectoderm during the initial steps of nervous system development. Neural crest cells delaminate from the neuroepithelium by undergoing a spatiotemporally regulated epithelial-mesenchymal transition (EMT) that proceeds in a coordinated wave head-to-tail to exit from the neural tube. While much is known about the transcriptional programs and membrane changes that promote EMT, there are additional levels of gene expression control that neural crest cells exert at the level of RNA to control EMT and migration. Yet, the role of post-transcriptional regulation, and how it drives and contributes to neural crest EMT, is not well understood. In this mini-review, we explore recent advances in our understanding of the role of post-transcriptional regulation during neural crest EMT.
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Affiliation(s)
- Mariann Guzman-Espinoza
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Minyoung Kim
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Oral and Craniofacial Sciences Graduate Program, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
| | - Cindy Ow
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Erica J. Hutchins
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Oral and Craniofacial Sciences Graduate Program, School of Dentistry, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
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15
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Li J, Chen J, Wang Z, Lei X. HoRDA: Learning higher-order structure information for predicting RNA-disease associations. Artif Intell Med 2024; 148:102775. [PMID: 38325924 DOI: 10.1016/j.artmed.2024.102775] [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: 11/14/2022] [Revised: 10/16/2023] [Accepted: 01/14/2024] [Indexed: 02/09/2024]
Abstract
CircRNA and miRNA are crucial non-coding RNAs, which are associated with biological diseases. Exploring the associations between RNAs and diseases often requires a significant time and financial investments, which has been greatly alleviated and improved with the application of deep learning methods in bioinformatics. However, existing methods often fail to achieve higher accuracy and cannot be universal between multiple RNAs. Moreover, complex RNA-disease associations hide important higher-order topology information. To address these issues, we learn higher-order structure information for predicting RNA-disease associations (HoRDA). Firstly, the correlations between RNAs and the correlations between diseases are fully explored by combining similarity and higher-order graph attention network. Then, a higher-order graph convolutional network is constructed to aggregate neighbor information, and further obtain the representations of RNAs and diseases. Meanwhile, due to the large number of complex and variable higher-order structures in biological networks, we design a higher-order negative sampling strategy to gain more desirable negative samples. Finally, the obtained embeddings of RNAs and diseases are feed into logistic regression model to acquire the probabilities of RNA-disease associations. Diverse simulation results demonstrate the superiority of the proposed method. In the end, the case study is conducted on breast neoplasms, colorectal neoplasms, and gastric neoplasms. We validate the proposed higher-order strategies through ablative and exploratory analyses and further demonstrate the practical applicability of HoRDA. HoRDA has a certain contribution in RNA-disease association prediction.
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Affiliation(s)
- Julong Li
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Jianrui Chen
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China.
| | - Zhihui Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
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16
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Chai F, Peng H, Qin L, Liu C, Zeng Y, Wang R, Xu G, Wang R, Wei G, Huang H, Lan Y, Chen W, Wang C. MicroRNA miR-181d-5p regulates the MAPK signaling pathway by targeting mitogen-activated protein kinase 8 (MAPK8) to improve lupus nephritis. Gene 2024; 893:147961. [PMID: 37931853 DOI: 10.1016/j.gene.2023.147961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/21/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Lupus nephritis (LN) is a common immune disease. The microRNA (miR)-181d-5p is a potential target for treating kidney injury. However, the therapeutic role of miR-181d-5p in LN has not been investigated. This study aimed to investigate the role of miR-181d-5p in targeting mitogen-activated protein kinase 8 (MAPK8) and stimulating the MAPK signaling pathway in LN. METHODS RT-qPCR was performed to identify the variations in miR-181d-5p expression in peripheral blood mononuclear cells (PBMCs) obtained from 42 LN patients, 30 healthy individuals, 6 MRL/lpr mice and 6 C57BL/6 mice. Western blot was used to detect the effect of miR-181d-5p on the MAPK signaling pathway in THP-1 cells and MRL/lpr mice. Enzyme-linked immunosorbent assay (ELISA) was utilized to detect the effect of miR-181d-5p on antinuclear antibodies and inflammatory factors. A dual-luciferase reporter assay was used to verify whether miR-181d-5p directly targets MAPK8. Flow cytometry was performed to evaluate apoptosis rates in transfected THP-1 cells. RESULTS miR-181d-5p expression was downregulated in PBMCs of LN patients (P < 0.01) and MRL/lpr mice (P < 0.05). A dual luciferase reporter assay demonstrated that miR-181d-5p inhibits MAPK8 (P < 0.01). Overexpression of miR-181d-5p inhibited the phosphorylation of p38 (P < 0.001) and p44/42 (P < 0.01). Moreover, miR-181d-5p decreased the apoptosis rate of THP-1 cells (P < 0.001), and reduced the secretion of IL-6 (P < 0.01) and TNF-α (P < 0.01). Furthermore, overexpression of miR-181d-5p decreased anti-dsDNA antibody (P < 0.05), anti-Sm antibody (P < 0.01), and fibrosis levels in MRL/lpr mice. CONCLUSION Upregulation of miR-181d-5p showed anti-inflammatory and anti-apoptotic effects on THP-1 cells in vitro and kidney injury in vivo. These effects were achieved by miR-181d-5p targeting MAPK8 to inhibit phosphorylation of p38 and p44/42. These results may offer new insights for improving therapeutic strategies against lupus nephritis.
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Affiliation(s)
- Fu Chai
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China; Graduate School of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Huixin Peng
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China; Graduate School of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Linxiu Qin
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China; Graduate School of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Chunhong Liu
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Yonglong Zeng
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Rong Wang
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Guidan Xu
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Rongqi Wang
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Huayi Huang
- Roswell Park Comprehensive Cancer Center, Surgical Oncology, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Yan Lan
- Department of Dermatology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Wencheng Chen
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China.
| | - Chunfang Wang
- Center for Medical Laboratory Science, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China.
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17
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Panagiotidou A, Chatzakis C, Ververi A, Eleftheriades M, Sotiriadis A. The Effect of Maternal Diet and Physical Activity on the Epigenome of the Offspring. Genes (Basel) 2024; 15:76. [PMID: 38254965 PMCID: PMC10815371 DOI: 10.3390/genes15010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The aim of this review was to examine the current literature regarding the effect of maternal lifestyle interventions (i.e., diet and physical activity) on the epigenome of the offspring. PubMed, Scopus and Cochrane-CENTRAL were screened until 8 July 2023. Only randomized controlled trials (RCTs) where a lifestyle intervention was compared to no intervention (standard care) were included. Outcome variables included DNA methylation, miRNA expression, and histone modifications. A qualitative approach was used for the consideration of the studies' results. Seven studies and 1765 mother-child pairs were assessed. The most common types of intervention were dietary advice, physical activity, and following a specific diet (olive oil). The included studies correlated the lifestyle and physical activity intervention in pregnancy to genome-wide or gene-specific differential methylation and miRNA expression in the cord blood or the placenta. An intervention of diet and physical activity in pregnancy was found to be associated with slight changes in the epigenome (DNA methylation and miRNA expression) in fetal tissues. The regions involved were related to adiposity, metabolic processes, type 2 diabetes, birth weight, or growth. However, not all studies showed significant differences in DNA methylation. Further studies with similar parameters are needed to have robust and comparable results and determine the biological role of such modifications.
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Affiliation(s)
- Anastasia Panagiotidou
- School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece; (A.P.); (C.C.); (A.V.)
| | - Christos Chatzakis
- School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece; (A.P.); (C.C.); (A.V.)
- Second Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece
| | - Athina Ververi
- School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece; (A.P.); (C.C.); (A.V.)
- Genetic Unit, First Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, “Papageorgiou” General Hospital, 564 03 Thessaloniki, Greece
| | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, 115 28 Athens, Greece;
| | - Alexandros Sotiriadis
- School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece; (A.P.); (C.C.); (A.V.)
- Second Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, 546 22 Thessaloniki, Greece
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18
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Zhao Y, Poudel P, Wang S. Detection of MicroRNAs Using Synthetic Toehold Switch in Mammalian Cells. Methods Mol Biol 2024; 2774:243-258. [PMID: 38441769 DOI: 10.1007/978-1-0716-3718-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Engineering synthetic gene circuits to control cellular functions has a broad application in the field of synthetic biology. Synthetic RNA-based switches that can operate at the transcriptional and posttranscriptional level have also drawn significant interest for the application of next-generation therapeutics and diagnostics. Thus, RNA-based switchable platforms are needed to report dynamic cellular mechanisms which play an important role in cell development and diseases. Recently, several RNA-based switches have been designed and utilized for biosensing and molecular diagnostics. However, miRNA-based switches have not been well established or characterized, especially for eukaryotic translational control. Here, we designed a novel synthetic toehold switch for detection of exogenously and endogenously expressed miRNAs in CHO, HeLa, HEK 293, and MDA-MB-231 breast cancer cells. Multiplex detection of miR-155 and miR-21 was tested using two toehold switches to evaluate the orthogonality and programmability of this synthetic platform.
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Affiliation(s)
- Yuwen Zhao
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Pratima Poudel
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA
| | - Shue Wang
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA.
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19
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Chen F, Shi B, Liu W, Gong J, Gao J, Sun Y, Yang P. Circulating exosomal microRNAs as biomarkers of lupus nephritis. Front Immunol 2023; 14:1326836. [PMID: 38223506 PMCID: PMC10785001 DOI: 10.3389/fimmu.2023.1326836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/08/2023] [Indexed: 01/16/2024] Open
Abstract
Objective Disruption in the delicate symphony of genes, microRNA (miRNA), or protein expression can result in the dysregulation of the immune system, leading to the devastating consequences such as lupus nephritis (LN). The capacity of exosomes to transport miRNAs between cells and modify the phenotype of recipient cells implies their involvement in persistent kidney inflammation. This study unveils identifying two previously undiscovered exosomal miRNAs in the serum of LN patients, offering potential solutions to the current challenges in LN diagnosis and management. Methods Initially, we used a reagent-based kit to isolate serum exosomes from patients with Systemic lupus erythematosus (SLE) and used Trizol method for total RNA extraction. Subsequently, we employed small RNA sequencing to screen for differential expression profiles of exosomal small RNAs. The RT-qPCR method was used to individually validate samples in both the screening and validation cohorts, enabling the identification of candidate small RNAs; specific to LN. We assessed the diagnostic potency using receiver operating characteristic (ROC) curve, and explored the biological roles of miRNAs using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Results Compared to SLE patients without LN, SLE patients accompanied by LN exhibited significantly spiked levels of exosomal hsa-miR-4796-5p and hsa-miR-7974. The duo of miRNAs, hsa-miR-4796-5p and hsa-miR-7974, exhibited promising potential as biomarkers for diagnosing LN, with an AUC exceeding 0.8. Correlation analysis revealed a strong positive association between these miRNAs and proteinuria, as well as the SLE Disease Activity Index (SLEDAI) score. Moreover, the levels of two miRNAs in LN patients were significantly elevated in comparison to other autoimmune nephritis conditions, such as immunoglobulin A nephropathy (IgAN) and diabetic nephropathy (DN). Furthermore, the bioinformatics analysis indicated that this miRNAs duo can play a pivotal role in the regulation of immune processes by modulating signal pathways, such as the mTOR and PI3K-Akt signaling pathway. Conclusion This study provides a new ground that serum exosomal miRNAs can effectively identify and predict LN in SLE patients.
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Affiliation(s)
- Fei Chen
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Bo Shi
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Wenjing Liu
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Jianmin Gong
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Jia Gao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yifan Sun
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Ping Yang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
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20
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Yang L, Feng H. Cross-kingdom regulation by plant-derived miRNAs in mammalian systems. Animal Model Exp Med 2023; 6:518-525. [PMID: 38064180 PMCID: PMC10757204 DOI: 10.1002/ame2.12358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/15/2023] [Indexed: 12/31/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules ubiquitously distributed across diverse organisms, serving as pivotal regulators of genetic expression. Notably, plant-derived miRNAs have been demonstrated to have unique bioactivity and certain stability in mammalian systems, thereby facilitating their capacity for cross-kingdom modulation of gene expression. While there is substantial evidence supporting the regulation of mammalian cells by plant-derived miRNAs, several questions remain unanswered. Specifically, a comprehensive investigation of the mechanisms underlying the stability and transport of plant miRNAs and their cross-kingdom regulation of gene expression in mammals remains to be done. In this review, we summarized the origin, processing, and functional mechanisms of plant miRNAs in mammalian tissues and circulation, emphasizing their greater resistance to mammalian digestion and circulation systems compared to animal miRNAs. Additionally, we introduce four well-known plant miRNAs that have been extensively studied for their functions and mechanisms in mammalian systems. By delving into these aspects, we aim to offer a fundamental understanding of this intriguing field and shed light on the complex interactions between plant miRNAs and mammalian biology.
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Affiliation(s)
- Linpu Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Han Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
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21
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Parsa-Kondelaji M, Musavi M, Barzegar F, Abbasian N, Rostami M, R Seyedtaghia M, S Hashemi S, Modi M, Nikfar B, A Momtazi-Borojeni A. Dysregulation of miRNA expression in patients with chronic myelogenous leukemia at diagnosis: a systematic review. Biomark Med 2023; 17:1021-1029. [PMID: 38230979 DOI: 10.2217/bmm-2023-0575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Aim: The present systematic review aimed to explore miRNAs as a potential biomarker for early diagnosis of chronic myeloid leukemia (CML). Materials & methods: A systematic search was conducted in three electronic databases, including Web of Science, Scopus and PubMed, to obtain relevant articles investigating the alteration of miRNA expression in patients with CML. Results: The authors found miRNAs whose expression changes are effective in the induction of CML disease. Among them, miR-21 and miR-155 were identified as the most common miRNAs with increased expression and miR-150 and miR-146 as the most common miRNAs with decreased expression. Conclusion: miRNAs can be used as an indicator for the early detection and treatment of CML phase.
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Affiliation(s)
- Mohammad Parsa-Kondelaji
- Department of Hematology & Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Musavi
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Faezeh Barzegar
- Department of Hematology & Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Abbasian
- Hematology & Blood Banking Center, Emam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Rostami
- Department of Hematology & Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad R Seyedtaghia
- Department of Medical Genetics & Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyyed S Hashemi
- Department of Medical Genetics & Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdiyeh Modi
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
- Department of Medical Biotechnology, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Banafsheh Nikfar
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Amir A Momtazi-Borojeni
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
- Department of Medical Biotechnology, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
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22
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Jouve M, Carpentier R, Kraiem S, Legrand N, Sobolewski C. MiRNAs in Alcohol-Related Liver Diseases and Hepatocellular Carcinoma: A Step toward New Therapeutic Approaches? Cancers (Basel) 2023; 15:5557. [PMID: 38067261 PMCID: PMC10705678 DOI: 10.3390/cancers15235557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 06/29/2024] Open
Abstract
Alcohol-related Liver Disease (ALD) is the primary cause of chronic liver disorders and hepatocellular carcinoma (HCC) development in developed countries and thus represents a major public health concern. Unfortunately, few therapeutic options are available for ALD and HCC, except liver transplantation or tumor resection for HCC. Deciphering the molecular mechanisms underlying the development of these diseases is therefore of major importance to identify early biomarkers and to design efficient therapeutic options. Increasing evidence indicate that epigenetic alterations play a central role in the development of ALD and HCC. Among them, microRNA importantly contribute to the development of this disease by controlling the expression of several genes involved in hepatic metabolism, inflammation, fibrosis, and carcinogenesis at the post-transcriptional level. In this review, we discuss the current knowledge about miRNAs' functions in the different stages of ALD and their role in the progression toward carcinogenesis. We highlight that each stage of ALD is associated with deregulated miRNAs involved in hepatic carcinogenesis, and thus represent HCC-priming miRNAs. By using in silico approaches, we have uncovered new miRNAs potentially involved in HCC. Finally, we discuss the therapeutic potential of targeting miRNAs for the treatment of these diseases.
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Affiliation(s)
- Mickaël Jouve
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Rodolphe Carpentier
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Sarra Kraiem
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Noémie Legrand
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Cyril Sobolewski
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France
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23
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Luo X, Liu J, Wang X, Yuan J, Zhang Y. Circ-DTL sponges miR-758-3p to accelerate cervical cancer malignant progression by regulating DCUN1D1 expression. J Biochem Mol Toxicol 2023; 37:e23462. [PMID: 37522575 DOI: 10.1002/jbt.23462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/26/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023]
Abstract
Circular RNAs (circRNAs) play important roles in regulating various cancer progression. However, the function and clinical significance of circ-denticleless E3 ubiquitin proteinligase homolog (DTL) in cervical cancer (CC) have not been studied. The present work explored the function and mechanism of circ-DTL in CC development. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to examine the expression of circ-DTL, miR-758-3p, and DCUN1D1. Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assays were used to detect cell proliferation. Cell cycle and cell apoptosis were investigated by flow cytometry. Wound-healing assay and transwell assay were conducted to assess cell migration and cell invasion. Western blot assay was carried out to determine protein expression. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were used to identify the relationship between miR-758-3p and circ-DTL or DCUN1D1. Xenograft mouse model assay was conducted to explore the role of circ-DTL in CC progression in vivo. Circ-DTL and DCUN1D1 expression were upregulated in CC tissues and CC cells, but miR-758-3p expression was downregulated. Knockdown of circ-DTL inhibited CC cell growth, migration, and invasion and promoted cell cycle arrest and cell apoptosis. Circ-DTL could sponge miR-758-3p to modulate CC cell progression. Moreover, miR-758-3p inhibited CC malignant development by suppressing DCUN1D1 expression. In addition, circ-DTL knockdown repressed CC cell tumor properties in vivo. Circ-DTL acted as a tumor promoter in CC development by regulating the miR-758-3p/DCUN1D1 pathway.
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Affiliation(s)
- Xiaoning Luo
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Jiewen Liu
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xiangcai Wang
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Jun Yuan
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Yu Zhang
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, Jiangxi, China
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24
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Jani PK, Petkau G, Kawano Y, Klemm U, Guerra GM, Heinz GA, Heinrich F, Durek P, Mashreghi MF, Melchers F. The miR-221/222 cluster regulates hematopoietic stem cell quiescence and multipotency by suppressing both Fos/AP-1/IEG pathway activation and stress-like differentiation to granulocytes. PLoS Biol 2023; 21:e3002015. [PMID: 37983263 PMCID: PMC10695376 DOI: 10.1371/journal.pbio.3002015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 12/04/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Throughout life, hematopoietic stem cells (HSCs), residing in bone marrow (BM), continuously regenerate erythroid/megakaryocytic, myeloid, and lymphoid cell lineages. This steady-state hematopoiesis from HSC and multipotent progenitors (MPPs) in BM can be perturbed by stress. The molecular controls of how stress can impact hematopoietic output remain poorly understood. MicroRNAs (miRNAs) as posttranscriptional regulators of gene expression have been found to control various functions in hematopoiesis. We find that the miR-221/222 cluster, which is expressed in HSC and in MPPs differentiating from them, perturbs steady-state hematopoiesis in ways comparable to stress. We compare pool sizes and single-cell transcriptomes of HSC and MPPs in unperturbed or stress-perturbed, miR-221/222-proficient or miR-221/222-deficient states. MiR-221/222 deficiency in hematopoietic cells was induced in C57BL/6J mice by conditional vav-cre-mediated deletion of the floxed miR-221/222 gene cluster. Social stress as well as miR-221/222 deficiency, alone or in combination, reduced HSC pools 3-fold and increased MPPs 1.5-fold. It also enhanced granulopoisis in the spleen. Furthermore, combined stress and miR-221/222 deficiency increased the erythroid/myeloid/granulocytic precursor pools in BM. Differential expression analyses of single-cell RNAseq transcriptomes of unperturbed and stressed, proficient HSC and MPPs detected more than 80 genes, selectively up-regulated in stressed cells, among them immediate early genes (IEGs). The same differential single-cell transcriptome analyses of unperturbed, miR-221/222-proficient with deficient HSC and MPPs identified Fos, Jun, JunB, Klf6, Nr4a1, Ier2, Zfp36-all IEGs-as well as CD74 and Ly6a as potential miRNA targets. Three of them, Klf6, Nr4a1, and Zfp36, have previously been found to influence myelogranulopoiesis. Together with increased levels of Jun, Fos forms increased amounts of the heterodimeric activator protein-1 (AP-1), which is known to control the expression of the selectively up-regulated expression of the IEGs. The comparisons of single-cell mRNA-deep sequencing analyses of socially stressed with miR-221/222-deficient HSC identify 5 of the 7 Fos/AP-1-controlled IEGs, Ier2, Jun, Junb, Klf6, and Zfp36, as common activators of HSC from quiescence. Combined with stress, miR-221/222 deficiency enhanced the Fos/AP-1/IEG pathway, extended it to MPPs, and increased the number of granulocyte precursors in BM, inducing selective up-regulation of genes encoding heat shock proteins Hspa5 and Hspa8, tubulin-cytoskeleton-organizing proteins Tuba1b, Tubb 4b and 5, and chromatin remodeling proteins H3f3b, H2afx, H2afz, and Hmgb2. Up-regulated in HSC, MPP1, and/or MPP2, they appear as potential regulators of stress-induced, miR-221/222-dependent increased granulocyte differentiation. Finally, stress by serial transplantations of miR-221/222-deficient HSC selectively exhausted their lymphoid differentiation capacities, while retaining their ability to home to BM and to differentiate to granulocytes. Thus, miR-221/222 maintains HSC quiescence and multipotency by suppressing Fos/AP-1/IEG-mediated activation and by suppressing enhanced stress-like differentiation to granulocytes. Since miR-221/222 is also expressed in human HSC, controlled induction of miR-221/222 in HSC should improve BM transplantations.
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Affiliation(s)
- Peter K. Jani
- Deutsches Rheuma Forschungszentrum (DRFZ), Berlin, Germany
| | - Georg Petkau
- Deutsches Rheuma Forschungszentrum (DRFZ), Berlin, Germany
| | - Yohei Kawano
- Deutsches Rheuma Forschungszentrum (DRFZ), Berlin, Germany
| | - Uwe Klemm
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | - Pawel Durek
- Deutsches Rheuma Forschungszentrum (DRFZ), Berlin, Germany
| | | | - Fritz Melchers
- Deutsches Rheuma Forschungszentrum (DRFZ), Berlin, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
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25
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Kumari P, Sarovar Bhavesh N. Birth and death view of DNA, RNA, and proteins. Gene 2023; 883:147672. [PMID: 37506987 DOI: 10.1016/j.gene.2023.147672] [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: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The potential of cells to guide their genome and configure genes to express at a given time and in response to specific stimuli is pivotal to regulate cellular processes such as tissue differentiation, organogenesis, organismal development, homeostasis, and disease. In this review, we focus on the diverse mechanisms involved in DNA replication and its degradation, mRNA synthesis, and associated regulation such as RNA capping, splicing, tailing, and export. mRNA turnover including Decapping, deadenylation, RNA interference, and Nonsense mediated mRNA decay followed by protein translation, post-translational modification, and protein turnover. We highlight recent advances in understanding the complex series of molecular mechanisms responsible for the remarkable cellular regulatory mechanisms.
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Affiliation(s)
- Pooja Kumari
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Neel Sarovar Bhavesh
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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26
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Shuaib M, Prajapati KS, Singh AK, Kumar S. Discovery of differentially expressed novel miRNAs in breast normal cells and their putative targets. Mol Cell Biochem 2023; 478:2361-2378. [PMID: 36680668 DOI: 10.1007/s11010-023-04665-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) play critical role in normal breast development and their altered expression may lead to breast cancer. Identification of new miRNAs allows us to understand the normal physiological process and associated disease pathophysiology. In the present study we identify the novel miRNAs in withaferin A treated breast normal cells (MCF-10A) using small RNA sequencing. The pathophysiological potential of the identified miRNAs was checked by studying their expression pattern in MDA-MB-231 and MCF-7 breast cancer cells using qRT-PCR technique. The secondary/tertiary structure of the identified miRNAs, target gene enrichment in Gene Ontology terms and KEGG pathway, miRNA-mRNA interaction of the sorted target genes, miRNA-mRNA/miRNA-argonaute protein/miRNA-mRNA-argonaute protein interaction and stability, were studied using bioinformatics tools/software, and molecular dynamics simulations. Hsa-miR-N88585 and hsa-miR-N461089 were identified and validated as novel miRNAs in normal breast cells. Up-expression of identified miRNAs in MDA-MB-231 and MCF-7 cells indicates their oncogenic nature. Identified target genes were enriched in classical signaling pathways (AMPK and Ras) and important GO terms. PLXDC2, BHLHE40, ARMC8, and PECAM1, CDC27, KCNK3 genes were sorted as putative targets for hsa-miR-N88585 and hsa-miR-N461089, respectively. MD simulation revealed stable hsa-miR-N88585/hsa-miR-N461089-AGO protein complex formation which indicates their further processing. In conclusion, the study identifies hsa-miR-N88585 and hsa-miR-N461089 as novel miRNAs in breast normal cells which are significantly inversely expressed in breast cancer cells. Further experiments are required to study the role of identified novel miRNAs in normal breast development and pathophysiology of breast cancer.
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Affiliation(s)
- Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India.
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27
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Liu C, Liu X, Li H, Kang Z. Advances in the regulation of adipogenesis and lipid metabolism by exosomal ncRNAs and their role in related metabolic diseases. Front Cell Dev Biol 2023; 11:1173904. [PMID: 37791070 PMCID: PMC10543472 DOI: 10.3389/fcell.2023.1173904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 08/15/2023] [Indexed: 10/05/2023] Open
Abstract
Exosomes are membrane-bound extracellular vesicles released following the fusion of multivesicular bodies (MVBs) with the cell membrane. Exosomes transport diverse molecules, including proteins, lipids, DNA and RNA, and regulate distant intercellular communication. Noncoding RNA (ncRNAs) carried by exosomes regulate cell-cell communication in tissues, including adipose tissue. This review summarizes the action mechanisms of ncRNAs carried by exosomes on adipocyte differentiation and modulation of adipogenesis by exosomal ncRNAs. This study aims to provide valuable insights for developing novel therapeutics.
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Affiliation(s)
- Cong Liu
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xilin Liu
- Department of Hand and Foot Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hong Li
- Department of Nursing, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhichen Kang
- Department of Rehabilitation, The Second Hospital of Jilin University, Changchun, China
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28
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Wang M, Yu F, Li P. Noncoding RNAs as an emerging resistance mechanism to immunotherapies in cancer: basic evidence and therapeutic implications. Front Immunol 2023; 14:1268745. [PMID: 37767098 PMCID: PMC10520974 DOI: 10.3389/fimmu.2023.1268745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The increasing knowledge in the field of oncoimmunology has led to extensive research into tumor immune landscape and a plethora of clinical immunotherapy trials in cancer patients. Immunotherapy has become a clinically beneficial alternative to traditional treatments by enhancing the power of the host immune system against cancer. However, it only works for a minority of cancers. Drug resistance continues to be a major obstacle to the success of immunotherapy in cancer. A fundamental understanding of the detailed mechanisms underlying immunotherapy resistance in cancer patients will provide new potential directions for further investigations of cancer treatment. Noncoding RNAs (ncRNAs) are tightly linked with cancer initiation and development due to their critical roles in gene expression and epigenetic modulation. The clear appreciation of the role of ncRNAs in tumor immunity has opened new frontiers in cancer research and therapy. Furthermore, ncRNAs are increasingly acknowledged as a key factor influencing immunotherapeutic treatment outcomes. Here, we review the available evidence on the roles of ncRNAs in immunotherapy resistance, with an emphasis on the associated mechanisms behind ncRNA-mediated immune resistance. The clinical implications of immune-related ncRNAs are also discussed, shedding light on the potential ncRNA-based therapies to overcome the resistance to immunotherapy.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | | | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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29
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Yu Y, Fan Z, Han Y, Sun X, Dong C, Liu G, Yin X, Liu L, Bai Y, Yang B. miR-135 protects against atrial fibrillation by suppressing intracellular calcium-mediated NLRP3 inflammasome activation. J Cell Commun Signal 2023; 17:813-825. [PMID: 36692633 PMCID: PMC10409699 DOI: 10.1007/s12079-023-00721-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/04/2023] [Indexed: 01/25/2023] Open
Abstract
Atrial fibrillation (AF), one of the most common types of arrhythmias, is associated with high morbidity and mortality, seriously endangering human health. Inflammation is closely associated with AF development. Activation of the nucleotide-binding domain-like receptor protein 3 (NLRP3) inflammasome in cardiomyocytes has been shown to promote AF progression. Here, we demonstrate the effect of miR-135 on NLRP3 inflammasome and study the cardioprotective role of miR-135 in AF. We observed that overexpression of miR-135 in mice reduced the AF incidence and duration, and inhibited both excessive activation of NLRP3 inflammasome and the increased intracellular calcium release during AF. However, the inhibitory effect of miR-135 on AF was partly abolished in the presence of a specific agonist of the calcium-sensing receptor (CaSR). We showed in the present study that miR-135 has a protective effect against AF by suppressing intracellular calcium-mediated NLRP3 inflammasome activation, suggesting the potential of miR-135 as a therapeutic agent in the treatment of AF.
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Affiliation(s)
- Yahan Yu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
- Zhuhai People's Hospital, Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, People's Republic of China
| | - Zheyu Fan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Yanna Han
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Xi Sun
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Chaorun Dong
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Guanqun Liu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Xinda Yin
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Linhe Liu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Yunlong Bai
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China.
- Joint International Research Laboratory of Cardiovascular Medicine, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, 150086, People's Republic of China.
| | - Baofeng Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China.
- Joint International Research Laboratory of Cardiovascular Medicine, Ministry of Education, College of Pharmacy, Harbin Medical University, Harbin, 150081, People's Republic of China.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, 150086, People's Republic of China.
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Hua X, Zou R, Bai X, Yang Y, Lu J, Huang C. Differential functions of RhoGDIβ in malignant transformation and progression of urothelial cell following N-butyl-N-(4-hydmoxybutyl) nitrosamine exposure. BMC Biol 2023; 21:181. [PMID: 37635218 PMCID: PMC10463823 DOI: 10.1186/s12915-023-01683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 08/15/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Functional role of Rho GDP-dissociation inhibitor beta (RhoGDIβ) in tumor biology appears to be contradictory across various studies. Thus, the exploration of the molecular mechanisms underlying the differential functions of this protein in urinary bladder carcinogenesis is highly significant in the field. Here, RhoGDIβ expression patterns, biological functions, and mechanisms leading to transformation and progression of human urothelial cells (UROtsa cells) were evaluated following varying lengths of exposure to the bladder carcinogen N-butyl-N-(4-hydmoxybutyl) nitrosamine (BBN). RESULTS It was seen that compared to expression in vehicle-treated control cells, RhoGDIβ protein expression was downregulated after 2-month of BBN exposure, but upregulated after 6-month of exposure. Assessments of cell function showed that RhoGDIβ inhibited UROtsa cell growth in cells with BBN for 2-month exposure, whereas it promoted the invasion of cells treated with BBN for 6 months. Mechanistic studies revealed that 2-month of BBN exposure markedly attenuated DNMT3a abundance, and this led to reduced miR-219a promoter methylation, increased miR-219a binding to the RhoGDIβ mRNA 3'UTR, and reduced RhoGDIβ protein translation. While after 6-mo of BBN treatment, the cells showed increased PP2A/JNK/C-Jun axis phosphorylation and this in turn mediated overall RhoGDIβ mRNA transcription and protein expression as well as invasion. CONCLUSIONS These findings indicate that RhoGDIβ is likely to inhibit the transformation of human urothelial cells during the early phase of BBN exposure, whereas it promotes invasion of the transformed/progressed urothelial cells in the late stage of BBN exposure. The studies also suggest that RhoGDIβ may be a useful biomarker for evaluating the progression of human bladder cancers.
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Affiliation(s)
- Xiaohui Hua
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ronghao Zou
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - Xiaoyue Bai
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - Yuyao Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - Juan Lu
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, Hefei, Anhui, 230032, People's Republic of China
| | - Chuanshu Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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31
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Hejenkowska ED, Mitash N, Donovan JE, Chandra A, Bertrand C, De Santi C, Greene CM, Mu F, Swiatecka-Urban A. TGF-β1 Inhibition of ACE2 Mediated by miRNA Uncovers Novel Mechanism of SARS-CoV-2 Pathogenesis. J Innate Immun 2023; 15:629-646. [PMID: 37579743 PMCID: PMC10601633 DOI: 10.1159/000533606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for COVID-19, utilizes receptor binding domain (RBD) of spike glycoprotein to interact with angiotensin (Ang)-converting enzyme 2 (ACE2). Altering ACE2 levels may affect entry of SARS-CoV-2 and recovery from COVID-19. Decreased cell surface density of ACE2 leads to increased local levels of Ang II and may contribute to mortality resulting from acute lung injury and fibrosis during COVID-19. Studies published early during the COVID-19 pandemic reported that people with cystic fibrosis (PwCF) had milder symptoms, compared to people without CF. This finding was attributed to elevated ACE2 levels and/or treatment with the high efficiency CFTR modulators. Subsequent studies did not confirm these findings reporting variable effects of CFTR gene mutations on ACE2 levels. Transforming growth factor (TGF)-β signaling is essential during SARS-CoV-2 infection and dominates the chronic immune response in severe COVID-19, leading to pulmonary fibrosis. TGF-β1 is a gene modifier associated with more severe lung disease in PwCF but its effects on the COVID-19 course in PwCF is unknown. To understand whether TGF-β1 affects ACE2 levels in the airway, we examined miRNAs and their gene targets affecting SARS-CoV-2 pathogenesis in response to TGF-β1. Small RNAseq and micro(mi)RNA profiling identified pathways uniquely affected by TGF-β1, including those associated with SARS-CoV-2 invasion, replication, and the host immune responses. TGF-β1 inhibited ACE2 expression by miR-136-3p and miR-369-5p mediated mechanism in CF and non-CF bronchial epithelial cells. ACE2 levels were higher in two bronchial epithelial cell models expressing the most common CF-causing mutation in CFTR gene F508del, compared to controls without the mutation. After TGF-β1 treatment, ACE2 protein levels were still higher in CF, compared to non-CF cells. TGF-β1 prevented the modulator-mediated rescue of F508del-CFTR function while the modulators did not prevent the TGF-β1 inhibition of ACE2 levels. Finally, TGF-β1 reduced the interaction between ACE2 and the recombinant spike RBD by lowering ACE2 levels and its binding to RBD. Our data demonstrate novel mechanism whereby TGF-β1 inhibition of ACE2 in CF and non-CF bronchial epithelial cells may modulate SARS-CoV-2 pathogenicity and COVID-19 severity. By reducing ACE2 levels, TGF-β1 may decrease entry of SARS-CoV-2 into the host cells while hindering the recovery from COVID-19 due to loss of the anti-inflammatory and regenerative effects of ACE2. The above outcomes may be modulated by other, miRNA-mediated effects exerted by TGF-β1 on the host immune responses, leading to a complex and yet incompletely understood circuitry.
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Affiliation(s)
| | - Nilay Mitash
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joshua E. Donovan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Anvita Chandra
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Carol Bertrand
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Catherine M. Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Fangping Mu
- Center for Research Computing, University of Pittsburgh, Pittsburgh, PA, USA
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Xiao W, Li P. Circ_0087862 promotes tumorigenesis and glycolysis in colorectal cancer by sponging miR-296-3p to regulate PGK1 expression. Pathol Res Pract 2023; 248:154695. [PMID: 37494801 DOI: 10.1016/j.prp.2023.154695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/13/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) exert crucial roles in tumor progression of multiple cancers, including colorectal cancer (CRC). However, the functions of most circRNAs are not been fully elucidated. In this study, the role and mechanism of circ_0087862 in CRC were investigated. METHODS The expression of circ_0087862, microRNA-296-3p (miR-296-3p) and phosphoglycerate kinase 1 (PGK1) was detected by quantitative real-time PCR (qRT-PCR). Cell Counting Kit-8 (CCK-8) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay were used to assess cell proliferation. Flow cytometry was employed to analyze cell apoptosis. Transwell assay was employed to evaluate cell invasion. Western blot assay was employed to detect the level of related protein markers and PGK1. The glucose consumption, lactate production were tested by corresponding kits. The relationship between miR-296-3p and circ_0087862 or PGK1 was verified by dual-luciferase reporter assay or RNA immunoprecipitation (RIP) assay. The in vivo function of circ_0087862 was examined by xenograft mice model. RESULTS The expression levels of circ_0087862 and PGK1 were up-regulated in CRC tissues and cells, while miR-296-3p was down-regulated. Circ_0087862 silencing suppressed cell proliferation, invasion and glycolysis and promoted cell apoptosis in CRC cells. Circ_0087862 targeted miR-296-3p in CRC cells. MiR-296-3p inhibition reversed circ_0087862 silencing-mediated inhibition effect on cell proliferation, invasion and glycolysis, as well as the promotion effect on cell apoptosis. PGK1 was a target of miR-296-3p, and the overexpression of PGK1 attenuated miR-296-3p-mediated tumor suppression effect on CRC progression. Moreover, knockdown of circ_0087862 inhibited tumorigenesis in vivo. CONCLUSION Circ_0087862 promoted CRC progression via miR-296-3p/PGK1 axis and might act as a potential target for CRC therapy.
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Affiliation(s)
- Weisheng Xiao
- Department of Gastroenterology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Peiyuan Li
- Department of Gastroenterology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China.
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Hussen BM, Rasul MF, Abdullah SR, Hidayat HJ, Faraj GSH, Ali FA, Salihi A, Baniahmad A, Ghafouri-Fard S, Rahman M, Glassy MC, Branicki W, Taheri M. Targeting miRNA by CRISPR/Cas in cancer: advantages and challenges. Mil Med Res 2023; 10:32. [PMID: 37460924 PMCID: PMC10351202 DOI: 10.1186/s40779-023-00468-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPR) has changed biomedical research and provided entirely new models to analyze every aspect of biomedical sciences during the last decade. In the study of cancer, the CRISPR/CRISPR-associated protein (Cas) system opens new avenues into issues that were once unknown in our knowledge of the noncoding genome, tumor heterogeneity, and precision medicines. CRISPR/Cas-based gene-editing technology now allows for the precise and permanent targeting of mutations and provides an opportunity to target small non-coding RNAs such as microRNAs (miRNAs). However, the development of effective and safe cancer gene editing therapy is highly dependent on proper design to be innocuous to normal cells and prevent introducing other abnormalities. This study aims to highlight the cutting-edge approaches in cancer-gene editing therapy based on the CRISPR/Cas technology to target miRNAs in cancer therapy. Furthermore, we highlight the potential challenges in CRISPR/Cas-mediated miRNA gene editing and offer advanced strategies to overcome them.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Kurdistan Region 44001 Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region 44001 Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region 44001 Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, Lebanese French University, Erbil, Kurdistan Region 44001 Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Kurdistan Region 44001 Iraq
| | - Goran Sedeeq Hama Faraj
- Department of Medical Laboratory Science, Komar University of Science and Technology, Sulaymaniyah, 46001 Iraq
| | - Fattma Abodi Ali
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region 44001 Iraq
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region 44001 Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, 44001 Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 374-37515 Iran
| | - Milladur Rahman
- Department of Clinical Sciences, Malmö, Section for Surgery, Lund University, 22100 Malmö, Sweden
| | - Mark C. Glassy
- Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, San Diego, CA 94720 USA
| | - Wojciech Branicki
- Faculty of Biology, Institute of Zoology and Biomedical Research, Jagiellonian University, 31-007 Kraków, Poland
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, 374-37515 Iran
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van den Berg PR, Bérenger-Currias NMLP, Budnik B, Slavov N, Semrau S. Integration of a multi-omics stem cell differentiation dataset using a dynamical model. PLoS Genet 2023; 19:e1010744. [PMID: 37167320 DOI: 10.1371/journal.pgen.1010744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/23/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023] Open
Abstract
Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.
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Affiliation(s)
| | | | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Leiden, Zuid-Holland, The Netherlands
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35
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Matai L, Slack FJ. MicroRNAs in Age-Related Proteostasis and Stress Responses. Noncoding RNA 2023; 9:26. [PMID: 37104008 PMCID: PMC10143298 DOI: 10.3390/ncrna9020026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
Aging is associated with the accumulation of damaged and misfolded proteins through a decline in the protein homeostasis (proteostasis) machinery, leading to various age-associated protein misfolding diseases such as Huntington's or Parkinson's. The efficiency of cellular stress response pathways also weakens with age, further contributing to the failure to maintain proteostasis. MicroRNAs (miRNAs or miRs) are a class of small, non-coding RNAs (ncRNAs) that bind target messenger RNAs at their 3'UTR, resulting in the post-transcriptional repression of gene expression. From the discovery of aging roles for lin-4 in C. elegans, the role of numerous miRNAs in controlling the aging process has been uncovered in different organisms. Recent studies have also shown that miRNAs regulate different components of proteostasis machinery as well as cellular response pathways to proteotoxic stress, some of which are very important during aging or in age-related pathologies. Here, we present a review of these findings, highlighting the role of individual miRNAs in age-associated protein folding and degradation across different organisms. We also broadly summarize the relationships between miRNAs and organelle-specific stress response pathways during aging and in various age-associated diseases.
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Affiliation(s)
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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36
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Xie X, Shirasu T, Li J, Guo LW, Kent KC. miR579-3p is an inhibitory modulator of neointimal hyperplasia and transcription factors c-MYB and KLF4. Cell Death Discov 2023; 9:73. [PMID: 36813774 PMCID: PMC9946956 DOI: 10.1038/s41420-023-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/28/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Neointimal hyperplasia (IH) is a common vascular pathology that typically manifests in in-stent restenosis and bypass vein graft failure. Smooth muscle cell (SMC) phenotypic switching is central to IH, both regulated by some microRNAs, yet the role of miR579-3p, a scarcely studied microRNA, is not known. Unbiased bioinformatic analysis suggested that miR579-3p was repressed in human primary SMCs treated with different pro-IH cytokines. Moreover, miR579-3p was software-predicted to target both c-MYB and KLF4 - two master transcription factors known to promote SMC phenotypic switching. Interestingly, treating injured rat carotid arteries via local infusion of miR579-3p-expressing lentivirus reduced IH 14 days after injury. In cultured human SMCs, transfection with miR579-3p inhibited SMC phenotypic switching, as indicated by decreased proliferation/migration and increased SMC contractile proteins. miR579-3p transfection downregulated c-MYB and KLF4, and luciferase assays indicated miR579-3p's targeting of the 3'UTRs of the c-MYB and KLF4 mRNAs. In vivo, immunohistochemistry showed that treatment of injured rat arteries with the miR579-3p lentivirus reduced c-MYB and KLF4 and increased SMC contractile proteins. Thus, this study identifies miR579-3p as a previously unrecognized small-RNA inhibitor of IH and SMC phenotypic switch involving its targeting of c-MYB and KLF4. Further studies on miR579-3p may provide an opportunity for translation to develop IH-mitigating new therapeutics.
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Affiliation(s)
- Xiujie Xie
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
| | - Takuro Shirasu
- grid.27755.320000 0000 9136 933XDepartment of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
| | - Jing Li
- grid.27755.320000 0000 9136 933XDepartment of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA. .,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA. .,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA.
| | - K. Craig Kent
- grid.27755.320000 0000 9136 933XDepartment of Surgery, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
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Tokić S, Jirouš M, Plužarić V, Mihalj M, Šola M, Tolušić Levak M, Glavaš K, Balogh P, Štefanić M. The miR-20a/miR-92b Profile Is Associated with Circulating γδ T-Cell Perturbations in Mild Psoriasis. Int J Mol Sci 2023; 24:4323. [PMID: 36901753 PMCID: PMC10001743 DOI: 10.3390/ijms24054323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
Psoriasis vulgaris (PV) is an autoinflammatory dermatosis of unknown etiology. Current evidence suggests a pathogenic role of γδT cells, but the growing complexity of this population has made the offending subset difficult to pinpoint. The work on γδTCRint and γδTCRhi subsets, which express intermediate and high levels of γδTCR at their surface, respectively, is particularly scarce, leaving their inner workings in PV essentially unresolved. We have shown here that the γδTCRint/γδTCRhi cell composition and their transcriptom are related to the differential miRNA expression by performing a targeted miRNA and mRNA quantification (RT-qPCR) in multiplexed, flow-sorted γδ blood T cells from healthy controls (n = 14) and patients with PV (n = 13). A significant loss of miR-20a in bulk γδT cells (~fourfold decrease, PV vs. controls) largely mirrored increasing Vδ1-Vδ2- and γδintVδ1-Vδ2- cell densities in the bloodstream, culminating in a relative excess of γδintVδ1-Vδ2- cells for PV. Transcripts encoding DNA-binding factors (ZBTB16), cytokine receptors (IL18R1), and cell adhesion molecules (SELPLG) were depleted in the process, closely tracking miR-20a availability in bulk γδ T-cell RNA. Compared to controls, PV was also associated with enhanced miR-92b expression (~13-fold) in bulk γδT cells that lacked association with the γδT cell composition. The miR-29a and let-7c expressions remained unaltered in case-control comparisons. Overall, our data expand the current landscape of the peripheral γδT cell composition, underlining changes in its mRNA/miRNA transcriptional circuits that may inform PV pathogenesis.
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Affiliation(s)
- Stana Tokić
- Department of Laboratory Medicine and Pharmacy, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
| | - Maja Jirouš
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
| | - Vera Plužarić
- Department of Dermatology and Venereology, University Hospital Osijek, 31000 Osijek, Croatia
| | - Martina Mihalj
- Department of Dermatology and Venereology, University Hospital Osijek, 31000 Osijek, Croatia
- Department of Physiology and Immunology, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
| | - Marija Šola
- Department of Dermatology and Venereology, University Hospital Osijek, 31000 Osijek, Croatia
| | - Maja Tolušić Levak
- Department of Dermatology and Venereology, University Hospital Osijek, 31000 Osijek, Croatia
- Department of Histology and Embryology, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
| | - Kristina Glavaš
- Department of Transfusion Medicine, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
| | - Peter Balogh
- Department of Immunology and Biotechnology, Faculty of Medicine, University of Pecs, 7622 Pecs, Hungary
| | - Mario Štefanić
- Department of Nuclear Medicine and Oncology, Faculty of Medicine, University of Osijek, 31000 Osijek, Croatia
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Liu D, Xiao H, Liu J, Zhang Y, Li J, Zhang T, Chen H. Circ_0000566 contributes oxygen-glucose deprivation and reoxygenation (OGD/R)-induced human brain microvascular endothelial cell injury via regulating miR-18a-5p/ACVR2B axis. Metab Brain Dis 2023; 38:1273-1284. [PMID: 36781583 DOI: 10.1007/s11011-023-01166-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023]
Abstract
Circular RNAs (circRNAs) exert regulatory roles in cerebrovascular disease. Human brain microvascular endothelial cells (HBMECs) participated in brain vascular dysfunction in ischemic stroke. Herein, the functions of circ_0000566 in oxygen-glucose deprivation and reoxygenation (OGD/R)-induced HBMECs were investigated. The expression of circ_0000566, miR-18a-5p, and Activin receptor type 2B (ACVR2B) was measured via quantitative real-time PCR (qRT-PCR). Cell Counting Kit-8 (CCK-8) and flow cytometry assays were utilized to detect cell viability and cell apoptosis. Western blot assay was employed to measure the levels of apoptotic-related proteins and ACVR2B. The secretion of IL-1β, IL-6, and TNF-α was detected via corresponding kits. The relationship between miR-18a-5p and circ_0000566 or ACVR2B was examined via dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Circ_0000566 and ACVR2B were highly expressed, while miR-18a-5p was down-regulated in OGD/R-treated HBMECs. OGD/R treatment promoted HBMECs apoptosis and inflammation and suppressed cell viability, which could be attenuated by silencing of circ_0000566. Circ_0000566 acted as a miR-18a-5p sponge to contribute to OGD/R-induced HBMECs injury. ACVR2B served as a direct target of miR-18a-5p, and ACVR2B overexpression might abolish the inhibitory role of miR-18a-5p on OGD/R-treated HBMEC injury. Circ_0000566 sponged miR-18a-5p to regulate OGD/R-induced HBMECs injury via regulating ACVR2B expression.
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Affiliation(s)
- Dan Liu
- Department of Acupuncture IV, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, No. 26, Heping Road, Xiangfang District, Harbin City, 150040, Heilongjiang Province, China
| | - Haitao Xiao
- Department of Chinese Internal Medicine, Suihua Hospital of Traditional Chinese Medicine, No. 90, Renhe Street, Beilin District, Suihua, Heilongjiang Province, China
| | - Jinxing Liu
- Heilongjiang University of Chinese Medicine, No. 24, Heping Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Yixin Zhang
- Heilongjiang University of Chinese Medicine, No. 24, Heping Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Jialiang Li
- Heilongjiang University of Chinese Medicine, No. 24, Heping Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Tingyu Zhang
- Heilongjiang University of Chinese Medicine, No. 24, Heping Road, Xiangfang District, Harbin, Heilongjiang Province, China
| | - Honglin Chen
- Department of Acupuncture IV, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, No. 26, Heping Road, Xiangfang District, Harbin City, 150040, Heilongjiang Province, China.
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Role of the MicroRNAs in the Pathogenic Mechanism of Painful Symptoms in Long COVID: Systematic Review. Int J Mol Sci 2023; 24:ijms24043574. [PMID: 36834984 PMCID: PMC9963913 DOI: 10.3390/ijms24043574] [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: 01/25/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The ongoing pandemic of COVID-19 has caused more than 6.7 million tragic deaths, plus, a large percentage of people who survived it present a myriad of chronic symptoms that last for at least 6 months; this has been named as long COVID. Some of the most prevalent are painful symptoms like headache, joint pain, migraine, neuropathic-like pain, fatigue and myalgia. MicroRNAs are small non-coding RNAs that regulate genes, and their involvement in several pathologies has been extensively shown. A deregulation of miRNAs has been observed in patients with COVID-19. The objective of the present systematic review was to show the prevalence of chronic pain-like symptoms of patients with long COVID and based on the expression of miRNAs in patients with COVID-19, and to present a proposal on how they may be involved in the pathogenic mechanisms of chronic pain-like symptoms. A systematic review was carried out in online databases for original articles published between March 2020 to April 2022; the systematic review followed the PRISMA guidelines, and it was registered in PROSPERO with registration number CRD42022318992. A total of 22 articles were included for the evaluation of miRNAs and 20 regarding long COVID; the overall prevalence of pain-like symptoms was around 10 to 87%, plus, the miRNAs that were commonly up and downregulated were miR-21-5p, miR-29a,b,c-3p miR-92a,b-3p, miR-92b-5p, miR-126-3p, miR-150-5p, miR-155-5p, miR-200a, c-3p, miR-320a,b,c,d,e-3p, and miR-451a. The molecular pathways that we hypothesized to be modulated by these miRNAs are the IL-6/STAT3 proinflammatory axis and the compromise of the blood-nerve barrier; these two mechanisms could be associated with the prevalence of fatigue and chronic pain in the long COVID population, plus they could be novel pharmacological targets in order to reduce and prevent these symptoms.
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Chen JW, Shrestha L, Green G, Leier A, Marquez-Lago TT. The hitchhikers' guide to RNA sequencing and functional analysis. Brief Bioinform 2023; 24:bbac529. [PMID: 36617463 PMCID: PMC9851315 DOI: 10.1093/bib/bbac529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 01/10/2023] Open
Abstract
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads' summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.
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Affiliation(s)
- Jiung-Wen Chen
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lisa Shrestha
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - George Green
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
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de Los Reyes-García AM, Zapata-Martínez L, Águila S, Lozano ML, Martínez C, González-Conejero R. microRNAs as biomarkers of risk of major adverse cardiovascular events in atrial fibrillation. Front Cardiovasc Med 2023; 10:1135127. [PMID: 36895835 PMCID: PMC9988920 DOI: 10.3389/fcvm.2023.1135127] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Atrial fibrillation is a complex and multifactorial disease. Although prophylactic anticoagulation has great benefits in avoiding comorbidities, adverse cardiovascular events still occur and thus in recent decades, many resources have been invested in the identification of useful markers in the prevention of the risk of MACE in these patients. As such, microRNAs, that are small non-coding RNAs whose function is to regulate gene expression post-transcriptionally, have a relevant role in the development of MACE. miRNAs, have been investigated for many years as potential non-invasive biomarkers of several diseases. Different studies have shown their utility in the diagnosis and prognosis of cardiovascular diseases. In particular, some studies have associated the presence of certain miRNAs in plasma with the development of MACE in AF. Despite these results, there are still many efforts to be done to allow the clinical use of miRNAs. The lack of standardization concerning the methodology in purifying and detecting miRNAs, still provides contradictory results. miRNAs also have a functional impact in MACE in AF through the dysregulation of immunothrombosis. Indeed, miRNAs may be a link between MACE and inflammation, through the regulation of neutrophil extracellular traps that are a key element in the establishment and evolution of thrombotic events. The use of miRNAs as therapy against thromboinflammatory processes should also be a future approach to avoid the occurrence of MACE in atrial fibrillation.
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Affiliation(s)
- Ascensión M de Los Reyes-García
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Laura Zapata-Martínez
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Sonia Águila
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Constantino Martínez
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
| | - Rocío González-Conejero
- Servicio de Hematología y Oncología Médica, Hospital General Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia IMIB Pascual Parrilla, Murcia, Spain
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Rai B, Pande A, Tiwari S. TRAIL and EGFR Pathways Targeting microRNAs are Predominantly Regulated in Human Diabetic Nephropathy. Microrna 2023; 12:143-155. [PMID: 37098997 DOI: 10.2174/2211536612666230407093841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Unbiased microRNA profiling of renal tissue and urinary extracellular vesicles (uEVs) from diabetic nephropathy (DN) subjects may unravel novel targets with diagnostic and therapeutic potential. Here we used the miRNA profile of uEVs and renal biopsies from DN subjects available on the GEO database. METHODS The miR expression profiles of kidney tissue (GSE51674) and urinary exosomes (GSE48318) from DN and control subjects were obtained by GEO2R tools from Gene Expression Omnibus (GEO) databases. Differentially expressed miRNAs in DN samples, relative to controls, were identified using a bioinformatic pipeline. Targets of miRs commonly regulated in both sample types were predicted by miRWalk, followed by functional gene enrichment analysis. Gene targets were identified by MiRTarBase, TargetScan and MiRDB. RESULTS Eight miRs, including let-7c, miR-10a, miR-10b and miR-181c, were significantly regulated in kidney tissue and uEVs in DN subjects versus controls. The top 10 significant pathways targeted by these miRs included TRAIL, EGFR, Proteoglycan syndecan, VEGF and Integrin Pathway. Gene target analysis by miRwalk upon validation using ShinyGO 70 targets with significant miRNA-mRNA interaction. CONCLUSION In silico analysis showed that miRs targeting TRAIL and EGFR signaling are predominately regulated in uEVs and renal tissue of DN subjects. After wet-lab validation, the identified miRstarget pairs may be explored for their diagnostic and/or therapeutic potential in diabetic nephropathy.
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Affiliation(s)
- Bhuvnesh Rai
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Akshara Pande
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Swasti Tiwari
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Zhao Y, Wang S. Detection of MicroRNA Expression Dynamics Using LNA/DNA Nanobiosensor. Methods Mol Biol 2023; 2630:75-87. [PMID: 36689177 DOI: 10.1007/978-1-0716-2982-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The investigation of complex biological processes requires effective tools for probing the spatiotemporal dynamics of individual cells. Single-cell gene expression analysis, such as RNA in situ hybridization and single-cell PCR, has been demonstrated in various biological applications (Tautz and Pfeifle, Chromosoma 98(2):81-5, 1989; Stahlberg and Bengtsson, Methods 50(4):282-288, 2010; Sanchez-Freire et al., Nat Protoc 7(5):829-838, 2012). However, existing techniques require cell lysis or fixation. The dynamic information and spatiotemporal regulation of the biological process cannot be obtained with these methods. Real-time gene expression analysis in living cells remains an outstanding challenge in the field. Here, we described a single-cell gene expression analysis method in living mammalian cells using a locked nucleic acid/DNA (LNA/DNA) nanobiosensor. This LNA/DNA nanobiosensor consists of a fluorophore-labeled detecting strand and a quenching strand. The fluorophore-labeled LNA probe is designed to hybridize with the target microRNA (miRNA) specifically and displace from the quenching strand, allowing the fluorophore to fluorescence. Large-scale single-cell dynamic gene expression monitoring can be performed using time-lapse microscopy to study spatiotemporal distribution and heterogeneity in gene expression. Multiplex detection of miRNAs can be achieved using different fluorophore-labeled LNA/DNA nanobiosensors. This LNA/DNA protocol is fast, generally applicable, and easily accessible.
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Affiliation(s)
- Yuwen Zhao
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Shue Wang
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, USA.
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Pang JM, Chien PC, Kao MC, Chiu PY, Chen PX, Hsu YL, Liu C, Liang X, Lin KT. MicroRNA-708 emerges as a potential candidate to target undruggable NRAS. PLoS One 2023; 18:e0284744. [PMID: 37083947 PMCID: PMC10120925 DOI: 10.1371/journal.pone.0284744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023] Open
Abstract
RAS, the most frequently mutated oncogene that drives tumorigenesis by promoting cell proliferation, survival, and motility, has been perceived as undruggable for the past three decades. However, intense research in the past has mainly focused on KRAS mutations, and targeted therapy for NRAS mutations remains an unmet medical need. NRAS mutation is frequently observed in several cancer types, including melanoma (15-20%), leukemia (10%), and occasionally other cancer types. Here, we report using miRNA-708, which targets the distinct 3' untranslated region (3'UTR) of NRAS, to develop miRNA-based precision medicine to treat NRAS mutation-driven cancers. We first confirmed that NRAS is a direct target of miRNA-708. Overexpression of miRNA-708 successfully reduced NRAS protein levels in melanoma, leukemia, and lung cancer cell lines with NRAS mutations, resulting in suppressed cell proliferation, anchorage-independent growth, and promotion of reactive oxygen species-induced apoptosis. Consistent with the functional data, the activities of NRAS-downstream effectors, the PI3K-AKT-mTOR or RAF-MEK-ERK signaling pathway, were impaired in miR-708 overexpressing cells. On the other hand, cell proliferation was not disturbed by miRNA-708 in cell lines carrying wild-type NRAS. Collectively, our data unveil the therapeutic potential of using miRNA-708 in NRAS mutation-driven cancers through direct depletion of constitutively active NRAS and thus inhibition of its downstream effectors to decelerate cancer progression. Harnessing the beneficial effects of miR-708 may therefore offer a potential avenue for small RNA-mediated precision medicine in cancer treatment.
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Affiliation(s)
- Jia Meng Pang
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Chen Chien
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Chien Kao
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Yun Chiu
- Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Pin-Xu Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Ling Hsu
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chengyang Liu
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaowei Liang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Kai-Ti Lin
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
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Sakshi, Ragini, Saini A, Verma C, Mani I. Epigenetics in renal diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:61-71. [DOI: 10.1016/bs.pmbts.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Gwarzo ID, Mohd Bohari SP, Abdul Wahab R, Zia A. Recent advances and future prospects in topical creams from medicinal plants to expedite wound healing: a review. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2053340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Iliyasu Datti Gwarzo
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
| | - Siti Pauliena Mohd Bohari
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
- Cosmetic and Fragrance Laboratory, Institute of Bioproduct Development, Universiti Teknologi Malaysia, UTM Johor, Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
- Advance Membrane Technology Research Centre, School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
| | - Arifullah Zia
- Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor, Malaysia
- Department of Biology, Faculty of Science, Nangarhar University, Darunta, Jalalabad, Afghanistan
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Petry S, Keraudren R, Nateghi B, Loiselle A, Pircs K, Jakobsson J, Sephton C, Langlois M, St-Amour I, Hébert SS. Widespread alterations in microRNA biogenesis in human Huntington’s disease putamen. Acta Neuropathol Commun 2022; 10:106. [PMID: 35869509 PMCID: PMC9308264 DOI: 10.1186/s40478-022-01407-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Altered microRNA (miRNA) expression is a common feature of Huntington’s disease (HD) and could participate in disease onset and progression. However, little is known about the underlying causes of miRNA disruption in HD. We and others have previously shown that mutant Huntingtin binds to Ago2, a central component of miRNA biogenesis, and disrupts mature miRNA levels. In this study, we sought to determine if miRNA maturation per se was compromised in HD. Towards this end, we characterized major miRNA biogenesis pathway components and miRNA maturation products (pri-miRNA, pre-miRNA, and mature) in human HD (N = 41, Vonsattel grades HD2-4) and healthy control (N = 25) subjects. Notably, the striatum (putamen) and cortex (BA39) from the same individuals were analyzed in parallel. We show that Ago2, Drosha, and Dicer were strongly downregulated in human HD at the early stages of the disease. Using a panel of HD-related miRNAs (miR-10b, miR-196b, miR-132, miR-212, miR-127, miR-128), we uncovered various types of maturation defects in the HD brain, the most prominent occurring at the pre-miRNA to mature miRNA maturation step. Consistent with earlier findings, we provide evidence that alterations in autophagy could participate in miRNA maturation defects. Notably, most changes occurred in the striatum, which is more prone to HTT aggregation and neurodegeneration. Likewise, we observed no significant alterations in miRNA biogenesis in human HD cortex and blood, strengthening tissue-specific effects. Overall, these data provide important clues into the underlying mechanisms behind miRNA alterations in HD-susceptible tissues. Further investigations are now required to understand the biological, diagnostic, and therapeutic implications of miRNA/RNAi biogenesis defects in HD and related neurodegenerative disorders.
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SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility. Int J Mol Sci 2022; 23:ijms232213725. [PMID: 36430200 PMCID: PMC9692299 DOI: 10.3390/ijms232213725] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.
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Hlynialuk C, Kemper L, Leinonen-Wright K, Petersen RC, Ashe K, Smith B. Caspase-2 mRNA levels are not elevated in mild cognitive impairment, Alzheimer's disease, Huntington's disease, or Lewy Body dementia. PLoS One 2022; 17:e0274784. [PMID: 36129947 PMCID: PMC9491574 DOI: 10.1371/journal.pone.0274784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
Caspase-2 is a member of the caspase family that exhibits both apoptotic and non-apoptotic properties, and has been shown to mediate synaptic deficits in models of several neurological conditions, including Alzheimer's disease (AD), Huntington's disease (HD), and Lewy Body dementia (LBD). Our lab previously reported that caspase-2 protein levels are elevated in these diseases, leading us to hypothesize that elevated caspase-2 protein levels are due to increased transcription of caspase-2 mRNA. There are two major isoforms of caspase-2 mRNA, caspase-2L and caspase-2S. We tested our hypothesis by measuring the levels of these mRNA isoforms normalized to levels of RPL13 mRNA, a reference gene that showed no disease-associated changes. Here, we report no increases in caspase-2L mRNA levels in any of the three diseases studied, AD (with mild cognitive impairment (MCI)), HD and LBD, disproving our hypothesis. Caspase-2S mRNA showed a non-significant downward trend in AD. We also analyzed expression levels of SNAP25 and βIII-tubulin mRNA. SNAP25 mRNA was significantly lower in AD and there were downward trends in MCI, LBD, and HD. βIII-tubulin mRNA expression remained unchanged between disease groups and controls. These findings indicate that factors besides transcriptional regulation cause increases in caspase-2 protein levels. The reduction of SNAP25 mRNA expression suggests that presynaptic dysfunction contributes to cognitive deficits in neurodegeneration.
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Affiliation(s)
- Chris Hlynialuk
- N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, United States of America
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States of America
| | - Lisa Kemper
- N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, United States of America
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States of America
| | - Kailee Leinonen-Wright
- N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, United States of America
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States of America
| | - Ronald C. Petersen
- Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Karen Ashe
- N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, United States of America
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States of America
- Minneapolis VA Medical Center, Minneapolis, MN, United States of America
| | - Benjamin Smith
- N. Bud Grossman Center for Memory Research and Care, University of Minnesota, Minneapolis, MN, United States of America
- Department of Neurology, University of Minnesota, Minneapolis, MN, United States of America
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miR-187/PDLIM1 Gets Involved in Gastric Cancer Progression and Cisplatin Sensitivity of Cisplatin by Mediating the Hippo-YAP Signaling Pathway. JOURNAL OF ONCOLOGY 2022; 2022:5456016. [PMID: 36164345 PMCID: PMC9509220 DOI: 10.1155/2022/5456016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/30/2022] [Accepted: 08/04/2022] [Indexed: 11/22/2022]
Abstract
Gastric cancer (GC) is one of the most prevalent malignancies in the digestive system across the world. The function and mechanism of PDLIM1, a cancer-suppressing gene, in gastric cancer progression remain unclear. This study is aimed at investigating the expression features and function of PDLIM1 in GC. RT-qPCR and western blot were used to compare the profiles of PDLIM1 and miR-187 between GC and normal tissues. The cell models of PDLIM1 overexpression and low expression were established in gastric cancer cell lines MKN45 and AGS. CCK8 and BrdU assays measured cell proliferation. Flow cytometry monitored cell apoptosis. Transwell analyzed cell invasion and migration. The influence of miR-187 overexpression on gastric cancer development was assessed. We predicted the targeted correlation between miR-187 and PDLIM1 through bioinformatics, which was corroborated via dual luciferase activity assay and RIP. Meanwhile, the cell model of PDLIM1 overexpression was built in AGS cells transfected with miR-187 mimics. A rescue experiment was conducted to assess the impact of PDLIM1 overexpression on the procancer function of miR-187. As a result, in contrast with normal paracancer tissues, PDLIM1 was substantially downregulated in GC tissues. Moreover, PDLIM1 overexpression considerably dampened proliferation, invasion, and migration in GC cells, boosted the cell apoptosis, and bolstered their sensitivity to cisplatin. PDLIM1 knockdown or miR-187 overexpression dramatically fostered GC cell proliferation, invasion, and migration and repressed cell apoptosis. Mechanism studies demonstrated that PDLIM1 vigorously restrained the profiles of the Hippo-YAP signaling pathway and the downstream target genes. miR-187 targeted PDLIM1, while miR-187 overexpression cramped PDLIM1 expression. The rescue experiment suggested that PDLIM1 overexpression weakened the procancer function of miR-187 in GC cells. In conclusion, our study demonstrated that PDLIM1 presented a low expression in GC tissues, while miR-187/PDLIM1 participated in GC development and cisplatin sensitivity by mediating the Hippo-YAP signaling pathway.
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