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Li T, Xing HM, Qian HD, Gao Q, Xu SL, Ma H, Chi ZL. Small extracellular vesicles derived from human induced pluripotent stem cell-differentiated neural progenitor cells mitigate retinal ganglion cell degeneration in a mouse model of optic nerve injury. Neural Regen Res 2025; 20:587-597. [PMID: 38819069 PMCID: PMC11317950 DOI: 10.4103/nrr.nrr-d-23-01414] [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: 08/22/2023] [Revised: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 06/01/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202502000-00034/figure1/v/2024-05-28T214302Z/r/image-tiff Several studies have found that transplantation of neural progenitor cells (NPCs) promotes the survival of injured neurons. However, a poor integration rate and high risk of tumorigenicity after cell transplantation limits their clinical application. Small extracellular vesicles (sEVs) contain bioactive molecules for neuronal protection and regeneration. Previous studies have shown that stem/progenitor cell-derived sEVs can promote neuronal survival and recovery of neurological function in neurodegenerative eye diseases and other eye diseases. In this study, we intravitreally transplanted sEVs derived from human induced pluripotent stem cells (hiPSCs) and hiPSCs-differentiated NPCs (hiPSC-NPC) in a mouse model of optic nerve crush. Our results show that these intravitreally injected sEVs were ingested by retinal cells, especially those localized in the ganglion cell layer. Treatment with hiPSC-NPC-derived sEVs mitigated optic nerve crush-induced retinal ganglion cell degeneration, and regulated the retinal microenvironment by inhibiting excessive activation of microglia. Component analysis further revealed that hiPSC-NPC derived sEVs transported neuroprotective and anti-inflammatory miRNA cargos to target cells, which had protective effects on RGCs after optic nerve injury. These findings suggest that sEVs derived from hiPSC-NPC are a promising cell-free therapeutic strategy for optic neuropathy.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hui-Min Xing
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai-Dong Qian
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qiao Gao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Sheng-Lan Xu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hua Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Zai-Long Chi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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2
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Nunes S, Bastos R, Marinho AI, Vieira R, Benício I, de Noronha MA, Lírio S, Brodskyn C, Tavares NM. Recent advances in the development and clinical application of miRNAs in infectious diseases. Noncoding RNA Res 2025; 10:41-54. [PMID: 39296638 PMCID: PMC11406675 DOI: 10.1016/j.ncrna.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/06/2024] [Accepted: 09/01/2024] [Indexed: 09/21/2024] Open
Abstract
In the search for new biomarkers and therapeutic targets for infectious diseases, several molecules have been investigated. Small RNAs, known as microRNAs (miRs), are important regulators of gene expression, and have emerged as promising candidates for these purposes. MiRs are a class of small, endogenous non-coding RNAs that play critical roles in several human diseases, including host-pathogen interaction mechanisms. Recently, miRs signatures have been reported in different infectious diseases, opening new perspectives for molecular diagnosis and therapy. MiR profiles can discriminate between healthy individuals and patients, as well as distinguish different disease stages. Furthermore, the possibility of assessing miRs in biological fluids, such as serum and whole blood, renders these molecules feasible for the development of new non-invasive diagnostic and prognostic tools. In this manuscript, we will comprehensively describe miRs as biomarkers and therapeutic targets in infectious diseases and explore how they can contribute to the advance of existing and new tools. Additionally, we will discuss different miR analysis platforms to understand the obstacles and advances of this molecular approach and propose their potential clinical applications and contributions to public health.
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Affiliation(s)
- Sara Nunes
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Rana Bastos
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Ananda Isis Marinho
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Raissa Vieira
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
| | - Ingra Benício
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | | | - Sofia Lírio
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Bahiana School of Medicine and Public Health, Salvador, Brazil
| | - Cláudia Brodskyn
- Federal University of Bahia (UFBA), Salvador, Brazil
- Laboratory of Parasite-Host Interaction and Epidemiology (LaIPHE), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Instituto Nacional de Ciência e Tecnologia (INCT) Iii - Instituto de Investigação Em Imunologia, São Paulo, Brazil
| | - Natalia Machado Tavares
- Laboratory of Medicine and Precision Public Health (MeSP), Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
- Federal University of Bahia (UFBA), Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia (INCT) Iii - Instituto de Investigação Em Imunologia, São Paulo, Brazil
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Cairns CA, Xiao L, Wang JY. Posttranscriptional Regulation of Intestinal Mucosal Growth and Adaptation by Noncoding RNAs in Critical Surgical Disorders. J INVEST SURG 2024; 37:2308809. [PMID: 38323630 PMCID: PMC11027105 DOI: 10.1080/08941939.2024.2308809] [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: 06/03/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
The human intestinal epithelium has an impressive ability to respond to insults and its homeostasis is maintained by well-regulated mechanisms under various pathophysiological conditions. Nonetheless, acute injury and inhibited regeneration of the intestinal epithelium occur commonly in critically ill surgical patients, leading to the translocation of luminal toxic substances and bacteria to the bloodstream. Effective therapies for the preservation of intestinal epithelial integrity and for the prevention of mucosal hemorrhage and gut barrier dysfunction are limited, primarily because of a poor understanding of the mechanisms underlying mucosal disruption. Noncoding RNAs (ncRNAs), which include microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and small vault RNAs (vtRNAs), modulate a wide array of biological functions and have been identified as orchestrators of intestinal epithelial homeostasis. Here, we feature the roles of many important ncRNAs in controlling intestinal mucosal growth, barrier function, and repair after injury-particularly in the context of postoperative recovery from bowel surgery. We review recent literature surrounding the relationships between lncRNAs, microRNAs, and RNA-binding proteins and how their interactions impact cell survival, proliferation, migration, and cell-to-cell interactions in the intestinal epithelium. With advancing knowledge of ncRNA biology and growing recognition of the importance of ncRNAs in maintaining the intestinal epithelial integrity, ncRNAs provide novel therapeutic targets for treatments to preserve the gut epithelium in individuals suffering from critical surgical disorders.
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Affiliation(s)
- Cassandra A. Cairns
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland 21201
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4
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Chen JY, Li YF, Zhou Z, Jiang XM, Bi X, Yang MF, Zhao B. De novo mutations promote inflammation in children with STAT3 gain-of-function syndrome by affecting IL-1β expression. Int Immunopharmacol 2024; 140:112755. [PMID: 39098225 DOI: 10.1016/j.intimp.2024.112755] [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: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
STAT3 gain-of-function syndrome, characterized by early-onset autoimmunity and primary immune regulatory disorder, remains poorly understood in terms of its immunological mechanisms. We employed whole-genome sequencing of familial trios to elucidate the pivotal role of de novo mutations in genetic diseases. We identified 37 high-risk pathogenic loci affecting 23 genes, including a novel STAT3 c.508G>A mutation. We also observed significant down-regulation of pathogenic genes in affected individuals, potentially associated with inflammatory responses regulated by PTPN14 via miR378c. These findings enhance our understanding of the pathogenesis of STAT3 gain-of-function syndrome and suggest potential therapeutic strategies. Notably, combined JAK inhibitors and IL-6R antagonists may offer promising treatment avenues for mitigating the severity of STAT3 gain-of-function syndrome.
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Affiliation(s)
- Ji-Yu Chen
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Yan-Fang Li
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Zhu Zhou
- Department of Nephrology, First Affiliated Hospital of Kunming Medical University, Yunnan Clinical Medical Research Center of Chronic Kidney Disease, Kunming 650032, Yunnan, China
| | - Xue-Mei Jiang
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Xin Bi
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Mi-Feng Yang
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Bo Zhao
- Department of Nephrology & Rheumatology, Kunming Children's Hospital, Kunming 650228, Yunnan, China.
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Roy U, Desai SS, Kumari S, Bushra T, Choudhary B, Raghavan SC. Understanding the Role of miR-29a in the Regulation of RAG1, a Gene Associated with the Development of the Immune System. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1125-1138. [PMID: 39269689 DOI: 10.4049/jimmunol.2300344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/16/2024] [Indexed: 09/15/2024]
Abstract
The process of Ag receptor diversity is initiated by RAGs consisting of RAG1 and RAG2 in developing lymphocytes. Besides its role as a sequence-specific nuclease during V(D)J recombination, RAGs can also act as a structure-specific nuclease leading to genome instability. Thus, regulation of RAG expression is essential to maintaining genome stability. Previously, the role of miR29c in the regulation of RAG1 was identified. In this article, we report the regulation of RAG1 by miR-29a in the lymphocytes of both mice (Mus musculus) and humans (Homo sapiens). The level of RAG1 could be modulated by overexpression of miR-29a and inhibition using anti-miRs. Argonaute2-immunoprecipitation and high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation studies established the association of miR-29a and RAG1 with Argonaute proteins. We observed a negative correlation between miR-29a and RAG1 levels in mouse B and T cells and leukemia patients. Overexpression of pre-miR-29a in the bone marrow cells of mice led to the generation of mature miR-29a transcripts and reduced RAG1 expression, which led to a significant reduction in V(D)J recombination in pro-B cells. Importantly, our studies are consistent with the phenotype reported in miR-29a knockout mice, which showed impaired immunity and survival defects. Finally, we show that although both miR-29c and miR-29a can regulate RAG1 at mRNA and protein levels, miR-29a substantially impacts immunity and survival. Our results reveal that the repression of RAG1 activity by miR-29a in B cells of mice and humans is essential to maintain Ig diversity and prevent hematological malignancies resulting from aberrant RAG1 expression in lymphocytes.
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Affiliation(s)
- Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sagar Sanjiv Desai
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Tanzeem Bushra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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6
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Li Y, Baumert BO, Stratakis N, Goodrich JA, Wu H, Liu SH, Wang H, Beglarian E, Bartell SM, Eckel SP, Walker D, Valvi D, La Merrill MA, Inge TH, Jenkins T, Ryder JR, Sisley S, Kohli R, Xanthakos SA, Vafeiadi M, Margetaki A, Roumeliotaki T, Aung M, McConnell R, Baccarelli A, Conti D, Chatzi L. Exposure to per- and polyfluoroalkyl substances and alterations in plasma microRNA profiles in children. ENVIRONMENTAL RESEARCH 2024; 259:119496. [PMID: 38936497 DOI: 10.1016/j.envres.2024.119496] [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: 05/12/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals that persist in the environment and can accumulate in humans, leading to adverse health effects. MicroRNAs (miRNAs) are emerging biomarkers that can advance the understanding of the mechanisms of PFAS effects on human health. However, little is known about the associations between PFAS exposures and miRNA alterations in humans. OBJECTIVE To investigate associations between PFAS concentrations and miRNA levels in children. METHODS Data from two distinct cohorts were utilized: 176 participants (average age 17.1 years; 75.6% female) from the Teen-Longitudinal Assessment of Bariatric Surgery (Teen-LABS) cohort in the United States, and 64 participants (average age 6.5 years, 39.1% female) from the Rhea study, a mother-child cohort in Greece. PFAS concentrations and miRNA levels were assessed in plasma samples from both studies. Associations between individual PFAS and plasma miRNA levels were examined after adjusting for covariates. Additionally, the cumulative effects of PFAS mixtures were evaluated using an exposure burden score. Ingenuity Pathways Analysis was employed to identify potential disease functions of PFAS-associated miRNAs. RESULTS Plasma PFAS concentrations were associated with alterations in 475 miRNAs in the Teen-LABs study and 5 miRNAs in the Rhea study (FDR p < 0.1). Specifically, plasma PFAS concentrations were consistently associated with decreased levels of miR-148b-3p and miR-29a-3p in both cohorts. Pathway analysis indicated that PFAS-related miRNAs were linked to numerous chronic disease pathways, including cardiovascular diseases, inflammatory conditions, and carcinogenesis. CONCLUSION Through miRNA screenings in two independent cohorts, this study identified both known and novel miRNAs associated with PFAS exposure in children. Pathway analysis revealed the involvement of these miRNAs in several cancer and inflammation-related pathways. Further studies are warranted to enhance our understanding of the relationships between PFAS exposure and disease risks, with miRNA emerging as potential biomarkers and/or mediators in these complex pathways.
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Affiliation(s)
- Yijie Li
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brittney O Baumert
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jesse A Goodrich
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Shelley H Liu
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hongxu Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily Beglarian
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Scott M Bartell
- Department of Environmental and Occupational Health and Department of Epidemiology and Biostatistics, University of California, Irvine, CA, USA
| | - Sandrah Proctor Eckel
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Douglas Walker
- Gangarosa Department of Environmental Health, Rollins School of Public Health, 1518 Clifton Road, NE, Atlanta, GA, USA
| | - Damaskini Valvi
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Thomas H Inge
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Todd Jenkins
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Justin R Ryder
- Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Stephanie Sisley
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Rohit Kohli
- Division of Gastroenterology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Stavra A Xanthakos
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Aikaterini Margetaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Theano Roumeliotaki
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; Department of Social Medicine, School of Medicine, University of Crete, Greece
| | - Max Aung
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rob McConnell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andrea Baccarelli
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - David Conti
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lida Chatzi
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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7
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Nguinkal JA, Zoclanclounon YAB, Brunner RM, Chen Y, Goldammer T. Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus). Sci Data 2024; 11:1095. [PMID: 39375414 PMCID: PMC11458897 DOI: 10.1038/s41597-024-03906-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 09/17/2024] [Indexed: 10/09/2024] Open
Abstract
Airbreathing catfish are stenohaline freshwater fish capable of withstanding various environmental conditions and farming practices, including breathing atmospheric oxygen. This unique ability has enabled them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological environments remain largely unexplored, primarily due to the limited availability of high-quality genomic resources. Here, we present a haplotype-resolved and near telomere-to-telomere (T2T) genome assembly of the African catfish (Clarias gariepinus), utilizing Oxford Nanopore, PacBio HiFi, Illumina and Hi-C sequencing technologies. The primary assembly spans 969.62 Mb with only 47 contigs, achieving a contig N50 of 33.71 Mb. Terminal telomeric signals were detected in 22 of 47 contigs, suggesting T2T assembled chromosomes. BUSCO analysis confirmed gene space completeness of 99% against the Actinopterygii dataset, highlighting the high quality of the assembly. Genome annotation identified 25,655 protein-coding genes and estimated 43.94% genome-wide repetitive elements. This data provides valuable genomic resources to advance aquaculture practices and to explore the genomic underpinnings of the ecological resilience of airbreathing catfish and related teleosts.
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Affiliation(s)
- Julien A Nguinkal
- Research Institute for Farm Animals (FBN), Fish Genetics Unit, Dummerstorf, 18196, Germany.
- Bernhard-Nocht Institute for Tropical Medicine, Department of Infectious Disease Epidemiology, Hamburg, 20359, Germany.
| | | | - Ronald M Brunner
- Research Institute for Farm Animals (FBN), Fish Genetics Unit, Dummerstorf, 18196, Germany
| | - Yutang Chen
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Tom Goldammer
- Research Institute for Farm Animals (FBN), Fish Genetics Unit, Dummerstorf, 18196, Germany.
- University of Rostock, Faculty of Agriculture and Environmental Sciences, Rostock, 18059, Germany.
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Gandhi G, Kodiappan R, Abdullah S, Teoh HK, Tai L, Cheong SK, Yeo WWY. Revealing the potential role of hsa-miR-663a in modulating the PI3K-Akt signaling pathway via miRNA microarray in spinal muscular atrophy patient fibroblast-derived iPSCs. J Neuropathol Exp Neurol 2024; 83:822-832. [PMID: 38894621 DOI: 10.1093/jnen/nlae065] [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] [Indexed: 06/21/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder due to deletion or mutation of survival motor neuron 1 (SMN1) gene. Although survival motor neuron 2 (SMN2) gene is still present in SMA patients, the production of full-length survival motor neuron (SMN) protein is insufficient owing to missing or mutated SMN1. No current disease-modifying therapies can cure SMA. The aim of this study was to explore microRNA (miRNA)-based therapies that may serve as a potential target for therapeutic intervention in delaying SMA progression or as treatment. The study screened for potentially dysregulated miRNAs in SMA fibroblast-derived iPSCs using miRNA microarray. Results from the miRNA microarray were validated using quantitative reverse transcription polymerase chain reaction. Bioinformatics analysis using various databases was performed to predict the potential putative gene targeted by hsa-miR-663a. The findings showed differential expression of hsa-miR-663a in SMA patients in relation to a healthy control. Bioinformatics analysis identified GNG7, IGF2, and TNN genes that were targeted by hsa-miR-663a to be involved in the PI3K-AKT pathway, which may be associated with disease progression in SMA. Thus, this study suggests the potential role of hsa-miR-663a as therapeutic target for the treatment of SMA patients in the near future.
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Affiliation(s)
- Gayatri Gandhi
- Perdana University Graduate School of Medicine, Perdana University, Kuala Lumpur, Malaysia
| | - Radha Kodiappan
- Department of Research and Training, MAHSA Specialist Hospital, Selangor, Malaysia
| | - Syahril Abdullah
- Medical Genetics Laboratory, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Genetics & Regenerative Medicine Research Group, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
| | - Hoon Koon Teoh
- Centre for Stem Cell Research, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
| | - Lihui Tai
- Centre for Stem Cell Research, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
- Cytopeutics Sdn. Bhd, Selangor, Malaysia
| | - Soon Keng Cheong
- Centre for Stem Cell Research, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia
| | - Wendy Wai Yeng Yeo
- Perdana University Graduate School of Medicine, Perdana University, Kuala Lumpur, Malaysia
- School of Pharmacy, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
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9
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Kwon J, Mori K, Maoka T, Sano T, Nakahara KS. Induction of necrosis symptoms by potato virus X in AGO2-silenced tomato plants associates with reduced transcript accumulation of copper chaperon for superoxide dismutase gene. Virus Res 2024; 348:199436. [PMID: 38996815 PMCID: PMC11315226 DOI: 10.1016/j.virusres.2024.199436] [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: 08/01/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
RNA silencing is a prominent antiviral defense mechanism in plants. When infected with a virus, RNA silencing-deficient plants tend to show exacerbated symptoms along with increased virus accumulation. However, how symptoms are exacerbated is little understood. Here, we investigated the role of the copper chaperon for superoxide dismutase (CCS) 1, in systemic necrosis observed in Argonaute (AGO)2-silenced tomato plants infected with potato virus X (PVX). While infection with the UK3 strain of PVX induced mosaic symptoms in tomato plants, systemic necrosis occurred when AGO2 was silenced. The CCS1 mRNA level was reduced and micro RNA398 (miR398), which potentially target CCS1, was increased in AGO2-knockdown tomato plants infected with PVX-UK3. Ectopic expression of CCS1 using recombinant PVX attenuated necrosis, suggesting that CCS1 alleviates systemic necrosis by activating superoxide dismutases to scavenge reactive oxygen species. Previous reports have indicated a decrease in the levels of CCS1 and superoxide dismutases along with an increased level of miR398 in plants infected with other viruses and viroids, and thus might represent shared regulatory mechanisms that exacerbate symptoms in these plants.
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Affiliation(s)
- Joon Kwon
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kento Mori
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Tetsuo Maoka
- Institute for Plant Protection, National Agriculture and Food Research Organization (NIPP, NARO), Tsukuba, Ibaraki, 305-8666, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Kenji S Nakahara
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan; Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan.
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Calderón-Peláez MA, Madroñero LJ, Castellanos JE, Velandia-Romero ML. Small extracellular vesicles from the human endothelial cell line EA.hy 926 exert a self-cell activation and modulate DENV-2 genome replication and infection in naïve endothelial cells. PLoS One 2024; 19:e0310735. [PMID: 39325758 PMCID: PMC11426460 DOI: 10.1371/journal.pone.0310735] [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: 04/24/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024] Open
Abstract
Extracellular vesicles (EVs) play crucial roles in cell signaling and communication, transporting molecules that convey a message to target cells. During infectious diseases, EVs can also carry viral molecules that may contribute to viral spread, as previously reported for dengue virus (DENV). EVs from infected endothelial cells (EC) may harbor viral segments and various sets of molecules that could contribute to endothelial dysfunction during severe dengue. However, the effect of these EVs on non-infected EC (NIC) remain unknown. We characterized the EVs produced by the human EC line EA.hy 926 infected with DENV-2 and assessed their functional impact on polarized NIC. Results showed that infection induced an increased in the quantity of produced EVs, which differentially carried proteins mainly involved in proteosome activity, along with a peptide of the NS5 viral protein. Additionally, all types of Y-RNAs were found, accompanied by a set of differentially loaded microRNAs (miRs) that could regulate DENV genome. Pre-treatment of polarized NIC with small EVs (sEVs) from infected EC before DENV-2 infection caused EC activation, a decrease in viral genome replication, and a protective effect against barrier disruption during the first 24h post-infection, suggesting that sEVs could be important in the pathology or resolution of DENV and a promising therapeutic tool for infectious diseases.
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Affiliation(s)
| | - L. Johana Madroñero
- Virology group, Vice-chancellor of research, Universidad El Bosque, Bogotá, Colombia
| | - Jaime E. Castellanos
- Virology group, Vice-chancellor of research, Universidad El Bosque, Bogotá, Colombia
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11
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Thivierge C, Bellefeuille M, Diwan SS, Dyakov BJA, Leventis R, Perron G, Najafabadi HS, Gravel SP, Gingras AC, Duchaine TF. Paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ. Cell Rep 2024; 43:114695. [PMID: 39250314 DOI: 10.1016/j.celrep.2024.114695] [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: 04/04/2024] [Revised: 06/28/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in physiological functions and disease, but the regulation of their nuclear biogenesis remains poorly understood. Here, BioID on Drosha, the catalytic subunit of the microprocessor complex, reveals its proximity to splicing factor proline- and glutamine (Q)-rich (SFPQ), a multifunctional RNA-binding protein (RBP) involved in forming paraspeckle nuclear condensates. SFPQ depletion impacts both primary and mature miRNA expression, while other paraspeckle proteins (PSPs) or the paraspeckle scaffolding RNA NEAT1 do not, indicating a paraspeckle-independent role. Comprehensive transcriptomic analyses show that SFPQ loss broadly affects RNAs and miRNA host gene (HG) expression, influencing both their transcription and the stability of their products. Notably, SFPQ protects the oncogenic miR-17∼92 polycistron from degradation by the nuclear exosome targeting (NEXT)-exosome complex and is tightly linked with its overexpression across a broad variety of cancers. Our findings reveal a dual role for SFPQ in regulating miRNA HG transcription and stability, as well as its significance in cancers.
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Affiliation(s)
- Caroline Thivierge
- Rosalind and Morris Goodman Cancer Institute, McGill Centre for RNA Sciences & Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Maxime Bellefeuille
- Rosalind and Morris Goodman Cancer Institute, McGill Centre for RNA Sciences & Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Sarah-Slim Diwan
- Rosalind and Morris Goodman Cancer Institute, McGill Centre for RNA Sciences & Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Boris J A Dyakov
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System & Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Rania Leventis
- Rosalind and Morris Goodman Cancer Institute, McGill Centre for RNA Sciences & Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Gabrielle Perron
- McGill Genome Centre & Department of Human Genetics, McGill University, Montréal, QC H3A 0G1, Canada
| | - Hamed S Najafabadi
- McGill Genome Centre & Department of Human Genetics, McGill University, Montréal, QC H3A 0G1, Canada
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System & Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Thomas F Duchaine
- Rosalind and Morris Goodman Cancer Institute, McGill Centre for RNA Sciences & Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada.
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12
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Cherlin T, Jing Y, Shah S, Kennedy A, Telonis AG, Pliatsika V, Wilson H, Thompson L, Vlantis PI, Loher P, Leiby B, Rigoutsos I. The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type. BMC Biol 2024; 22:205. [PMID: 39267057 PMCID: PMC11397057 DOI: 10.1186/s12915-024-01970-6] [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] [Received: 12/07/2022] [Accepted: 08/01/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND MicroRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), and rRNA-derived fragments (rRFs) represent most of the small non-coding RNAs (sncRNAs) found in cells. Members of these three classes modulate messenger RNA (mRNA) and protein abundance and are dysregulated in diseases. Experimental studies to date have assumed that the subcellular distribution of these molecules is well-understood, independent of cell type, and the same for all isoforms of a sncRNA. RESULTS We tested these assumptions by investigating the subcellular distribution of isomiRs, tRFs, and rRFs in biological replicates from three cell lines from the same tissue and same-sex donors that model the same cancer subtype. In each cell line, we profiled the isomiRs, tRFs, and rRFs in the nucleus, cytoplasm, whole mitochondrion (MT), mitoplast (MP), and whole cell. Using a rigorous mathematical model we developed, we accounted for cross-fraction contamination and technical errors and adjusted the measured abundances accordingly. Analyses of the adjusted abundances show that isomiRs, tRFs, and rRFs exhibit complex patterns of subcellular distributions. These patterns depend on each sncRNA's exact sequence and the cell type. Even in the same cell line, isoforms of the same sncRNA whose sequences differ by a few nucleotides (nts) can have different subcellular distributions. CONCLUSIONS SncRNAs with similar sequences have different subcellular distributions within and across cell lines, suggesting that each isoform could have a different function. Future computational and experimental studies of isomiRs, tRFs, and rRFs will need to distinguish among each molecule's various isoforms and account for differences in each isoform's subcellular distribution in the cell line at hand. While the findings add to a growing body of evidence that isomiRs, tRFs, rRFs, tRNAs, and rRNAs follow complex intracellular trafficking rules, further investigation is needed to exclude alternative explanations for the observed subcellular distribution of sncRNAs.
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Affiliation(s)
- Tess Cherlin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Yi Jing
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
| | - Siddhartha Shah
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
| | - Anne Kennedy
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- University of Miami, Miami, FL, USA
| | - Venetia Pliatsika
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- New York University, New York, NY, USA
| | - Haley Wilson
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lily Thompson
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Panagiotis I Vlantis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
- Independent Scholar, Athens, Greece
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA
| | - Benjamin Leiby
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA, 19017, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19017, USA.
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13
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Reese KL, Pantel K, Smit DJ. Multibiomarker panels in liquid biopsy for early detection of pancreatic cancer - a comprehensive review. J Exp Clin Cancer Res 2024; 43:250. [PMID: 39218911 PMCID: PMC11367781 DOI: 10.1186/s13046-024-03166-w] [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: 03/18/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is frequently detected in late stages, which leads to limited therapeutic options and a dismal overall survival rate. To date, no robust method for the detection of early-stage PDAC that can be used for targeted screening approaches is available. Liquid biopsy allows the minimally invasive collection of body fluids (typically peripheral blood) and the subsequent analysis of circulating tumor cells or tumor-associated molecules such as nucleic acids, proteins, or metabolites that may be useful for the early diagnosis of PDAC. Single biomarkers may lack sensitivity and/or specificity to reliably detect PDAC, while combinations of these circulating biomarkers in multimarker panels may improve the sensitivity and specificity of blood test-based diagnosis. In this narrative review, we present an overview of different liquid biopsy biomarkers for the early diagnosis of PDAC and discuss the validity of multimarker panels.
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Affiliation(s)
- Kim-Lea Reese
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
| | - Daniel J Smit
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
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14
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Wu J, Zhu Y, Liu D, Cong Q, Bai C. Biological functions and potential mechanisms of miR‑143‑3p in cancers (Review). Oncol Rep 2024; 52:113. [PMID: 38994765 PMCID: PMC11253085 DOI: 10.3892/or.2024.8772] [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: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 07/13/2024] Open
Abstract
In recent years, microRNAs (miRNAs or miRs) have been increasingly studied for their role in cancer and have shown potential as cancer biomarkers. miR‑143‑3p and miR‑143‑5p are the mature miRNAs derived from pre‑miRNA‑143. At present, there are numerous studies on the function of miR‑143‑3p in cancer progression, but there are no systematic reviews describing the function of miR‑143‑3p in cancer. It is widely considered that miR‑143‑3p is downregulated in most malignant tumors and that upstream regulators can act on this gene, which in turn regulates the corresponding target to act on the tumor. In addition, miRNA‑143‑3p can regulate target genes to affect the biological process of tumors through various signaling pathways, such as the PI3K/Akt, Wnt/β‑catenin, AKT/STAT3 and Ras‑Raf‑MEK‑ERK pathways. The present review comprehensively described the biogenesis of miR‑143‑3p, the biological functions of miR‑143‑3p and the related roles and mechanisms in different cancer types. The potential of miR‑143‑3p as a biomarker for cancer was also highlighted and valuable future research directions were discussed.
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Affiliation(s)
- Jia Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116000, P.R. China
| | - Ying Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116000, P.R. China
| | - Dandan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116000, P.R. China
| | - Qingwei Cong
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116000, P.R. China
| | - Changchuan Bai
- Dalian Hospital of Traditional Chinese Medicine, Dalian, Liaoning 116013, P.R. China
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15
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Li D, Xiang B, Peng J, Li H, Peng L, Chen X. Association of genetic variations of 3'-UTR in clopidogrel pharmacokinetic-relevant genes with clopidogrel response in Han Chinese patients with coronary artery disease. Eur J Pharm Sci 2024; 200:106830. [PMID: 38878906 DOI: 10.1016/j.ejps.2024.106830] [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: 01/17/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
Dual antiplatelet therapy with aspirin and clopidogrel has reduced ischemic vascular events significantly. Genetic influence, especially those in clopidogrel pharmacokinetic-relevant genes partially accounts for interindividual pharmacodynamic variability of clopidogrel. However, most studies have concentrated on the genetic variations in introns, exons, or promoters of the candidate genes, and the association between genetic variations in 3'-UTR in clopidogrel pharmacokinetic-relevant genes and clopidogrel response is unknown. In our study, ten different algorithms were applied to pick potential miRNAs targeting the clopidogrel pharmacokinetic-relevant genes. Furthermore, the correlation between miRNA expression profiles and mRNA expression of corresponding clopidogrel pharmacokinetic-relevant genes was analyzed. Through comprehensive analysis, including bioinformatics prediction and correlation analysis of miRNA and mRNA expression profiles, miR-218-5p and miR-506-5p were supposed to regulate the expression of PON1 via binding with its 3'-UTR. Moreover, PON1 rs854551 and rs854552 were located in miRNA recognizing sequences and may serve as potential miRSNPs possibly affecting PON1 expression. The rs854552 polymorphism was genotyped and platelet reactivity index (PRI) indicative of clopidogrel response was measured in 341 Chinese coronary artery disease (CAD) patients 24 h after administration of 300 mg clopidogrel. Our results showed that PON1 rs854552 had a significant influence on PRI in CAD patients, especially in patients with CYP2C19 extensive metabolic phenotype. In conclusion, PON1 rs854552 polymorphisms may affect clopidogrel response. Bioinformatics prediction followed by functional validation could aid in decoding the contribution of unexplained variations in the 3'-UTR in drug-metabolizing enzymes on clopidogrel response.
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Affiliation(s)
- Dongjie Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China; Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Boyu Xiang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jingxuan Peng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - He Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
| | - Liming Peng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China; Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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16
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He Z, Sun H, Zhao F, Ma L, Wang J, Liu X, Li M, Hao Z, Li S. MicroRNA expression profiles reveal wool development and fineness regulation in Gansu alpine fine-wool sheep. Genomics 2024; 116:110922. [PMID: 39178999 DOI: 10.1016/j.ygeno.2024.110922] [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: 05/28/2024] [Revised: 07/04/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
The development of wool has a complex regulatory mechanism both influenced by genetic and environmental factors. MicroRNAs (miRNA) were involved in various biological processes of animals, and may play an important role in the regulation of wool development. In this study, we comprehensively analyzed and identified the histological parameters of hair follicles, as well as the miRNAs, target genes, pathways, and Gene Ontology terms related to wool fineness regulation and wool growth and development using HE staining and RNA-Seqs methods. Both coarse (group C, mean fiber diameter (MFD) = 22.26 ± 0.69 μm, n = 6) and fine (group F, MFD = 16.91 ± 0.29 μm, n = 6) of Gansu alpine fine-wool sheep with different wool fineness were used in this study. The results showed that the primary follicle diameter and secondary wool fiber diameter in group C were significantly higher than those in group F (P < 0.05). And the number of primary and secondary hair follicles in group C was significantly lower than that in group F (P < 0.05). Furthermore, a total of 67 DE miRNAs and 290 potential DE miRNAs target genes were screened in the skin tissues of sheep from groups F and C, and some potential target genes related to wool fineness regulation were screened, such as CDH2, KRT82, FOXN1, LOC101106296, KRT20, MCOLN3, KRT71, and TERT. These genes were closely related to Glutathione metabolism, epidermal cell differentiation, keratinization, and regulation of hair cycle. Moreover, the regulatory network of miRNAs-mRNAs suggested that miRNAs (miR-129-x, novel m0079-3p, miR-2484-z, novel m0025-5P, etc.) may play a key role in the wool development and wool fineness regulation of Gansu alpine fine-wool sheep. In summary, this study expands the existing miRNAs database and provides new information for studying the regulation of wool development in Gansu alpine fine wool sheep.
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Affiliation(s)
- Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Hongxian Sun
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Longxia Ma
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China.
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17
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Chan YL, Ho CSH, Tay GWN, Tan TWK, Tang TB. MicroRNA classification and discovery for major depressive disorder diagnosis: Towards a robust and interpretable machine learning approach. J Affect Disord 2024; 360:326-335. [PMID: 38788856 DOI: 10.1016/j.jad.2024.05.066] [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: 02/08/2024] [Revised: 04/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Major depressive disorder (MDD) is notably underdiagnosed and undertreated due to its complex nature and subjective diagnostic methods. Biomarker identification would help provide a clearer understanding of MDD aetiology. Although machine learning (ML) has been implemented in previous studies to study the alteration of microRNA (miRNA) levels in MDD cases, clinical translation has not been feasible due to the lack of interpretability (i.e. too many miRNAs for consideration) and stability. METHODS This study applied logistic regression (LR) model to the blood miRNA expression profile to differentiate patients with MDD (n = 60) from healthy controls (HCs, n = 60). Embedded (L1-regularised logistic regression) feature selector was utilised to extract clinically relevant miRNAs, and optimized for clinical application. RESULTS Patients with MDD could be differentiated from HCs with the area under the receiver operating characteristic curve (AUC) of 0.81 on testing data when all available miRNAs were considered (which served as a benchmark). Our LR model selected miRNAs up to 5 (known as LR-5 model) emerged as the best model because it achieved a moderate classification ability (AUC = 0.75), relatively high interpretability (feature number = 5) and stability (ϕ̂Z=0.55) compared to the benchmark. The top-ranking miRNAs identified by our model have demonstrated associations with MDD pathways involving cytokine signalling in the immune system, the reelin signalling pathway, programmed cell death and cellular responses to stress. CONCLUSION The LR-5 model, which is optimised based on ML design factors, may lead to a robust and clinically usable MDD diagnostic tool.
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Affiliation(s)
- Yee Ling Chan
- Centre for Intelligent Signal and Imaging Research (CISIR), Universiti Teknologi PETRONAS (UTP), Bandar Seri Iskandar 32610, Perak, Malaysia
| | - Cyrus S H Ho
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117543, Singapore
| | - Gabrielle W N Tay
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117543, Singapore
| | - Trevor W K Tan
- Centre for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117543, Singapore; Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117543, Singapore; Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore; N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore 117456, Singapore; Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore 119077, Singapore
| | - Tong Boon Tang
- Centre for Intelligent Signal and Imaging Research (CISIR), Universiti Teknologi PETRONAS (UTP), Bandar Seri Iskandar 32610, Perak, Malaysia.
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18
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Zhang Q, Lu B. The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs. Int J Mol Sci 2024; 25:9225. [PMID: 39273174 PMCID: PMC11395517 DOI: 10.3390/ijms25179225] [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: 07/18/2024] [Revised: 08/18/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Newts are excellent vertebrate models for investigating tissue regeneration due to their remarkable regenerative capabilities. To investigate the mRNA and microRNAs (miRNAs) profiles within the blastema niche of regenerating newt limbs, we amputated the limbs of Chinese fire belly newts (Cynops orientalis) and conducted comprehensive analyses of the transcriptome and microRNA profiles at five distinct time points post-amputation (0 hours, 1 day, 5 days 10 days and 20 days). We identified 24 significantly differentially expressed (DE) genes and 20 significantly DE miRNAs. Utilizing weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) enrichment analysis, we identified four genes likely to playing crucial roles in the early stages of limb regeneration: Cemip, Rhou, Gpd2 and Pcna. Moreover, mRNA-miRNA integration analysis uncovered seven human miRNAs (miR-19b-1, miR-19b-2, miR-21-5p, miR-127-5p, miR-150-5p, miR-194-5p, and miR-210-5p) may regulate the expression of these four key genes. The temporal expression patterns of these key genes and miRNAs further validated the robustness of the identified mRNA-miRNA landscape. Our study successfully identified candidate key genes and elucidated a portion of the genetic regulatory mechanisms involved in newt limb regeneration. These findings offer valuable insights for further exploration of the intricate processes of tissue regeneration.
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Affiliation(s)
- Qi Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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19
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Mohajeri Khorasani A, Raghibi A, Haj Mohammad Hassani B, Bolbolizadeh P, Amali A, Sadeghi M, Farshidi N, Dehghani A, Mousavi P. Decoding the Role of NEIL1 Gene in DNA Repair and Lifespan: A Literature Review with Bioinformatics Analysis. Adv Biol (Weinh) 2024:e2300708. [PMID: 39164210 DOI: 10.1002/adbi.202300708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/21/2024] [Indexed: 08/22/2024]
Abstract
Longevity, the length of an organism's lifespan, is impacted by environmental factors, metabolic processes, and genetic determinants. The base excision repair (BER) pathway is crucial for maintaining genomic integrity by repairing oxidatively modified base lesions. Nei-like DNA Glycosylase 1 (NEIL1), part of the BER pathway, is vital in repairing oxidative bases in G-rich DNA regions, such as telomeres and promoters. Hence, in this comprehensive review, it have undertaken a meticulous investigation of the intricate association between NEIL1 and longevity. The analysis delves into the multifaceted aspects of the NEIL1 gene, its various RNA transcripts, and the diverse protein isoforms. In addition, a combination of bioinformatic analysis is conducted to identify NEIL1 mutations, transcription factors, and epigenetic modifications, as well as its lncRNA/pseudogene/circRNA-miRNA-mRNA regulatory network. The findings suggest that the normal function of NEIL1 is a significant factor in human health and longevity, with defects in NEIL1 potentially leading to various cancers and related syndromes, Alzheimer's disease, obesity, and diabetes.
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Affiliation(s)
- Amirhossein Mohajeri Khorasani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Alireza Raghibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1416634793, Iran
| | - Behzad Haj Mohammad Hassani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pedram Bolbolizadeh
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Arian Amali
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mahboubeh Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Narges Farshidi
- Department of Pharmaceutics, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- USERN Office, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Aghdas Dehghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
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20
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Das S, Rai SN. Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers. Noncoding RNA 2024; 10:45. [PMID: 39195574 DOI: 10.3390/ncrna10040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
Gene regulation is crucial for cellular function and homeostasis. It involves diverse mechanisms controlling the production of specific gene products and contributing to tissue-specific variations in gene expression. The dysregulation of genes leads to disease, emphasizing the need to understand these mechanisms. Computational methods have jointly studied transcription factors (TFs), microRNA (miRNA), and messenger RNA (mRNA) to investigate gene regulatory networks. However, there remains a knowledge gap in comprehending gene regulatory networks. On the other hand, super-enhancers (SEs) have been implicated in miRNA biogenesis and function in recent experimental studies, in addition to their pivotal roles in cell identity and disease progression. However, statistical/computational methodologies harnessing the potential of SEs in deciphering gene regulation networks remain notably absent. However, to understand the effect of miRNA on mRNA, existing statistical/computational methods could be updated, or novel methods could be developed by accounting for SEs in the model. In this review, we categorize existing computational methods that utilize TF and miRNA data to understand gene regulatory networks into three broad areas and explore the challenges of integrating enhancers/SEs. The three areas include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in the identification of therapeutic targets and disease biomarkers. We believe that constructing statistical/computational models that dissect the role of SEs in predicting the effect of miRNA on gene regulation is crucial for tackling these challenges.
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Affiliation(s)
- Sarmistha Das
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shesh N Rai
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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21
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Xia W, Wang S, Liu X, Chen Y, Lin C, Liu R, Liu H, Li J, Zhu J. Chromosome-level genome provides new insight into the overwintering process of Korla pear (Pyrus sinkiangensis Yu). BMC PLANT BIOLOGY 2024; 24:773. [PMID: 39138412 PMCID: PMC11323677 DOI: 10.1186/s12870-024-05490-x] [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: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
Korla pear has a unique taste and aroma and is a breeding parent of numerous pear varieties. It is susceptible to Valsa mali var. pyri, which invades bark wounded by freezing injury. Its genetic relationships have not been fully defined and could offer insight into the mechanism for freezing tolerance and disease resistance. We generated a high-quality, chromosome-level genome assembly for Korla pear via the Illumina and PacBio circular consensus sequencing (CCS) platforms and high-throughput chromosome conformation capture (Hi-C). The Korla pear genome is ~ 496.63 Mb, and 99.18% of it is assembled to 17 chromosomes. Collinearity and phylogenetic analyses indicated that Korla might be derived from Pyrus pyrifolia and that it diverged ~ 3.9-4.6 Mya. During domestication, seven late embryogenesis abundant (LEA), two dehydrin (DHN), and 54 disease resistance genes were lost from Korla pear compared with P. betulifolia. Moreover, 21 LEA and 31 disease resistance genes were common to the Korla pear and P. betulifolia genomes but were upregulated under overwintering only in P. betulifolia because key cis elements were missing in Korla pear. Gene deletion and downregulation during domestication reduced freezing tolerance and disease resistance in Korla pear. These results could facilitate the breeding of novel pear varieties with high biotic and abiotic stress resistance.
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Affiliation(s)
- Wenwen Xia
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Saisai Wang
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Xiaoyan Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yifei Chen
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Caixia Lin
- Xinjiang Production and Construction Crops, Institute of Agricultural Sciences, Tiemenguan, 841007, China
| | - Ruina Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Hailiang Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Jin Li
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
| | - Jianbo Zhu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
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22
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Ferreira SS, Pandey S, Hemminger J, Bozdag S, Antunes MS. Early changes in microRNA expression in Arabidopsis plants infected with the fungal pathogen Fusarium graminearum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596347. [PMID: 39149262 PMCID: PMC11326132 DOI: 10.1101/2024.05.29.596347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Plants respond to biotic stressors by modulating various processes in an attempt to limit the attack by a pathogen or herbivore. Triggering these different defense processes requires orchestration of a network of proteins and RNA molecules that includes microRNAs (miRNAs). These short RNA molecules (20-22 nucleotides) have been shown to be important players in the early responses of plants to stresses because they can rapidly regulate the expression levels of a network of downstream genes. The ascomycete Fusarium graminearum is an important fungal pathogen that causes significant losses in cereal crops worldwide. Using the well-characterized Fusarium-Arabidopsis pathosystem, we investigated how plants change expression of their miRNAs globally during the early stages of infection by F. graminearum. In addition to miRNAs that have been previously implicated in stress responses, we have also identified evolutionarily young miRNAs whose levels change significantly in response to fungal infection. Some of these young miRNAs have homologs present in cereals. Thus, manipulating expression of these miRNAs may provide a unique path toward development of plants with increased resistance to fungal pathogens.
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Affiliation(s)
- Savio S. Ferreira
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Current address: Dept. of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN
| | - Suman Pandey
- Dept. of Computer Science & Engineering, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
| | - Jesseca Hemminger
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
| | - Serdar Bozdag
- Dept. of Computer Science & Engineering, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Dept. of Mathematics, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
| | - Mauricio S. Antunes
- Dept. of Biological Sciences, University of North Texas, Denton, TX
- BioDiscovery Institute, University of North Texas, Denton, TX
- Center for Computational Life Sciences, University of North Texas, Denton, TX
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23
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Shen C, Li X, Qin J, Duan L. Characterization of miRNA profiling in konjac-derived exosome-like nanoparticles and elucidation of their multifaceted roles in human health. FRONTIERS IN PLANT SCIENCE 2024; 15:1444683. [PMID: 39175488 PMCID: PMC11338808 DOI: 10.3389/fpls.2024.1444683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Plant-derived exosome-like nanoparticles (ELNs) have demonstrated cross-kingdom capabilities in regulating intercellular communication, facilitating drug delivery, and providing therapeutic interventions in humans. However, the functional attributes of konjac-derived ELNs (K-ELNs) remain largely unexplored. This study investigates the isolation, characterization, and functional analysis of K-ELNs, along with the profiling and differential expression analysis of associated miRNAs in both K-ELNs and Konjac tissues. K-ELNs were successfully isolated and characterized from two konjac species using ultracentrifugation, followed by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Small RNA sequencing identified a total of 3,259 miRNAs across all samples. Differential expression analysis revealed significant differences in miRNA profiles between K-ELNs and tissue samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of target genes provided insights into their roles in modulating pathways associated with diseases such as cancer and neurodegenerative disorders. Additionally, six miRNAs were selected for validation of sequencing results via RT-qPCR. The 5'RLM-RACE method was employed to validate the cleavage sites between differentially expressed miRNAs (DEMs) and their predicted target genes, further substantiating the regulatory roles of miRNAs in konjac. The findings of this study enhance our understanding of the molecular mechanisms underlying the biological functions and applications of K-ELNs, laying the groundwork for future research into their potential therapeutic roles in human health.
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Affiliation(s)
- Chuan Shen
- Shaannan Eco-economy Research Center, Ankang University, Ankang, China
| | - Xia Li
- Department of Electronic and Information Engineering, Ankang University, Ankang, China
| | - Jianfeng Qin
- Ankang Municipality Agricultural Science Research Institute, Ankang, China
| | - Longfei Duan
- Ankang Municipality Agricultural Science Research Institute, Ankang, China
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24
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Trivedi TS, Shaikh AM, Mankad AU, Rawal RM, Patel SK. Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny. Biochem Genet 2024; 62:2766-2795. [PMID: 38017284 DOI: 10.1007/s10528-023-10575-7] [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: 05/29/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (Anethum foeniculum) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their Arabidopsis thaliana and Homo sapience targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the Anethum foeniculum genome and assessed its impact on Arabidopsis thaliana and Homo sapience transcriptomes. In addition, functional enrichment analysis was evaluated for both species' targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in Homo sapiens and 1314 genes in Arabidopsis thaliana. Functional enrichment analysis reveals 56 Arabidopsis thaliana targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein-protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely MAPK1, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4, have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the CSPP1 target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of Anethum foeniculum miRNAs and the biological processes and diseases with which they are associated.
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Affiliation(s)
- Tithi S Trivedi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Aafrinbanu M Shaikh
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Archana U Mankad
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Rakesh M Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Saumya K Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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25
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Hao H, Ren X, Ma Z, Chen Z, Yang K, Wang Q, Liu S. Comprehensive analysis of the differential expression of mRNAs, lncRNAs, and miRNAs in Zi goose testis with high and low sperm mobility. Poult Sci 2024; 103:103895. [PMID: 38917609 PMCID: PMC11255893 DOI: 10.1016/j.psj.2024.103895] [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: 02/28/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Sperm mobility (SM) is an objective index for measuring sperm motility; however, the mechanisms underlying its regulation in geese remain unclear. The present study sought to elucidate the genetic mechanism underlying SM traits in Zi geese (Anser cygnoides L.). To this end, three successive experiments were performed. In Experiment I, SM was determined in 40 ganders; the 3 ganders with the highest mobility and three with the lowest mobility were assigned to the high and low sperm mobility rank (SMR) groups, respectively. In Experiment II, the differences in fertility between the two SMR groups were assessed within two breeding flocks comprising the selected six ganders from Experiment I and 30 females (each flock had 3 ganders and 15 females). In Experiment III, the testes of the 6 ganders were harvested for histological observation and whole-transcriptome sequencing. Results revealed better fertility, well-developed seminiferous tubules, and abundant mature sperm in the high-SMR-flock compared to those of the low-SMR-flock (89 vs. 81%) (P < 0.05). Differential expression (DE) analysis identified 76 mRNAs, 344 lncRNAs, and 17 miRNAs between the SMR groups, with LOC106049708, XPNPEP3, GNB3, ADCY8, PRKAG3, oha-miR-182-5p, and ocu-miR-10b-5p identified as key mRNAs and miRNAs contributing to SM. Enrichment analysis implicated these DE RNAs in pathways related to ATP binding, cell metabolism, apelin signaling, Wnt signaling, and Adherens junctions. Additionally, competing endogenous RNA (ceRNA) networks comprising 9 DE mRNAs, 17 DE miRNAs, and 169 DE lncRNAs were constructed. Two ceRNA network pathways (LOC106049708-oha-miR-182-5p-MSTRG.2479.6 and PRKAG3-ocu-miR-10b-5p-MSTRG.9047.14) were identified as key regulators of SM in geese. These findings offer crucial insights into the identification of key genes and ceRNA pathways influencing sperm mobility in geese.
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Affiliation(s)
- Hongrun Hao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Xiaofang Ren
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Zhigang Ma
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Zhifeng Chen
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Kun Yang
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Qiuju Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Shengjun Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China.
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26
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Hany M, Demerdash HM, Abouelnasr AA, Torensma B. Expression and Relations of Unique miRNAs Investigated in Metabolic Bariatric Surgery: A Systematic Review. Obes Surg 2024; 34:3038-3057. [PMID: 38916799 PMCID: PMC11289332 DOI: 10.1007/s11695-024-07302-5] [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: 04/12/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
Several studies have indicated that miRNAs play crucial roles in adipogenesis, insulin resistance, and inflammatory pathways associated with obesity and change after metabolic bariatric surgery (MBS). This systematic review explores and maps the existing literature on how miRNAs are expressed and investigates the unique miRNAs with the effects after MBS. The Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, and EMBASE were searched from 2019 until February 2024. This SR found 825 miRNAs from 25 studies, identifying 507 unique ones not used twice in the same study. A total of 21 studies (84%) measured RNA before and after surgery. The miRNA used per study ranged from 1 to 146 miRNA types, with a median study sample size of just 27 patients per study, raising concerns about some conclusions' robustness. From the 507 unique miRNAs, only 16 were consistently analyzed in 4 to 7 studies, which gave 77 different outcomes in relation to miRNA after MBS. MiRNA 122 and 122-5p were analyzed the most. Others were 106b-5p, 140-5p, 183-5p, 199b-5p, 20b-5p, 424-5p, 486-5p, 7-5p, 92a, 93-5p, 194-5p, 21-5p, 221, 320a, and 223-3p. A gap was observed in many studies, whereby the results were not the same, or there was no explanation for the effects after MBS was given within the same miRNA. Fifteen miRNAs were reported to have the same upward and downward trend, although not within the same study, and only 26.1% employed some form of statistical modeling to account for bias or confounding factors. Directions and effects in miRNA are visible, but still, inconsistent outcomes linked to the same miRNA after MBS, underscoring the need for clarity in miRNA-outcome relationships. Collaborative efforts, consensus-driven miRNA dictionaries, and larger, more rigorous studies are necessary to improve methodology designs and improve outcomes.
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Affiliation(s)
- Mohamed Hany
- Department of Surgery, Medical Research Institute, Alexandria University, Alexandria, Egypt.
- Madina Women's Hospital (IFSO certified center, European chapter), Alexandria, Egypt.
| | - Hala M Demerdash
- Consultant and Professor of Clinical Pathology, Alexandria University, Alexandria, Egypt
| | | | - Bart Torensma
- Leiden University Medical Center (LUMC), Leiden, The Netherlands
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27
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Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells. Respir Res 2024; 25:289. [PMID: 39080656 PMCID: PMC11290275 DOI: 10.1186/s12931-024-02919-7] [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: 04/16/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Sarcoidosis is a heterogeneous granulomatous disease with no accurate biomarkers of disease progression. Therefore, we profiled and integrated the DNA methylome, mRNAs, and microRNAs to identify molecular changes associated with sarcoidosis and disease progression that might illuminate underlying mechanisms of disease and potential biomarkers. METHODS Bronchoalveolar lavage cells from 64 sarcoidosis subjects and 16 healthy controls were used. DNA methylation was profiled on Illumina HumanMethylationEPIC arrays, mRNA by RNA-sequencing, and miRNAs by small RNA-sequencing. Linear models were fit to test for effect of sarcoidosis diagnosis and progression phenotype, adjusting for age, sex, smoking, and principal components of the data. We built a supervised multi-omics model using a subset of features from each dataset. RESULTS We identified 1,459 CpGs, 64 mRNAs, and five miRNAs associated with sarcoidosis versus controls and four mRNAs associated with disease progression. Our integrated model emphasized the prominence of the PI3K/AKT1 pathway, which is important in T cell and mTOR function. Novel immune related genes and miRNAs including LYST, RGS14, SLFN12L, and hsa-miR-199b-5p, distinguished sarcoidosis from controls. Our integrated model also demonstrated differential expression/methylation of IL20RB, ABCC11, SFSWAP, AGBL4, miR-146a-3p, and miR-378b between non-progressive and progressive sarcoidosis. CONCLUSIONS Leveraging the DNA methylome, transcriptome, and miRNA-sequencing in sarcoidosis BAL cells, we detected widespread molecular changes associated with disease, many which are involved in immune response. These molecules may serve as diagnostic/prognostic biomarkers and/or drug targets, although future testing is required for confirmation.
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Affiliation(s)
- Iain R Konigsberg
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
| | - Nancy W Lin
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA.
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Shu-Yi Liao
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Cuining Liu
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Kristyn MacPhail
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Margaret M Mroz
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Elizabeth Davidson
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Clara I Restrepo
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Sunita Sharma
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Li Li
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Division of Environmental and Occupational Health Sciences, Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
- Division of Pulmonary and Critical Care Sciences, Department of Medicine, School of Medicine, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
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28
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Hacimoto SYS, Cressoni ACL, da Silva LECM, Padovan CC, Ferriani RA, Rosa-e-Silva JC, Meola J. Selection of reference miRNAs for RT-qPCR assays in endometriosis menstrual blood-derived mesenchymal stem cells. PLoS One 2024; 19:e0306657. [PMID: 39078824 PMCID: PMC11288454 DOI: 10.1371/journal.pone.0306657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
Choosing appropriate reference genes or internal controls to normalize RT-qPCR data is mandatory for the interexperimental reproducibility of gene expression data obtained by RT-qPCR in most studies, including those on endometriosis. Particularly for miRNAs, the choice for reference genes is challenging because of their physicochemical and biological characteristics. Moreover, the retrograde menstruation theory, mesenchymal stem cells in menstrual blood (MenSCs), and changes in post-transcriptional regulatory processes through miRNAs have gained prominence in the scientific community as important players in endometriosis. Therefore, we originally explored the stability of 10 miRNAs expressions as internal control candidates in conditions involving the two-dimensional culture of MenSCs from healthy women and patients with endometriosis. Here, we applied multiple algorithms (geNorm, NormFinder, Bestkeeper, and delta Ct) to screen reference genes and assessed the comprehensive stability classification of miRNAs using RefFinder. Pairwise variation calculated using geNorm identified three miRNAs as a sufficient number of reference genes for accurate normalization. MiR-191-5p, miR-24-3p, and miR-103a-3p were the best combination for suitable gene expression normalization. This study will benefit similar research, but is also attractive for regenerative medicine and clinics that use MenSCs, miRNA expression, and RT-qPCR.
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Affiliation(s)
- Sabrina Yukari Santos Hacimoto
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ana Clara Lagazzi Cressoni
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Cristiana Carolina Padovan
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute of Hormones and Women’s Health (Hormona), CNPq, Porto Alegre, Rio Grande do Sul, Brazil
| | - Júlio César Rosa-e-Silva
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Juliana Meola
- Department of Gynecology and Obstetrics of Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute of Hormones and Women’s Health (Hormona), CNPq, Porto Alegre, Rio Grande do Sul, Brazil
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Gan L, Zheng L, Zou J, Luo P, Chen T, Zou J, Li W, Chen Q, Cheng L, Zhang F, Qian B. MicroRNA-21 in urologic cancers: from molecular mechanisms to clinical implications. Front Cell Dev Biol 2024; 12:1437951. [PMID: 39114567 PMCID: PMC11304453 DOI: 10.3389/fcell.2024.1437951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024] Open
Abstract
The three most common kinds of urologic malignancies are prostate, bladder, and kidney cancer, which typically cause substantial morbidity and mortality. Early detection and effective treatment are essential due to their high fatality rates. As a result, there is an urgent need for innovative research to improve the clinical management of patients with urologic cancers. A type of small noncoding RNAs of 22 nucleotides, microRNAs (miRNAs) are well-known for their important roles in a variety of developmental processes. Among these, microRNA-21 (miR-21) stands out as a commonly studied miRNA with implications in tumorigenesis and cancer development, particularly in urological tumors. Recent research has shed light on the dysregulation of miR-21 in urological tumors, offering insights into its potential as a prognostic, diagnostic, and therapeutic tool. This review delves into the pathogenesis of miR-21 in prostate, bladder, and renal cancers, its utility as a cancer biomarker, and the therapeutic possibilities of targeting miR-21.
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Affiliation(s)
- Lifeng Gan
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Tao Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Jun Zou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Le Cheng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Fangtao Zhang
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
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Guo X, Lan G, Jiang Q, Guo Y, Ouyang Y, Liang J, Zhang M. Expression mechanisms of mir-486-5p and its host gene sANK1 in porcine muscle. Mol Biol Rep 2024; 51:840. [PMID: 39042282 DOI: 10.1007/s11033-024-09773-2] [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: 12/13/2023] [Accepted: 07/01/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND MiR-486-5p has been identified as a crucial regulator of the PI3K/AKT signalling pathway, which plays a significant role in skeletal muscle development. Its host gene, sANK1, is also essential for skeletal muscle development. However, the understanding of porcine miR-486-5p and sANK1 has been limited. METHODS AND RESULTS In this study, PCR analyses revealed a positive correlation between the expression of miR-486-5p and sANK1 in the longissimus dorsi muscle of the Bama mini-pig and Landrace-pig, as well as during myoblast differentiation. Furthermore, the expression of miR-486-5p/sANK1 was higher in the Bama mini-pig compared to the Landrace-pig. There was a total of 18 single nucleotide polymorphisms (SNP) present in the sANK1 promoter region. Among these SNPs, 14 of them resulted in alterations in transcription factor binding sites (TFBs). Additionally, the promoter fluorescence assay demonstrated that the activity of the sANK1 promoter derived from the Bama mini-pig was significantly higher compared to Landrace-pig. It is worth noting that ten regulatory SNPs have the potential to influence the activity of the sANK1 promoter. A nuclear mutation A-G located at position - 401 (relative to the transcription start site) in the Bama mini-pig was identified, which creates a putative TFB motif for MyoD. CONCLUSIONS The findings presented in this study offer fundamental molecular knowledge and expression patterns of miR-486-5p/sANK1, which can be valuable for gaining a deeper understanding of the gene's involvement in porcine skeletal muscle development, and meat quality.
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Affiliation(s)
- Xiaoping Guo
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Mingyuan Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China.
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31
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Hohmann T, Hohmann U, Dehghani F, Grisk O, Jasinski-Bergner S. Analyzing the Impact of the Highest Expressed Epstein-Barr Virus-Encoded microRNAs on the Host Cell Transcriptome. Int J Mol Sci 2024; 25:7838. [PMID: 39063079 PMCID: PMC11276978 DOI: 10.3390/ijms25147838] [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: 06/12/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The Epstein-Barr virus (EBV) has a very high prevalence (>90% in adults), establishes a lifelong latency after primary infection, and exerts an oncogenic potential. This dsDNA virus encodes for various molecules, including microRNAs (miRs), which can be detected in the latent and lytic phases with different expression levels and affect, among others, immune evasion and malignant transformation. In this study, the different EBV miRs are quantified in EBV-positive lymphomas, and the impact on the host cell transcriptome of the most abundant EBV miRs will be analyzed using comparative RNA sequencing analyses. The EBV miRs ebv-miR-BART1, -BART4, -BART17, and -BHRF1-1 were most highly expressed, and their selective overexpression in EBV-negative human cells resulted in a large number of statistically significantly down- and up-regulated host cell genes. Functional analyses showed that these dysregulated target genes are involved in important cellular processes, including growth factor pathways such as WNT, EGF, FGF, and PDGF, as well as cellular processes such as apoptosis regulation and inflammation. Individual differences were observed between these four analyzed EBV miRs. In particular, ebv-miR-BHRF1-1 appears to be more important for malignant transformation and immune evasion than the other EBV miRs.
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Affiliation(s)
- Tim Hohmann
- Department of Anatomy and Cell Biology, Medical Faculty, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06108 Halle (Saale), Germany; (T.H.); (U.H.); (F.D.)
| | - Urszula Hohmann
- Department of Anatomy and Cell Biology, Medical Faculty, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06108 Halle (Saale), Germany; (T.H.); (U.H.); (F.D.)
| | - Faramarz Dehghani
- Department of Anatomy and Cell Biology, Medical Faculty, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06108 Halle (Saale), Germany; (T.H.); (U.H.); (F.D.)
| | - Olaf Grisk
- Institute of Physiology, Brandenburg Medical School (MHB), Theodor Fontane, Hochstraße 29, Haus 11, 2.OG, 14770 Brandenburg an der Havel, Germany;
| | - Simon Jasinski-Bergner
- Institute of Physiology, Brandenburg Medical School (MHB), Theodor Fontane, Hochstraße 29, Haus 11, 2.OG, 14770 Brandenburg an der Havel, Germany;
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, 14770 Brandenburg an der Havel, Germany
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32
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Chowdhury D, Nayeem M, Vanderven HA, Sarker S. Role of miRNA in Highly Pathogenic H5 Avian Influenza Virus Infection: An Emphasis on Cellular and Chicken Models. Viruses 2024; 16:1102. [PMID: 39066264 PMCID: PMC11281567 DOI: 10.3390/v16071102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/01/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The avian influenza virus, particularly the H5N1 strain, poses a significant and ongoing threat to both human and animal health. Recent outbreaks have affected domestic and wild birds on a massive scale, raising concerns about the virus' spread to mammals. This review focuses on the critical role of microRNAs (miRNAs) in modulating pro-inflammatory signaling pathways during the pathogenesis of influenza A virus (IAV), with an emphasis on highly pathogenic avian influenza (HPAI) H5 viral infections. Current research indicates that miRNAs play a significant role in HPAI H5 infections, influencing various aspects of the disease process. This review aims to synthesize recent findings on the impact of different miRNAs on immune function, viral cytopathogenicity, and respiratory viral replication. Understanding these mechanisms is essential for developing new therapeutic strategies to combat avian influenza and mitigate its effects on both human and animal populations.
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Affiliation(s)
- Dibakar Chowdhury
- Laboratory of Influenza Research, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Md. Nayeem
- One Health Institute, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh;
| | - Hillary A. Vanderven
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC 3010, Australia
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
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Lenart M, Siemińska I, Szatanek R, Mordel A, Szczepanik A, Rubinkiewicz M, Siedlar M, Baj-Krzyworzeka M. Identification of miRNAs Present in Cell- and Plasma-Derived Extracellular Vesicles-Possible Biomarkers of Colorectal Cancer. Cancers (Basel) 2024; 16:2464. [PMID: 39001526 PMCID: PMC11240749 DOI: 10.3390/cancers16132464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024] Open
Abstract
Globally, an increasing prevalence of colorectal cancer (CRC) prompts a need for the development of new methods for early tumor detection. MicroRNAs (also referred to as miRNAs) are short non-coding RNA molecules that play a pivotal role in the regulation of gene expression. MiRNAs are effectively transferred to extracellular vesicle (EVs) membrane sacs commonly released by cells. Our study aimed to examine the expression of miRNAs in four CRC cell lines and EVs derived from them (tumor EVs) in comparison to the normal colon epithelium cell line and its EVs. EVs were isolated by ultracentrifugation from the culture supernatant of SW480, SW620, SW1116, HCT116 and normal CCD841CoN cell lines and characterized according to the MISEV2023 guidelines. MiRNAs were analyzed by small RNA sequencing and validated by quantitative PCR. The performed analysis revealed 22 common miRNAs highly expressed in CRC cell lines and effectively transferred to tumor EVs, including miR-9-5p, miR-182-5p, miR-196b-5p, miR-200b-5p, miR-200c-3p, miR-425-5p and miR-429, which are associated with development, proliferation, invasion and migration of colorectal cancer cells, as well as in vesicle maturation and transport-associated pathways. In parallel, normal cells expressed miRNAs, such as miR-369 and miR-143, which play a role in proinflammatory response and tumor suppression. The analysis of selected miRNAs in plasma-derived EVs and tumor samples from CRC patients showed the similarity of miRNA expression profile between the patients' samples and CRC cell lines. Moreover, miR-182-5p, miR-196-5p, miR-425-5p and miR-429 were detected in several EV samples isolated from patients' plasma. Our results suggest that miR-182-5p, miR-196b-5p and miR-429 are differentially expressed between EVs from CRC patients and healthy donors, which might have clinical implications.
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Affiliation(s)
- Marzena Lenart
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Izabela Siemińska
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
- Institute of Veterinary Sciences, University Center of Veterinary Medicine JU-AU, University of Agriculture in Krakow, 30-059 Krakow, Poland
| | - Rafał Szatanek
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Anna Mordel
- Department of Clinical Immunology, University Children's Hospital of Cracow, 30-663 Krakow, Poland
| | - Antoni Szczepanik
- Third Department of Surgery, Faculty of Medicine, Jagiellonian University Medical College, 31-202 Krakow, Poland
| | - Mateusz Rubinkiewicz
- Second Department of Surgery, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
| | - Monika Baj-Krzyworzeka
- Department of Clinical Immunology, Medical College, Jagiellonian University, 30-663 Krakow, Poland
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Engel A, Rishik S, Hirsch P, Keller V, Fehlmann T, Kern F, Keller A. SingmiR: a single-cell miRNA alignment and analysis tool. Nucleic Acids Res 2024; 52:W374-W380. [PMID: 38572750 PMCID: PMC11223861 DOI: 10.1093/nar/gkae225] [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: 02/19/2024] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.
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Affiliation(s)
- Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Shusruto Rishik
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
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35
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Kamens HM, Anziano EK, Horton WJ, Cavigelli SA. Chronic Adolescent Restraint Stress Downregulates miRNA-200a Expression in Male and Female C57BL/6J and BALB/cJ Mice. Genes (Basel) 2024; 15:873. [PMID: 39062652 PMCID: PMC11275362 DOI: 10.3390/genes15070873] [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: 05/20/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Adolescence is a critical developmental period when the brain is plastic, and stress exposure can have lasting physiological consequences. One mechanism through which adolescent stress may have lasting effects is by altering microRNAs (miRNAs), leading to wide-scale gene expression changes. Three prior independent studies used unbiased approaches (RNA sequencing or microarray) to identify miRNAs differentially expressed by chronic variable stress in male rodents. In all three studies, miRNA-200a was differentially expressed in areas of the brain associated with emotion regulation. The current study extends this research to determine if chronic non-variable adolescent stress downregulates miRNA-200a expression by looking at two strains (BALB/cJ and C57BL/6J) of male and female mice. We utilized a 14-day (2 h/day) restraint stress protocol and verified stress effects on adolescent body weight gain and circulating corticosterone concentrations relative to non-restraint controls. Mice were then left undisturbed until they were euthanized in adulthood, at which time brains were collected to measure miRNA-200a in the ventral hippocampus. Three weeks after adolescent stress ended, differences in body weight between groups were no longer significant; however, animals exposed to stress had less miRNA-200a expression in the ventral hippocampus than control animals. These data implicate miRNA-200a expression as a potential mechanism by which adolescent stress can have persistent impacts on multiple outcomes in both male and female mice.
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Affiliation(s)
- Helen M. Kamens
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA 16801, USA (W.J.H.); (S.A.C.)
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Ferreira T, da Costa RMG, Dias F, Gama A, Gaspar VM, Mano JF, Oliveira PA, Medeiros R. Exploring the role of microRNAs as diagnostic and prognostic biomarkers in canine mammary tumors. GeroScience 2024:10.1007/s11357-024-01260-7. [PMID: 38954129 DOI: 10.1007/s11357-024-01260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Canine mammary tumors (CMTs) represent a significant health concern in dogs, with a high incidence among intact female dogs. CMTs are a promising comparative model for human breast cancer, due to sharing several pathophysiological features. Additionally, CMTs have a strong genetic correlation with their human counterpart, including the expression of microRNAs (miRNAs). MiRNAs are a class of non-coding RNAs that play important roles in post-translational regulation of gene expression, being implicated in carcinogenesis, tumor progression, and metastasis. Moreover, miRNAs hold promise as diagnostic, prognostic, and metastatic biomarkers. Understanding the molecular mechanisms underlying CMTs is crucial for improving diagnosis, prognosis, and monitoring of treatments. Herein, we provide a comprehensive overview of the current knowledge on miRNAs in CMTs, highlighting their roles in carcinogenesis and their potential as biomarkers. Additionally, we highlight the current limitations and critically discuss the overarching challenges in this field, emphasizing the need for future research to translate miRNA findings into veterinary clinical practice.
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Affiliation(s)
- Tiago Ferreira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal.
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal.
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Rui M Gil da Costa
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Postgraduate Program in Adult Health (PPGSAD), Federal University of Maranhão (UFMA), São Luís, Brazil
| | - Francisca Dias
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - João F Mano
- Department of Chemistry, CICECO - Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Paula A Oliveira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), UTAD, 5000-801, Vila Real, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal.
- Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal.
- Research Department of the Portuguese League against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal.
- Virology Service, Portuguese Institute of Oncology (IPO), 4200-072, Porto, Portugal.
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of the Fernando Pessoa University, 4249-004, Porto, Portugal.
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Evans LW, Durbin-Johnson B, Sutton KJ, Yam P, Bouzid YY, Cervantes E, Bonnel E, Stephenson CB, Bennett BJ. Specific circulating miRNAs are associated with plasma lipids in a healthy American cohort. Physiol Genomics 2024; 56:492-505. [PMID: 38557280 PMCID: PMC11368566 DOI: 10.1152/physiolgenomics.00087.2023] [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: 08/11/2023] [Revised: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Low-density lipoprotein cholesterol (LDL-c) is both a therapeutic target and a risk factor for cardiovascular disease (CVD). MicroRNA (miRNA) has been shown to regulate cholesterol homeostasis, and miRNA in blood circulation has been linked to hypercholesterolemia. However, few studies to date have associated miRNA with phenotypes like LDL-c in a healthy population. To this end, we analyzed circulating miRNA in relation to LDL-c in a healthy cohort of 353 participants using two separate bioinformatic approaches. The first approach found that miR-15b-5p and miR-16-5p were upregulated in individuals with at-risk levels of LDL-c. The second approach identified two miRNA clusters, one that positively and a second that negatively correlated with LDL-c. Included in the cluster that positively correlated with LDL-c were miR-15b-5p and miR-16-5p, as well as other miRNA from the miR-15/107, miR-30, and let-7 families. Cross-species analyses suggested that several miRNAs that associated with LDL-c are conserved between mice and humans. Finally, we examined the influence of diet on circulating miRNA. Our results robustly linked circulating miRNA with LDL-c, suggesting that miRNA could be used as biomarkers for hypercholesterolemia or targets for developing cholesterol-lowering drugs.NEW & NOTEWORTHY This study explored the association between circulating microRNA (miRNA) and low-density lipoprotein cholesterol (LDL-c) in a healthy population of 353 participants. Two miRNAs, miR-15b-5p and miR-16-5p, were upregulated in individuals with at-risk LDL-c levels. Several miRNA clusters were positively and negatively correlated with LDL-c and are known to target mRNA involved in lipid metabolism. The study also investigated the influence of diet on circulating miRNA, suggesting potential biomarkers for hypercholesterolemia.
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Affiliation(s)
- Levi W Evans
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
| | - Blythe Durbin-Johnson
- Division of Biostatistics, University of California, Davis, California, United States
| | - Kristen J Sutton
- Department of Nutrition, University of California, Davis, California, United States
| | - Phoebe Yam
- Department of Nutrition, University of California, Davis, California, United States
| | - Yasmine Y Bouzid
- Department of Nutrition, University of California, Davis, California, United States
| | - Eduardo Cervantes
- Department of Nutrition, University of California, Davis, California, United States
| | - Ellen Bonnel
- Department of Nutrition, University of California, Davis, California, United States
| | - Charles B Stephenson
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
- Department of Nutrition, University of California, Davis, California, United States
| | - Brian J Bennett
- USDA-ARS-Western Human Nutrition Research Center, Davis, California, United States
- Department of Nutrition, University of California, Davis, California, United States
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Hu L, Zheng X, Zhou M, Wang J, Tong L, Dong M, Xu T, Li Z. Optimized AF4 combined with density cushion ultracentrifugation enables profiling of high-purity human blood extracellular vesicles. J Extracell Vesicles 2024; 13:e12470. [PMID: 39001700 PMCID: PMC11245685 DOI: 10.1002/jev2.12470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/11/2024] [Indexed: 07/15/2024] Open
Abstract
Extracellular vesicles (EVs) have emerged as a promising tool for clinical liquid biopsy. However, the identification of EVs derived from blood samples is hindered by the presence of abundant plasma proteins, which impairs the downstream biochemical analysis of EV-associated proteins and nucleic acids. Here, we employed optimized asymmetric flow field-flow fractionation (AF4) combined with density cushion ultracentrifugation (UC) to obtain high-purity and intact EVs with very low lipoprotein contamination from human plasma and serum. Further proteomic analysis revealed more than 1000 EV-associated proteins, a large proportion of which has not been previously reported. Specifically, we found that cell-line-derived EV markers are incompatible with the identification of plasma-EVs and proposed that the proteins MYCT1, TSPAN14, MPIG6B and MYADM, as well as the traditional EV markers CD63 and CD147, are plasma-EV markers. Benefiting from the high-purity of EVs, we conducted comprehensive miRNA profiling of plasma EVs and nanosized particles (NPs), as well as compared plasma- and serum-derived EVs, which provides a valuable resource for the EV research community. Overall, our findings provide a comprehensive assessment of human blood EVs as a basis for clinical biopsy applications.
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Affiliation(s)
- Liqiao Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Guangzhou National LaboratoryGuangzhouChina
| | - Xinyue Zheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Maoge Zhou
- Guangzhou National LaboratoryGuangzhouChina
| | - Jifeng Wang
- Laboratory of Proteomics, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Lingjun Tong
- Jinan Central Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Ming Dong
- Guangzhou National LaboratoryGuangzhouChina
| | - Tao Xu
- Guangzhou National LaboratoryGuangzhouChina
- Jinan Central Hospital, Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of SciencesBeijingChina
- School of Biomedical EngineeringGuangzhou Medical UniversityGuangzhouChina
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Aravind VA, Kouznetsova VL, Kesari S, Tsigelny IF. Using Machine Learning and miRNA for the Diagnosis of Esophageal Cancer. J Appl Lab Med 2024; 9:684-695. [PMID: 38721901 DOI: 10.1093/jalm/jfae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/20/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND Esophageal cancer (EC) remains a global health challenge, often diagnosed at advanced stages, leading to high mortality rates. Current diagnostic tools for EC are limited in their efficacy. This study aims to harness the potential of microRNAs (miRNAs) as novel, noninvasive diagnostic biomarkers for EC. Our objective was to determine the diagnostic accuracy of miRNAs, particularly in distinguishing miRNAs associated with EC from control miRNAs. METHODS We applied machine learning (ML) techniques in WEKA (Waikato Environment for Knowledge Analysis) and TensorFlow Keras to a dataset of miRNA sequences and gene targets, assessing the predictive power of several classifiers: naïve Bayes, multilayer perceptron, Hoeffding tree, random forest, and random tree. The data were further subjected to InfoGain feature selection to identify the most informative miRNA sequence and gene target descriptors. The ML models' abilities to distinguish between miRNA implicated in EC and control group miRNA was then tested. RESULTS Of the tested WEKA classifiers, the top 3 performing ones were random forest, Hoeffding tree, and naïve Bayes. The TensorFlow Keras neural network model was subsequently trained and tested, the model's predictive power was further validated using an independent dataset. The TensorFlow Keras gave an accuracy 0.91. The WEKA best algorithm (naïve Bayes) model yielded an accuracy of 0.94. CONCLUSIONS The results demonstrate the potential of ML-based miRNA classifiers in diagnosing EC. However, further studies are necessary to validate these findings and explore the full clinical potential of this approach.
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Affiliation(s)
- Vishnu A Aravind
- REHS program, San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
- BiAna, La Jolla, CA, United States
- CureScience Institute, San Diego, CA, United States
| | - Santosh Kesari
- Pacific Neuroscience Institute, Department of Translational Neurosciences, Santa Monica, United States
| | - Igor F Tsigelny
- San Diego Supercomputer Center, UC San Diego, San Diego, CA, United States
- BiAna, La Jolla, CA, United States
- CureScience Institute, San Diego, CA, United States
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
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Jang D, Kim CJ, Shin BH, Lim DH. The Biological Roles of microRNAs in Drosophila Development. INSECTS 2024; 15:491. [PMID: 39057224 PMCID: PMC11277110 DOI: 10.3390/insects15070491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Drosophila is a well-established insect model system for studying various physiological phenomena and developmental processes, with a focus on gene regulation. Drosophila development is controlled by programmed regulatory mechanisms specific to individual tissues. When key developmental processes are shared among various insects, the associated regulatory networks are believed to be conserved across insects. Thus, studies of developmental regulation in Drosophila have substantially contributed to our understanding of insect development. Over the past two decades, studies on microRNAs (miRNAs) in Drosophila have revealed their crucial regulatory roles in various developmental processes. This review focuses on the biological roles of miRNAs in specific tissues and processes associated with Drosophila development. Additionally, as a future direction, we discuss sequencing technologies that can analyze the interactions between miRNAs and their target genes, with the aim of enhancing miRNA studies in Drosophila development.
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Affiliation(s)
| | | | | | - Do-Hwan Lim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea; (D.J.); (C.J.K.); (B.H.S.)
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Ausserhofer P, Kiss I, Witte A, Klein R. Anti-Adenoviral Effect of Human Argonaute 2 Alone and in Combination with Artificial microRNAs. Cells 2024; 13:1117. [PMID: 38994969 PMCID: PMC11240694 DOI: 10.3390/cells13131117] [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: 05/27/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
During infection, adenoviruses inhibit the cellular RNA interference (RNAi) machinery by saturating the RNA-induced silencing complex (RISC) of the host cells with large amounts of virus-derived microRNAs (mivaRNAs) that bind to the key component of the complex, Argonaute 2 (AGO2). In the present study, we investigated AGO2 as a prominent player at the intersection between human adenovirus 5 (HAdV-5) and host cells because of its ability to interfere with the HAdV-5 life cycle. First, the ectopic expression of AGO2 had a detrimental effect on the ability of the virus to replicate. In addition, in silico and in vitro analyses suggested that endogenous microRNAs (miRNAs), particularly hsa-miR-7-5p, have similar effects. This miRNA was found to be able to target the HAdV-5 DNA polymerase mRNA. The inhibitory effect became more pronounced upon overexpression of AGO2, likely due to elevated AGO2 levels, which abolished the competition between cellular miRNAs and mivaRNAs for RISC incorporation. Collectively, our data suggest that endogenous miRNAs would be capable of significantly inhibiting viral replication if adenoviruses had not developed a mechanism to counteract this function. Eventually, AGO2 overexpression-mediated relief of the RISC-saturating action of mivaRNAs strongly enhanced the effectiveness of artificial miRNAs (amiRNAs) directed against the HAdV-5 preterminal protein (pTP) mRNA, suggesting a substantial benefit of co-expressing amiRNAs and AGO2 in RNAi-based strategies for the therapeutic inhibition of adenoviruses.
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Affiliation(s)
- Philipp Ausserhofer
- Institute of Biotechnology, IMC University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria; (P.A.)
| | - Izabella Kiss
- Institute of Biotechnology, IMC University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria; (P.A.)
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Angela Witte
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1090 Vienna, Austria
| | - Reinhard Klein
- Institute of Biotechnology, IMC University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria; (P.A.)
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Gao X, Ma Q, Zhang X, Wang X, Wang N, Cui Y, Li S, Ma S, Wang H, Zhang K. The reference genome sequence of Artemisia argyi provides insights into secondary metabolism biosynthesis. FRONTIERS IN PLANT SCIENCE 2024; 15:1406592. [PMID: 39006964 PMCID: PMC11239399 DOI: 10.3389/fpls.2024.1406592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Artemisia argyi, a perennial herb of the genus Artemisia in the family Asteraceae, holds significant importance in Chinese traditional medicine, referred to as "Aicao". Here, we report a high-quality reference genome of Artemisia argyi L. cv. beiai, with a genome size up to 4.15 Gb and a contig N50 of 508.96 Kb, produced with third-generation Nanopore sequencing technology. We predicted 147,248 protein-coding genes, with approximately 68.86% of the assembled sequences comprising repetitive elements, primarily long terminal repeat retrotransposons(LTRs). Comparative genomics analysis shows that A. argyi has the highest number of specific gene families with 5121, and much more families with four or more members than the other 6 plant species, which is consistent with its more expanded gene families and fewer contracted gene families. Furthermore, through transcriptome sequencing of A. argyi in response to exogenous MeJA treatment, we have elucidated acquired regulatory insights into MeJA's impact on the phenylpropanoid, flavonoid, and terpenoid biosynthesis pathways of A. argyi. The whole-genome information obtained in this study serves as a valuable resource for delving deeper into the cultivation and molecular breeding of A. argyi. Moreover, it holds promise for enhancing genome assemblies across other members of the Asteraceae family. The identification of key genes establishes a solid groundwork for developing new varieties of Artemisia with elevated concentrations of active compounds.
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Affiliation(s)
- Xinqiang Gao
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Qiang Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xiaomeng Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xingyun Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yupeng Cui
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Shuyan Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Shengming Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hong Wang
- Henan Artemisia Argyi Medical Research Center, Anyang, China
| | - Kunpeng Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
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Zeng X, Wei Z, Du Q, Li J, Xie Z, Wang X. Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network. Bioinformatics 2024; 40:i381-i389. [PMID: 38940172 PMCID: PMC11211823 DOI: 10.1093/bioinformatics/btae262] [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] [Indexed: 06/29/2024] Open
Abstract
SUMMARY Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements and their impact plays a crucial role in understanding the regulation of the mRNA translation process, which supports the development of mRNA-based medicine or vaccines. Deep neural networks (DNN) can learn complex cis-regulatory codes from RNA sequences. However, extracting these cis-regulatory codes efficiently from DNN remains a significant challenge. Here, we propose a method based on our toolkit NeuronMotif and motif mutagenesis, which not only enables the discovery of diverse and high-quality motifs but also efficiently reveals motif interactions. By interpreting deep-learning models, we have discovered several crucial motifs that impact mRNA translation efficiency and stability, as well as some unknown motifs or motif syntax, offering novel insights for biologists. Furthermore, we note that it is challenging to enrich motif syntax in datasets composed of randomly generated sequences, and they may not contain sufficient biological signals. AVAILABILITY AND IMPLEMENTATION The source code and data used to produce the results and analyses presented in this manuscript are available from GitHub (https://github.com/WangLabTHU/combmotif).
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Affiliation(s)
- Xiaocheng Zeng
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Zheng Wei
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Qixiu Du
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Jiaqi Li
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Zhen Xie
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China
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Cappelli E, Ravera S, Bertola N, Grilli F, Squillario M, Regis S, Degan P. Advanced Analysis and Validation of a microRNA Signature for Fanconi Anemia. Genes (Basel) 2024; 15:820. [PMID: 39062599 PMCID: PMC11276059 DOI: 10.3390/genes15070820] [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: 05/17/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Some years ago, we reported the generation of a Fanconi anemia (FA) microRNA signature. This study aims to develop an analytical strategy to select a smaller and more reliable set of molecules that could be tested for potential benefits for the FA phenotype, elucidate its biochemical and molecular mechanisms, address experimental activity, and evaluate its possible impact on FA therapy. In silico analyses of the data obtained in the original study were thoroughly processed and anenrichment analysis was employed to identify the classes of genes that are over-represented in the FA-miRNA population under study. Primary bone marrow mononuclear cells (MNCs) from sixFA patients and sixhealthy donors as control samples were employed in the study. RNAs containing the small RNA fractions were reverse-transcribed and real-time PCR was performed in triplicate using the specific primers. Experiments were performed in triplicate.The in-silico analysis reported six miRNAs as likely contributors to the complex pathological spectrum of FA. Among these, three miRNAs were validated by real-time PCR. Primary bone marrow mononuclear cells (MNCs) reported a significant reduction in the expression level of miRNA-1246 and miRNA-206 in the FA samples in comparison to controls.This study highlights several biochemical pathways as culprits in the phenotypic manifestations and the pathophysiological mechanisms acting in FA. A relatively low number of miRNAs appear involved in all these different phenotypes, demonstrating the extreme plasticity of the gene expression modulation. This study further highlights miR-206 as a pivotal player in regulatory functions and signaling in the bone marrow mesenchymal stem cell (BMSC) process in FA. Due to this evidence, the activity of miR-206 in FA deserves specific experimental scrutiny. The results, here presented, might be relevant in the management of FA.
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Affiliation(s)
- Enrico Cappelli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy;
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genoa, Via De Toni 14, 16132 Genova, Italy;
| | - Nadia Bertola
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, L. go R. Benzi 10, 16132 Genoa, Italy;
| | - Federica Grilli
- Haematology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy;
| | | | - Stefano Regis
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16148 Genova, Italy;
| | - Paolo Degan
- Mutagenesi e Prevenzione Oncologica Unit—IRCCS Ospedale Policlinico San Martino, L. go R. Benzi 10, 16132 Genoa, Italy;
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Doyle C, Callaghan B, Roodnat AW, Armstrong L, Lester K, Simpson DA, Atkinson SD, Sheridan C, McKenna DJ, Willoughby CE. The TGFβ Induced MicroRNAome of the Trabecular Meshwork. Cells 2024; 13:1060. [PMID: 38920689 PMCID: PMC11201560 DOI: 10.3390/cells13121060] [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: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is a progressive optic neuropathy with a complex, multifactorial aetiology. Raised intraocular pressure (IOP) is the most important clinically modifiable risk factor for POAG. All current pharmacological agents target aqueous humour dynamics to lower IOP. Newer therapeutic agents are required as some patients with POAG show a limited therapeutic response or develop ocular and systemic side effects to topical medication. Elevated IOP in POAG results from cellular and molecular changes in the trabecular meshwork driven by increased levels of transforming growth factor β (TGFβ) in the anterior segment of the eye. Understanding how TGFβ affects both the structural and functional changes in the outflow pathway and IOP is required to develop new glaucoma therapies that target the molecular pathology in the trabecular meshwork. In this study, we evaluated the effects of TGF-β1 and -β2 treatment on miRNA expression in cultured human primary trabecular meshwork cells. Our findings are presented in terms of specific miRNAs (miRNA-centric), but given miRNAs work in networks to control cellular pathways and processes, a pathway-centric view of miRNA action is also reported. Evaluating TGFβ-responsive miRNA expression in trabecular meshwork cells will further our understanding of the important pathways and changes involved in the pathogenesis of glaucoma and could lead to the development of miRNAs as new therapeutic modalities in glaucoma.
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Affiliation(s)
- Chelsey Doyle
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Breedge Callaghan
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Anton W. Roodnat
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Lee Armstrong
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Karen Lester
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - David A. Simpson
- Wellcome Wolfson Institute for Experimental Medicine, Queens’ University, Belfast BT9 7BL, UK;
| | - Sarah D. Atkinson
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Carl Sheridan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK;
| | - Declan J. McKenna
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Colin E. Willoughby
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
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Nazou E, Potiris A, Mavrogianni D, Drakaki E, Vogiatzis AA, Sarli V, Vrantza T, Zikopoulos A, Louis K, Skentou C, Panagopoulos P, Drakakis P, Stavros S. Oocyte Maturation and miRNAs: Studying a Complicate Interaction to Reveal Possible Biomarkers for Female Infertility. Diseases 2024; 12:121. [PMID: 38920553 PMCID: PMC11202488 DOI: 10.3390/diseases12060121] [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: 03/25/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
Cellular metabolism, apoptosis, fertilization, and proliferation of granulosa cells belong to a battery of processes where microRNAs can be detected and associated with infertility. The aim of the present review is to focus on mammalian oocyte maturation events and the association between oocyte growth and miRNA expression. PubMed/Medline, Google Scholar and Scopus databases were searched, and 33 studies were included. Regarding the correlation among miRNA expression and the regulation of granulosa cells and cumulus cells, the most important miRNAs were let-7b, let-7c and miR-21. Additionally, the loss of Dicer, an enzyme involved in miRNA biogenesis, is probably a crucial factor in oogenesis, oocyte maturation and embryogenesis. Furthermore, miRNAs interfere with different cellular mechanisms like apoptosis, steroidogenesis, genome integrity, angiogenesis, antioxidative response and, consequently, oocyte maturation. Hence, it is of major importance to clarify the role and mechanism of each miRNA as understanding its action may develop new tools and establish new diagnostic and treatment approaches for infertility and ovarian disorders.
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Affiliation(s)
- Eleni Nazou
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Anastasios Potiris
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Despoina Mavrogianni
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece; (D.M.); (E.D.)
| | - Eirini Drakaki
- First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece; (D.M.); (E.D.)
| | - Aris-Anargyros Vogiatzis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Vaia Sarli
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Tereza Vrantza
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Athanasios Zikopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Konstantinos Louis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Chara Skentou
- Department of Obstetrics and Gynecology, Medical School, University of Ioannina, 45110 Ioannina, Greece;
| | - Periklis Panagopoulos
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Peter Drakakis
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
| | - Sofoklis Stavros
- Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece; (E.N.); (A.-A.V.); (V.S.); (T.V.); (A.Z.); (K.L.); (P.P.); (P.D.); (S.S.)
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Lu P, Jiang J. AE-RW: Predicting miRNA-disease associations by using autoencoder and random walk on miRNA-gene-disease heterogeneous network. Comput Biol Chem 2024; 110:108085. [PMID: 38754260 DOI: 10.1016/j.compbiolchem.2024.108085] [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: 02/28/2024] [Revised: 04/04/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Since scientific investigations have demonstrated that aberrant expression of miRNAs brings about the incidence of numerous intricate diseases, precise determination of miRNA-disease relationships greatly contributes to the advancement of human medical progress. To tackle the issue of inefficient conventional experimental approaches, numerous computational methods have been proposed to predict miRNA-disease association with enhanced accuracy. However, constructing miRNA-gene-disease heterogeneous network by incorporating gene information has been relatively under-explored in existing computational techniques. Accordingly, this paper puts forward a technique to predict miRNA-disease association by applying autoencoder and implementing random walk on miRNA-gene-disease heterogeneous network(AE-RW). Firstly, we integrate association information and similarities between miRNAs, genes, and diseases to construct a miRNA-gene-disease heterogeneous network. Subsequently, we consolidate two network feature representations extracted independently via an autoencoder and a random walk procedure. Finally, deep neural network(DNN) are utilized to conduct association prediction. The experimental results demonstrate that the AE-RW model achieved an AUC of 0.9478 through 5-fold CV on the HMDD v3.2 dataset, outperforming the five most advanced existing models. Additionally, case studies were implemented for breast and lung cancer, further validated the superior predictive capabilities of our model.
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Affiliation(s)
- Pengli Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
| | - Jicheng Jiang
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
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Pang S, Chen B, Li Y, Wu S, Chen L. miR-92a-3p promotes pulmonary fibrosis progression by regulating KLF2-mediated endothelial-to-mesenchymal transition. Cytotechnology 2024; 76:291-300. [PMID: 38736725 PMCID: PMC11082104 DOI: 10.1007/s10616-024-00617-2] [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: 06/29/2023] [Accepted: 01/10/2024] [Indexed: 05/14/2024] Open
Abstract
Pulmonary fibrosis (PF) is a chronic lung disease that has a poor prognosis and a serious impact on the quality of life of patients. Here, we investigated the potential role of miR-92a-3p in PF. The mRNA level of miR-92a-3p was significantly increased in both the lung tissues of bleomycin (BLM)--treated mice and pulmonary microvascular endothelial cells (PMVECs). Overexpressing miR-92a-3p increased the mRNA and protein levels of α‑SMA, vimentin, and Col-1 but downregulated E-cadherin. Additionally, the protein and mRNA expression levels of KLF2 were significantly decreased in the lung tissues of BLM-treated mice, suggesting that KLF2 participated in the progression of BLM-induced PF. Downregulating miR-92a-3p upregulated the expression of KLF2 and inhibited the endothelial-to-mesenchymal transition (EndoMT) process, thus alleviating PF in vivo. Altogether, a miR-92a-3p deficiency could significantly reduce the development of myofibroblasts and ameliorate PF progression.
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Affiliation(s)
- Sisi Pang
- Division of Geriatric Cardiology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029 People’s Republic of China
| | - Bo Chen
- Division of Geriatric Respiratory, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029 People’s Republic of China
| | - Yan Li
- Division of Geriatric Respiratory, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029 People’s Republic of China
| | - Shuangshuang Wu
- Division of Geriatric Respiratory, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029 People’s Republic of China
| | - Lei Chen
- Division of Geriatric Respiratory, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029 People’s Republic of China
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Craig T, Richwine K, Ishmael FT. Plasma microRNAs as biomarkers in hereditary angioedema. Ann Allergy Asthma Immunol 2024; 132:723-729.e4. [PMID: 38412917 DOI: 10.1016/j.anai.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Hereditary angioedema (HAE) is an autosomal dominant disease with variable expression. In some families with identical genetic abnormalities, the expression can range from several attacks per month to no attacks at all. It is hypothesized that post-transcriptional gene regulation accounts for the variable expression of the disease. OBJECTIVE To identify candidate microRNAs (miRNAs) that could play a role in HAE by determining whether miRNAs are differentially expressed in patients with HAE vs non-HAE individuals and whether expression profiles are tracked with severity. METHODS This study compared serum miRNA expression in patients with HAE vs non-HAE using RNA sequencing. Associations between miRNA expression and HAE severity were assessed in patients with mild disease (<6 attacks a year) vs severe disease (>1 attack per month). The functions of candidate miRNAs were analyzed using in silico methods. RESULTS There were robust miRNA expression differences between patients with HAE and non-HAE controls. A cluster analysis identified subgroups of patients with HAE having unique miRNA profiles that tracked with frequency of attacks. Two miRNAs, miR-99b-5p and miR-127-3p, were differentially expressed between mild and severe HAE (adjusted P < .05). In silico analysis revealed a function of differentially expressed miRNAs in regulation of C1 esterase inhibitor, kininogen, the bradykinin B2 receptor, and adherens junction function. CONCLUSION Candidate microRNAs were identified that could distinguish patients with and without HAE and may be used to identify phenotypes of HAE.
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Affiliation(s)
- Timothy Craig
- Department of Medicine, Penn State University, Hershey, Pennsylvania
| | - Kristina Richwine
- Department of Medicine, Penn State University, Hershey, Pennsylvania
| | - Faoud T Ishmael
- Department of Medicine, Penn State University, Hershey, Pennsylvania; Department of Allergy and Sleep Medicine, Mount Nittany Physician Group, State College, Pennsylvania.
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Garley M, Nowak K, Jabłońska E. Neutrophil microRNAs. Biol Rev Camb Philos Soc 2024; 99:864-877. [PMID: 38148491 DOI: 10.1111/brv.13048] [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: 02/01/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023]
Abstract
Neutrophils are considered 'first-line defence' cells as they can be rapidly recruited to the site of the immune response. As key components of non-specific immune mechanisms, neutrophils use phagocytosis, degranulation, and formation of neutrophil extracellular traps (NETs) to fight pathogens. Recently, immunoregulatory abilities of neutrophils associated with the secretion of several mediators, including cytokines and extracellular vesicles (EVs) containing, among other components, microRNAs (miRNAs), have also been reported. EVs are small structures released by cells into the extracellular space and are present in all body fluids. Microvesicles show the composition and status of the releasing cell, its physiological state, and pathological changes. Currently, EVs have gained immense scientific interest as they act as transporters of epigenetic information in intercellular communication. This review summarises findings from recent scientific reports that have evaluated the utility of miRNA molecules as biomarkers for effective diagnostics or even as start-points for new therapeutic strategies in neutrophil-mediated immune reactions. In addition, this review describes the current state of knowledge on miRNA molecules, which are endogenous regulators of gene expression besides being involved in the regulation of the immune response.
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Affiliation(s)
- Marzena Garley
- Department of Immunology, Medical University of Bialystok, Waszyngtona 15A, Bialystok, 15-269, Poland
| | - Karolina Nowak
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Ewa Jabłońska
- Department of Immunology, Medical University of Bialystok, Waszyngtona 15A, Bialystok, 15-269, Poland
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