1
|
Ismaeel A, Peck BD, Montgomery MM, Burke BI, Goh J, Kang G, Franco AB, Xia Q, Goljanek-Whysall K, McDonagh B, McLendon JM, Koopmans PJ, Jacko D, Schaaf K, Bloch W, Gehlert S, Wen Y, Murach KA, Peterson CA, Boudreau RL, Fisher-Wellman KH, McCarthy JJ. microRNA-1 Regulates Metabolic Flexibility in Skeletal Muscle via Pyruvate Metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607377. [PMID: 39149347 PMCID: PMC11326265 DOI: 10.1101/2024.08.09.607377] [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
MicroRNA-1 (miR-1) is the most abundant miRNA in adult skeletal muscle. To determine the function of miR-1 in adult skeletal muscle, we generated an inducible, skeletal muscle-specific miR-1 knockout (KO) mouse. Integration of RNA-sequencing (RNA-seq) data from miR-1 KO muscle with Argonaute 2 enhanced crosslinking and immunoprecipitation sequencing (AGO2 eCLIP-seq) from human skeletal muscle identified miR-1 target genes involved with glycolysis and pyruvate metabolism. The loss of miR-1 in skeletal muscle induced cancer-like metabolic reprogramming, as shown by higher pyruvate kinase muscle isozyme M2 (PKM2) protein levels, which promoted glycolysis. Comprehensive bioenergetic and metabolic phenotyping combined with skeletal muscle proteomics and metabolomics further demonstrated that miR-1 KO induced metabolic inflexibility as a result of pyruvate oxidation resistance. While the genetic loss of miR-1 reduced endurance exercise performance in mice and in C. elegans, the physiological down-regulation of miR-1 expression in response to a hypertrophic stimulus in both humans and mice causes a similar metabolic reprogramming that supports muscle cell growth. Taken together, these data identify a novel post-translational mechanism of adult skeletal muscle metabolism regulation mediated by miR-1.
Collapse
Affiliation(s)
- Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Bailey D Peck
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - McLane M Montgomery
- Department of Physiology, East Carolina University, Brody School of Medicine, Greenville, NC, USA
| | - Benjamin I Burke
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Jensen Goh
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Gyumin Kang
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Abigail B Franco
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Mass Spectrometry and Proteomics Core, University of Kentucky, Lexington, KY, USA
| | - Qin Xia
- Discipline of Physiology, School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Katarzyna Goljanek-Whysall
- Discipline of Physiology, School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Jared M McLendon
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, United States
| | - Pieter J Koopmans
- Department Health, Human Performance, & Recreation, University of Arkansas, Fayetteville, AR, USA
- Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, USA
| | - Daniel Jacko
- Institute of Cardiovascular Research and Sports Medicine, German Sport University, Cologne, Germany
- Olympic Base Center, North Rhine-Westphalia/Rhineland, Cologne, Germany
| | - Kirill Schaaf
- Institute of Cardiovascular Research and Sports Medicine, German Sport University, Cologne, Germany
- Olympic Base Center, North Rhine-Westphalia/Rhineland, Cologne, Germany
| | - Wilhelm Bloch
- Institute of Cardiovascular Research and Sports Medicine, German Sport University, Cologne, Germany
| | - Sebastian Gehlert
- Institute of Cardiovascular Research and Sports Medicine, German Sport University, Cologne, Germany
- Department for the Biosciences of Sports, Institute of Sports Science, University of Hildesheim, Hildesheim, Germany
| | - Yuan Wen
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Kevin A Murach
- Department Health, Human Performance, & Recreation, University of Arkansas, Fayetteville, AR, USA
- Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, USA
| | - Charlotte A Peterson
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Ryan L Boudreau
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kelsey H Fisher-Wellman
- Department of Physiology, East Carolina University, Brody School of Medicine, Greenville, NC, USA
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
2
|
Qadeer A, Wajid A, Rafey HA, Nawaz S, Khan S, Rahman SU, Alzahrani KJ, Khan MZ, Alsabi MNS, Ullah H, Safi SZ, Xia Z, Zahoor M. Exploring extracellular vesicles in zoonotic helminth biology: implications for diagnosis, therapeutic and delivery. Front Cell Infect Microbiol 2024; 14:1424838. [PMID: 39165921 PMCID: PMC11333462 DOI: 10.3389/fcimb.2024.1424838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/03/2024] [Indexed: 08/22/2024] Open
Abstract
Extracellular vesicles (EVs) have emerged as key intercellular communication and pathogenesis mediators. Parasitic organisms' helminths, cause widespread infections with significant health impacts worldwide. Recent research has shed light on the role of EVs in the lifecycle, immune evasion, and disease progression of these parasitic organisms. These tiny membrane-bound organelles including microvesicles and exosomes, facilitate the transfer of proteins, lipids, mRNAs, and microRNAs between cells. EVs have been isolated from various bodily fluids, offering a potential diagnostic and therapeutic avenue for combating infectious agents. According to recent research, EVs from helminths hold great promise in the diagnosis of parasitic infections due to their specificity, early detection capabilities, accessibility, and the potential for staging and monitoring infections, promote intercellular communication, and are a viable therapeutic tool for the treatment of infectious agents. Exploring host-parasite interactions has identified promising new targets for diagnostic, therapy, and vaccine development against helminths. This literature review delves into EVS's origin, nature, biogenesis, and composition in these parasitic organisms. It also highlights the proteins and miRNAs involved in EV release, providing a comprehensive summary of the latest findings on the significance of EVs in the biology of helminths, promising targets for therapeutic and diagnostic biomarkers.
Collapse
Affiliation(s)
- Abdul Qadeer
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Abdul Wajid
- Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Hafiz Abdul Rafey
- Shifa College of Pharmaceutical Sciences, Faculty of Pharmaceutical and Allied Health Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Saqib Nawaz
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Sawar Khan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sajid Ur Rahman
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Muhammad Zahoor Khan
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Mohammad Nafi Solaiman Alsabi
- Department of Basic Veterinary Medical Sciences, Faculty of Veterinary Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Hanif Ullah
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- West China School of Nursing/West China Hospital, Sichuan University, Chengdu, China
| | - Sher Zaman Safi
- Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom, Selangor, Malaysia
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Muhammad Zahoor
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
3
|
Sampilo NF, Song JL. microRNA-1 regulates sea urchin skeletogenesis by directly targeting skeletogenic genes and modulating components of signaling pathways. Dev Biol 2024; 508:123-137. [PMID: 38290645 PMCID: PMC10985635 DOI: 10.1016/j.ydbio.2024.01.010] [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: 05/08/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
microRNAs are evolutionarily conserved non-coding RNAs that direct post-transcriptional regulation of target transcripts. In vertebrates, microRNA-1 (miR-1) is expressed in muscle and has been found to play critical regulatory roles in vertebrate angiogenesis, a process that has been proposed to be analogous to sea urchin skeletogenesis. Results indicate that both miR-1 inhibitor and miR-1 mimic-injected larvae have significantly less F-actin enriched circumpharyngeal muscle fibers and fewer gut contractions. In addition, miR-1 regulates the positioning of skeletogenic primary mesenchyme cells (PMCs) and skeletogenesis of the sea urchin embryo. Interestingly, the gain-of-function of miR-1 leads to more severe PMC patterning and skeletal branching defects than its loss-of-function. The results suggest that miR-1 directly suppresses Ets1/2, Tbr, and VegfR7 of the skeletogenic gene regulatory network, and Nodal, and Wnt1 signaling components. This study identifies potential targets of miR-1 that impacts skeletogenesis and muscle formation and contributes to a deeper understanding of miR-1's function during development.
Collapse
Affiliation(s)
- Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| |
Collapse
|
4
|
Xu W, Liu J, Qi H, Si R, Zhao Z, Tao Z, Bai Y, Hu S, Sun X, Cong Y, Zhang H, Fan D, Xiao L, Wang Y, Li Y, Du Z. A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis. Nat Commun 2024; 15:2783. [PMID: 38555276 PMCID: PMC10981687 DOI: 10.1038/s41467-024-47055-4] [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: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024] Open
Abstract
Elucidating the expression of microRNAs in developing single cells is critical for functional discovery. Here, we construct scCAMERA (single-cell cartography of microRNA expression based on reporter assay), utilizing promoter-driven fluorescent reporters in conjunction with imaging and lineage tracing. The cartography delineates the transcriptional activity of 54 conserved microRNAs in lineage-resolved single cells throughout C. elegans embryogenesis. The combinatorial expression of microRNAs partitions cells into fine clusters reflecting their function and anatomy. Notably, the expression of individual microRNAs exhibits high cell specificity and divergence among family members. Guided by cellular expression patterns, we identify developmental functions of specific microRNAs, including miR-1 in pharynx development and physiology, miR-232 in excretory canal morphogenesis by repressing NHR-25/NR5A, and a functional synergy between miR-232 and miR-234 in canal development, demonstrating the broad utility of scCAMERA. Furthermore, integrative analysis reveals that tissue-specific fate determinants activate microRNAs to repress protein production from leaky transcripts associated with alternative, especially neuronal, fates, thereby enhancing the fidelity of developmental fate differentiation. Collectively, our study offers rich opportunities for multidimensional expression-informed analysis of microRNA biology in metazoans.
Collapse
Affiliation(s)
- Weina Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyi Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huan Qi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ruolin Si
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhiguang Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiju Tao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuchuan Bai
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shipeng Hu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xiaohan Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yulin Cong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haoye Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duchangjiang Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yangyang Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
5
|
Kotagama K, McJunkin K. Recent advances in understanding microRNA function and regulation in C. elegans. Semin Cell Dev Biol 2024; 154:4-13. [PMID: 37055330 PMCID: PMC10564972 DOI: 10.1016/j.semcdb.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
MicroRNAs (miRNAs) were first discovered in C. elegans as essential post-transcriptional regulators of gene expression. Since their initial discovery, miRNAs have been implicated in numerous areas of physiology and disease in all animals examined. In recent years, the C. elegans model continues to contribute important advances to all areas of miRNA research. Technological advances in tissue-specific miRNA profiling and genome editing have driven breakthroughs in understanding biological functions of miRNAs, mechanism of miRNA action, and regulation of miRNAs. In this review, we highlight these new C. elegans findings from the past five to seven years.
Collapse
Affiliation(s)
- Kasuen Kotagama
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA.
| |
Collapse
|
6
|
Rezaee D, Saadatpour F, Akbari N, Zoghi A, Najafi S, Beyranvand P, Zamani-Rarani F, Rashidi MA, Bagheri-Mohammadi S, Bakhtiari M. The role of microRNAs in the pathophysiology of human central nervous system: A focus on neurodegenerative diseases. Ageing Res Rev 2023; 92:102090. [PMID: 37832609 DOI: 10.1016/j.arr.2023.102090] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
microRNAs (miRNAs) are suggested to play substantial roles in regulating the development and various physiologic functions of the central nervous system (CNS). These include neurogenesis, cell fate and differentiation, morphogenesis, formation of dendrites, and targeting non-neural mRNAs. Notably, deregulation of an increasing number of miRNAs is associated with several neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and CNS tumors. They are particularly known to affect the amyloid β (Aβ) cleavage and accumulation, tau protein homeostasis, and expression of alpha-synuclein (α-syn), Parkin, PINK1, and brain-derived neurotrophic factor (BDNF) that play pivotal roles in the pathogenesis of neurodegenerative diseases. These include miR-16, miR-17-5p, miR-20a, miR-106a, miR-106b, miR-15a, miR-15b, miR-103, miR-107, miR-298, miR-328, miR-195, miR-485, and miR-29. In CNS tumors, several miRNAs, including miR-31, miR-16, and miR-21 have been identified to modulate tumorigenesis through impacting tumor invasion and apoptosis. In this review article, we have a look at the recent advances on our knowledge about the role of miRNAs in human brain development and functions, neurodegenerative diseases, and their clinical potentials.
Collapse
Affiliation(s)
- Delsuz Rezaee
- School of Allied Medical Sciences, Ilam University of Medical Sciences, Ilam, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nayyereh Akbari
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anahita Zoghi
- Brain Mapping Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Parisa Beyranvand
- Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fahimeh Zamani-Rarani
- Department of Anatomical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Rashidi
- Student Research Committee, Department of Occupational Health and Safety, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Bagheri-Mohammadi
- Department of Physiology and Neurophysiology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Bakhtiari
- Department of Anatomical Sciences, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| |
Collapse
|
7
|
Guiducci L, Cabiati M, Santocchi E, Prosperi M, Morales MA, Muratori F, Randazzo E, Federico G, Calderoni S, Del Ry S. Expression of miRNAs in Pre-Schoolers with Autism Spectrum Disorders Compared with Typically Developing Peers and Its Effects after Probiotic Supplementation. J Clin Med 2023; 12:7162. [PMID: 38002774 PMCID: PMC10672692 DOI: 10.3390/jcm12227162] [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: 10/25/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Alteration of the microbiota-gut-brain axis has been recently recognized as a possible contributor to the physiopathology of autism spectrum disorder (ASD). In this context, microRNA (miRNAs) dysfunction, implicated both in several neuropathological conditions including ASD and in different gastrointestinal disorders (GIDs), could represent an important modulating factor. In this contextual framework, we studied the transcriptional profile of specific circulating miRNAs associated with both ASD (miR-197-5p, miR-424-5p, miR-500a-5p, miR-664a-5p) and GID (miR-21-5p, miR-320a-5p, miR-31-5p, miR-223-5p) in a group of pre-schoolers with ASD and in typically developing (TD) peers. In the ASD group, we also assessed the same miRNAs after a 6-month supplementation with probiotics and their correlation with plasma levels of zonulin and lactoferrin. At baseline, the expression of miRNAs involved in ASD were significantly reduced in ASD pre-schoolers vs. TD controls. Regarding the miRNAs involved in GID, the expression levels of miR-320-5p, miR-31-5p, and miR-223-5p were significantly higher in ASD than in TD subjects, whereas miR-21-5p showed significantly reduced expression in the ASD group vs. TD group. Supplementation with probiotics did not significantly change the expression of miRNAs in the ASD population. We found a significative negative correlation between zonulin and miR-197-5p and miR-21-5p at baseline, as well as between lactoferrin and miR-223-5p after 6 months of probiotic supplementation. Our study confirms the presence of an altered profile of the miRNAs investigated in ASD versus TD peers that was not modified by supplementation with probiotics.
Collapse
Affiliation(s)
- Letizia Guiducci
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Manuela Cabiati
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Elisa Santocchi
- UFSMIA Zona Valle del Serchio, Azienda USL Toscana Nord Ovest, 55032 Castelnuovo di Garfagnana, Italy;
| | - Margherita Prosperi
- UFSMIA Valdera-Alta Val di Cecina, Azienda USL Toscana Nord Ovest, 56128 Pisa, Italy;
| | - Maria Aurora Morales
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Filippo Muratori
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Emioli Randazzo
- Unit of Pediatric Endocrinology and Diabetes, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (E.R.); (G.F.)
| | - Giovanni Federico
- Unit of Pediatric Endocrinology and Diabetes, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (E.R.); (G.F.)
| | - Sara Calderoni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Silvia Del Ry
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| |
Collapse
|
8
|
Paneru BD, Hill DA. The role of extracellular vesicle-derived miRNAs in adipose tissue function and metabolic health. IMMUNOMETABOLISM (COBHAM, SURREY) 2023; 5:e00027. [PMID: 37501663 PMCID: PMC10371064 DOI: 10.1097/in9.0000000000000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
Extracellular vesicles (EVs) are nanometer size lipid particles that are released from virtually every cell type. Recent studies have shown that miRNAs carried by EVs play important roles in intercellular and interorgan communication. In the context of obesity and insulin resistance, EV-derived miRNAs functionally bridge major metabolic organs, including the adipose tissue, skeletal muscle, liver, and pancreas, to regulate insulin secretion and signaling. As a result, many of these EV-derived miRNAs have been proposed as potential disease biomarkers and/or therapeutic agents. However, the field's knowledge of EV miRNA-mediated regulation of mammalian metabolism is still in its infancy. Here, we review the evidence indicating that EV-derived miRNAs provide cell-to-cell and organ-to-organ communication to support metabolic health, highlight the potential medical relevance of these discoveries, and discuss the most important knowledge gaps and future directions for this field.
Collapse
Affiliation(s)
- Bam D. Paneru
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David A. Hill
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Institute for Immunology, and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
9
|
Quesnelle DC, Bendena WG, Chin-Sang ID. A Compilation of the Diverse miRNA Functions in Caenorhabditis elegans and Drosophila melanogaster Development. Int J Mol Sci 2023; 24:ijms24086963. [PMID: 37108126 PMCID: PMC10139094 DOI: 10.3390/ijms24086963] [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: 03/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs are critical regulators of post-transcriptional gene expression in a wide range of taxa, including invertebrates, mammals, and plants. Since their discovery in the nematode, Caenorhabditis elegans, miRNA research has exploded, and they are being identified in almost every facet of development. Invertebrate model organisms, particularly C. elegans, and Drosophila melanogaster, are ideal systems for studying miRNA function, and the roles of many miRNAs are known in these animals. In this review, we compiled the functions of many of the miRNAs that are involved in the development of these invertebrate model species. We examine how gene regulation by miRNAs shapes both embryonic and larval development and show that, although many different aspects of development are regulated, several trends are apparent in the nature of their regulation.
Collapse
Affiliation(s)
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ian D Chin-Sang
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
10
|
Sun L, Zhou H, Zhao X, Zhang H, Wang Y, Li G. Small RNA sequencing identified miR-3180 as a potential prognostic biomarker for Chinese hepatocellular carcinoma patients. Front Genet 2023; 14:1102171. [PMID: 37051592 PMCID: PMC10083302 DOI: 10.3389/fgene.2023.1102171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/10/2023] [Indexed: 03/28/2023] Open
Abstract
MicroRNAs (miRNAs) and their target genes are aberrantly expressed in many cancers and are linked to carcinogenesis and metastasis, especially among hepatocellular carcinoma (HCC) patients. This study sought to identify new biomarkers related to HCC prognosis using small RNA sequencing from the tumor and matched normal adjacent tissue of 32 patients with HCC. Eight miRNAs were downregulated and 61 were upregulated more than twofold. Of these, five miRNAs, hsa-miR-3180, hsa-miR-5589-5p, hsa-miR-490-5p, hsa-miR-137, and hsa-miR-378i, were significantly associated with 5-year overall survival (OS) rates. Differential upregulation of hsa-miR-3180 and downregulation of hsa-miR-378i in tumor samples supported the finding that low and high concentrations of hsa-miR-3180 (p = 0.029) and hsa-miR-378i (p = 0.047), respectively, were associated with higher 5-year OS. Cox regression analyses indicated that hsa-miR-3180 (HR = 0.08; p = 0.013) and hsa-miR-378i (HR = 18.34; p = 0.045) were independent prognostic factors of poor survival. However, high hsa-miR-3180 expression obtained larger AUCs for OS and progression-free survival (PFS) and had better nomogram prediction than hsa-miR-378i. These findings indicate that hsa-miR-3180 may be associated with HCC progression and could serve as a potential biomarker for this disease.
Collapse
Affiliation(s)
- Libo Sun
- General Surgery Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Hansheng Zhou
- Department of Pharmacy, Linyi People’s Hospital, Linyi, Shandong, China
| | - Xiaofei Zhao
- General Surgery Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Haitao Zhang
- General Surgery Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- CAS Key Lab of Mental Health, Institute of Psychology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yan Wang, ; Guangming Li,
| | - Guangming Li
- General Surgery Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
- *Correspondence: Yan Wang, ; Guangming Li,
| |
Collapse
|
11
|
Lépine S, Castellanos-Montiel MJ, Durcan TM. TDP-43 dysregulation and neuromuscular junction disruption in amyotrophic lateral sclerosis. Transl Neurodegener 2022; 11:56. [PMID: 36575535 PMCID: PMC9793560 DOI: 10.1186/s40035-022-00331-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a disease characterized by upper and lower motor neuron (MN) loss with a signature feature of cytoplasmic aggregates containing TDP-43, which are detected in nearly all patients. Mutations in the gene that encodes TDP-43 (TARBDP) are known to result in both familial and sporadic ALS. In ALS, disruption of neuromuscular junctions (NMJs) constitutes a critical event in disease pathogenesis, leading to denervation atrophy, motor impairments and disability. Morphological defects and impaired synaptic transmission at NMJs have been reported in several TDP-43 animal models and in vitro, linking TDP-43 dysregulation to the loss of NMJ integrity in ALS. Through the lens of the dying-back and dying-forward hypotheses of ALS, this review discusses the roles of TDP-43 related to synaptic function, with a focus on the potential molecular mechanisms occurring within MNs, skeletal muscles and glial cells that may contribute to NMJ disruption in ALS.
Collapse
Affiliation(s)
- Sarah Lépine
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada ,grid.14709.3b0000 0004 1936 8649Faculty of Medicine and Health Sciences, McGill University, 3605 De La Montagne, Montreal, QC H3G 2M1 Canada
| | - Maria José Castellanos-Montiel
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada
| | - Thomas Martin Durcan
- grid.14709.3b0000 0004 1936 8649The Neuro’s Early Drug Discovery Unit (EDDU), Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, 3801 University Street, Montreal, QC H3A 2B4 Canada
| |
Collapse
|
12
|
Roy C, Molin L, Alcolei A, Solyga M, Bonneau B, Vachon C, Bessereau JL, Solari F. DAF-2/insulin IGF-1 receptor regulates motility during aging by integrating opposite signaling from muscle and neuronal tissues. Aging Cell 2022; 21:e13660. [PMID: 35808897 PMCID: PMC9381905 DOI: 10.1111/acel.13660] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 05/27/2022] [Accepted: 06/05/2022] [Indexed: 12/11/2022] Open
Abstract
During aging, preservation of locomotion is generally considered an indicator of sustained good health, in elderlies and in animal models. In Caenorhabditis elegans, mutants of the insulin‐IGF‐1 receptor DAF2/IIRc represent a paradigm of healthy aging, as their increased lifespan is accompanied by a delay in age‐related loss of motility. Here, we investigated the DAF‐2/IIRc‐dependent relationship between longevity and motility using an auxin‐inducible degron to trigger tissue‐specific degradation of endogenous DAF‐2/IIRc. As previously reported, inactivation of DAF‐2/IIRc in neurons or intestine was sufficient to extend the lifespan of worms, whereas depletion in epidermis, germline, or muscle was not. However, neither intestinal nor neuronal depletion of DAF‐2/IIRc prevented the age‐related loss of motility. In 1‐day‐old adults, DAF‐2/IIRc depletion in neurons reduced motility in a DAF‐16/FOXO dependent manner, while muscle depletion had no effect. By contrast, DAF‐2 depletion in the muscle of middle‐age animals improved their motility independently of DAF‐16/FOXO but required UNC‐120/SRF. Yet, neuronal or muscle DAF‐2/IIRc depletion both preserved the mitochondria network in aging muscle. Overall, these results show that the motility pattern of daf‐2 mutants is determined by the sequential and opposing impact of neurons and muscle tissues and can be dissociated from the regulation of the lifespan. This work also provides the characterization of a versatile tool to analyze the tissue‐specific contribution of insulin‐like signaling in integrated phenotypes at the whole organism level.
Collapse
Affiliation(s)
- Charline Roy
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Laurent Molin
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Allan Alcolei
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Mathilde Solyga
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Benjamin Bonneau
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Camille Vachon
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Jean-Louis Bessereau
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| | - Florence Solari
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR5284, INSERMU1314, Institut NeuroMyoGène, MeLis, Lyon, France
| |
Collapse
|
13
|
Li Z, Guo Y, Ndandala CB, Chen H, Huang C, Zhao G, Huang H, Li G, Chen H. Analysis of circRNA and miRNA expression profiles in IGF3-induced ovarian maturation in spotted scat ( Scatophagus argus). Front Endocrinol (Lausanne) 2022; 13:998207. [PMID: 36506051 PMCID: PMC9732426 DOI: 10.3389/fendo.2022.998207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/03/2022] [Indexed: 11/26/2022] Open
Abstract
Insulin-like growth factor 3 (IGF3) induces ovarian maturation in teleosts; however, research on its molecular regulatory mechanism remains deficient. Circular RNAs (circRNAs) and microRNAs (miRNAs) are involved in various biological processes, including reproduction. In this study, circRNAs and miRNAs involved in IGF3-induced ovarian maturation were evaluated in spotted scat (Scatophagus argus). In ovarian tissues, we identified 176 differentially expressed (DE) circRNAs and 52 DE miRNAs between IGF3 treatment and control groups. Gene Ontology (GO) enrichment analyses showed that host genes of DE circRNAs and target genes of DE miRNAs were enriched for various processes with a high degree of overlap, including cellular process, reproduction, reproductive process, biological adhesion, growth, extracellular region, cell junction, catalytic activity, and transcription factor activity. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included cell adhesion molecules, ECM-receptor interaction, regulation of actin cytoskeleton, focal adhesion, cell cycle, Hedgehog signaling pathway, phosphatidylinositol signaling system, PI3K-Akt signaling pathway, Apelin signaling pathway, Notch signaling pathway, insulin signaling pathway, and Rap1 signaling pathway. A circRNA-miRNA-mRNA regulatory network was constructed, including DE genes involved in reproduction (e.g., oocyte maturation, oocyte meiosis, and ECM remodeling), such as ccnd2, hecw2, dnm2, irs1, adam12, and cdh13. According to the regulatory network and tissue distribution, we identified one circRNA (Lachesis_group5:6245955|6270787) and three miRNAs (novel_miR_622, novel_miR_980, and novel_miR_64) that may exert regulatory effects in IGF3-induced ovarian maturation in S. argus. Taken together, this study provides a novel insight into the molecular mechanisms by which IGF3 functions in ovaries and highlights the effects of circRNAs and miRNAs in reproduction in S. argus.
Collapse
Affiliation(s)
- Zhiyuan Li
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yuwen Guo
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Charles Brighton Ndandala
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Huadong Chen
- Guangdong Havwii Agriculture Group Co., LTD, Zhanjiang, China
| | | | | | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya, China
- *Correspondence: Huapu Chen, ; Hai Huang,
| | - Guangli Li
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Huapu Chen
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya, China
- *Correspondence: Huapu Chen, ; Hai Huang,
| |
Collapse
|
14
|
Zhou C, Zhang Y, Wu S, Wang Z, Tuersong W, Wang C, Liu F, Hu M. Genome-Wide Identification of CircRNAs of Infective Larvae and Adult Worms of Parasitic Nematode, Haemonchus contortus. Front Cell Infect Microbiol 2021; 11:764089. [PMID: 34881194 PMCID: PMC8645938 DOI: 10.3389/fcimb.2021.764089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
CircRNAs, a novel class of ncRNA family, are endogenous transcriptional products involved in various biological and physiological processes in plants and animals. However, almost no information is available for circRNAs of parasitic helminths. In the present study, the circRNAs repertoire was comprehensively explored in Haemonchus contortus, a blood-sucking parasitic nematode of ruminants. In total, 20073 circRNAs were identified and annotated from three key developmental stages/genders of H. contortus including the free-living infective third-stage larvae (L3, 18883), parasitic adult female (Af, 3491), and male worms (Am, 2550) via deep-sequencing technology and bioinformatic analysis. Among these identified circRNAs, 71% were derived from exonic regions of protein-coding genes. The number of circRNAs transcribed from the X chromosome (4704) was higher than that from Chromosome I-V (3143, 3273, 3041, 3030, 2882). The amount of highly expressed circRNAs in third-stage larvae was significantly more abundant than that in adult stage. 15948 and 16847 circRNAs were differentially expressed between Af and L3s and between Am and L3, respectively. Among them, 13409 circRNAs existed in both comparisons. Furthermore, 1119 circRNAs were differentially expressed between Af_and_Am. GO enrichment analysis indicated that source genes of circRNAs differentially expressed between Am and L3 as well as between Af and L3 were significantly enriched in many biological processes, primarily including signaling, signal transduction and cell communication terms. KEGG analysis revealed that parental genes of differentially expressed circRNAs were mainly related to metabolism (pyruvate metabolism, glycerophospholipid metabolism, and carbon metabolism), MAPK signaling pathway, and phosphatidylinositol signaling system. Moreover, many circRNAs contained one or more miRNA potential binding sites, suggesting that they could regulate gene expression at the post-transcriptional level. Furthermore, the correctness of head-to-tail back splicing site and alternative circularization events were verified by Sanger sequencing using both divergent and convergent primers. Finally, the reliability of RNA-Seq data and the resistance of circRNAs to RNase R digestion were confirmed by quantitative RT-PCR. Taken together, our findings provide a foundation for elucidating the regulatory mechanisms of circRNAs in H. contortus, which will advance the understanding of circRNAs in parasitic nematodes.
Collapse
Affiliation(s)
- Caixian Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Simin Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiheng Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Waresi Tuersong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chunqun Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Feng Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
15
|
Ghafouri-Fard S, Noroozi R, Brand S, Hussen BM, Eghtedarian R, Taheri M, Ebrahimzadeh K. Emerging Role of Non-coding RNAs in Autism Spectrum Disorder. J Mol Neurosci 2021; 72:201-216. [PMID: 34767189 DOI: 10.1007/s12031-021-01934-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023]
Abstract
Autism spectrum disorders (ASD) embrace a diverse set of neurodevelopmental diseases with a multifaceted genetic basis. Non-coding RNAs (ncRNAs) are among putative loci with critical participation in the development of ASD. Expression of some lncRNAs, namely RP11-466P24.2, SYP-AS1, STXBP5-AS1, and IFNG-AS1 has been decreased in ASD, while AK128569, CTD-2516F10.2, MSNP1AS, RPS10P2-AS1, LINC00693, LINC00689, NEAT1, TUG1, and Shank2-AS lncRNAs have been over-expressed in ASD. Expression of several miRNAs which are implicated in the immunological developmental, immune responses, and protein synthesis as well as those participating in the regulation of PI3K/Akt/mTOR and EGFR signaling pathways is dysregulated in the context of ASD. In the present article, we describe investigations which appraised the role of lncRNAs, miRNAs, and circRNAs in the pathobiology of ASD.
Collapse
Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Serge Brand
- Psychiatric Clinics, Center for Affective, Stress and Sleep Disorders, University of Basel, Basel, Switzerland
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Reyhane Eghtedarian
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Institute of Human Genetics, Jena University Hospital, 07740, Jena, Germany.
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
16
|
Gutiérrez-Pérez P, Santillán EM, Lendl T, Wang J, Schrempf A, Steinacker TL, Asparuhova M, Brandstetter M, Haselbach D, Cochella L. miR-1 sustains muscle physiology by controlling V-ATPase complex assembly. SCIENCE ADVANCES 2021; 7:eabh1434. [PMID: 34652942 PMCID: PMC8519577 DOI: 10.1126/sciadv.abh1434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/23/2021] [Indexed: 05/13/2023]
Abstract
Muscle function requires unique structural and metabolic adaptations that can render muscle cells selectively vulnerable, with mutations in some ubiquitously expressed genes causing myopathies but sparing other tissues. We uncovered a muscle cell vulnerability by studying miR-1, a deeply conserved, muscle-specific microRNA whose ablation causes various muscle defects. Using Caenorhabditis elegans, we found that miR-1 represses multiple subunits of the ubiquitous vacuolar adenosine triphosphatase (V-ATPase) complex, which is essential for internal compartment acidification and metabolic signaling. V-ATPase subunits are predicted miR-1 targets in animals ranging from C. elegans to humans, and we experimentally validated this in Drosophila. Unexpectedly, up-regulation of V-ATPase subunits upon miR-1 deletion causes reduced V-ATPase function due to defects in complex assembly. These results reveal V-ATPase assembly as a conserved muscle cell vulnerability and support a previously unknown role for microRNAs in the regulation of protein complexes.
Collapse
Affiliation(s)
- Paula Gutiérrez-Pérez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Emilio M. Santillán
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Thomas Lendl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Anna Schrempf
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Mila Asparuhova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Brandstetter
- Electron Microscopy Facility, Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| |
Collapse
|
17
|
Schiffer I, Gerisch B, Kawamura K, Laboy R, Hewitt J, Denzel MS, Mori MA, Vanapalli S, Shen Y, Symmons O, Antebi A. miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging. eLife 2021; 10:e66768. [PMID: 34311841 PMCID: PMC8315803 DOI: 10.7554/elife.66768] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/03/2021] [Indexed: 01/02/2023] Open
Abstract
Muscle function relies on the precise architecture of dynamic contractile elements, which must be fine-tuned to maintain motility throughout life. Muscle is also plastic, and remodeled in response to stress, growth, neural and metabolic inputs. The conserved muscle-enriched microRNA, miR-1, regulates distinct aspects of muscle development, but whether it plays a role during aging is unknown. Here we investigated Caenorhabditis elegans miR-1 in muscle function in response to proteostatic stress. mir-1 deletion improved mid-life muscle motility, pharyngeal pumping, and organismal longevity upon polyQ35 proteotoxic challenge. We identified multiple vacuolar ATPase subunits as subject to miR-1 control, and the regulatory subunit vha-13/ATP6V1A as a direct target downregulated via its 3'UTR to mediate miR-1 physiology. miR-1 further regulates nuclear localization of lysosomal biogenesis factor HLH-30/TFEB and lysosomal acidification. Our studies reveal that miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact muscle function and health during aging.
Collapse
Affiliation(s)
| | - Birgit Gerisch
- Max Planck Institute for Biology of AgeingCologneGermany
| | | | - Raymond Laboy
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Jennifer Hewitt
- Max Planck Institute for Biology of AgeingCologneGermany
- Department of Chemical Engineering, Texas Tech UniversityLubbockUnited States
| | - Martin Sebastian Denzel
- Max Planck Institute for Biology of AgeingCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of CologneCologneGermany
| | - Marcelo A Mori
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP)CampinasBrazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas (UNICAMP)CampinasBrazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas (UNICAMP)CampinasBrazil
| | - Siva Vanapalli
- Department of Chemical Engineering, Texas Tech UniversityLubbockUnited States
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | | | - Adam Antebi
- Max Planck Institute for Biology of AgeingCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of CologneCologneGermany
| |
Collapse
|
18
|
Brosnan CA, Palmer AJ, Zuryn S. Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading. Nat Commun 2021; 12:2194. [PMID: 33850152 PMCID: PMC8044110 DOI: 10.1038/s41467-021-22503-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/18/2021] [Indexed: 12/13/2022] Open
Abstract
Multicellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.
Collapse
Affiliation(s)
- Christopher A Brosnan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia.
| | - Alexander J Palmer
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
| |
Collapse
|
19
|
Kinser HE, Mosley MC, Plutzer IB, Pincus Z. Global, cell non-autonomous gene regulation drives individual lifespan among isogenic C. elegans. eLife 2021; 10:e65026. [PMID: 33522488 PMCID: PMC7864635 DOI: 10.7554/elife.65026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Across species, lifespan is highly variable among individuals within a population. Even genetically identical Caenorhabditis elegans reared in homogeneous environments are as variable in lifespan as outbred human populations. We hypothesized that persistent inter-individual differences in expression of key regulatory genes drives this lifespan variability. As a test, we examined the relationship between future lifespan and the expression of 22 microRNA promoter::GFP constructs. Surprisingly, expression of nearly half of these reporters, well before death, could effectively predict lifespan. This indicates that prospectively long- vs. short-lived individuals have highly divergent patterns of transgene expression and transcriptional regulation. The gene-regulatory processes reported on by two of the most lifespan-predictive transgenes do not require DAF-16, the FOXO transcription factor that is a principal effector of insulin/insulin-like growth factor (IGF-1) signaling. Last, we demonstrate a hierarchy of redundancy in lifespan-predictive ability among three transgenes expressed in distinct tissues, suggesting that they collectively report on an organism-wide, cell non-autonomous process that acts to set each individual's lifespan.
Collapse
Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. LouisSt. LouisUnited States
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
| | - Matthew C Mosley
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
- Program in Developmental, Regenerative, and Stem Cell Biology, Washington University in St. LouisSt. LouisUnited States
| | - Isaac B Plutzer
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. LouisSt. LouisUnited States
| |
Collapse
|
20
|
Galagali H, Kim JK. The multifaceted roles of microRNAs in differentiation. Curr Opin Cell Biol 2020; 67:118-140. [PMID: 33152557 DOI: 10.1016/j.ceb.2020.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are major drivers of cell fate specification and differentiation. The post-transcriptional regulation of key molecular factors by microRNAs contributes to the progression of embryonic and postembryonic development in several organisms. Following the discovery of lin-4 and let-7 in Caenorhabditis elegans and bantam microRNAs in Drosophila melanogaster, microRNAs have emerged as orchestrators of cellular differentiation and developmental timing. Spatiotemporal control of microRNAs and associated protein machinery can modulate microRNA activity. Additionally, adaptive modulation of microRNA expression and function in response to changing environmental conditions ensures that robust cell fate specification during development is maintained. Herein, we review the role of microRNAs in the regulation of differentiation during development.
Collapse
Affiliation(s)
- Himani Galagali
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| |
Collapse
|
21
|
Dexheimer PJ, Wang J, Cochella L. Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans. Curr Biol 2020; 30:5058-5065.e5. [PMID: 33125867 PMCID: PMC7758728 DOI: 10.1016/j.cub.2020.09.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/25/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are a class of post-transcriptional repressors with diverse roles in animal development and physiology [1]. The Microprocessor complex, composed of Drosha and Pasha/DGCR8, is necessary for the biogenesis of all canonical miRNAs and essential for the early stages of animal embryogenesis [2, 3, 4, 5, 6, 7, 8]. However, the cause for this requirement is largely unknown. Animals often express hundreds of miRNAs, and it remains unclear whether the Microprocessor is required to produce one or few essential miRNAs or many individually non-essential miRNAs. Additionally, both Drosha and Pasha/DGCR8 bind and cleave a variety of non-miRNA substrates [9, 10, 11, 12, 13, 14, 15], and it is unknown whether these activities account for the Microprocessor’s essential requirement. To distinguish between these possibilities, we developed a system in C. elegans to stringently deplete embryos of Microprocessor activity. Using a combination of auxin-inducible degradation (AID) and RNA interference (RNAi), we achieved Drosha and Pasha/DGCR8 depletion starting in the maternal germline, resulting in Microprocessor and miRNA-depleted embryos, which fail to undergo morphogenesis or form organs. Using a Microprocessor-bypass strategy, we show that this early embryonic arrest is rescued by the addition of just two miRNAs, one miR-35 and one miR-51 family member, resulting in morphologically normal larvae. Thus, just two out of ∼150 canonical miRNAs are sufficient for morphogenesis and organogenesis, and the processing of these miRNAs accounts for the essential requirement for Drosha and Pasha/DGCR8 during the early stages of C. elegans embryonic development. Video Abstract
Depletion of Drosha and Pasha results in embryos that fail to undergo morphogenesis The mirtron pathway enables expression of miRNAs in the absence of Drosha and Pasha Two miRNAs are sufficient to rescue embryogenesis in the absence of Drosha and Pasha miR-35 and miR-51 play an unexplored, likely conserved role in animal development
Collapse
Affiliation(s)
- Philipp J Dexheimer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
| |
Collapse
|
22
|
Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
Collapse
Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| |
Collapse
|
23
|
Liang S, Duan J, Hu H, Zhang J, Gao S, Jing H, Li G, Sun Z. Comprehensive Analysis of SiNPs on the Genome-Wide Transcriptional Changes in Caenorhabditis elegans. Int J Nanomedicine 2020; 15:5227-5237. [PMID: 32801688 PMCID: PMC7399461 DOI: 10.2147/ijn.s251269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022] Open
Abstract
Background Large-scale production and application of amorphous silica nanoparticles (SiNPs) have enhanced the risk of human exposure to SiNPs. However, the toxic effects and the underlying biological mechanisms of SiNPs on Caenorhabditis elegans remain largely unclear. Purpose This study was to investigate the genome-wide transcriptional alteration of SiNPs on C. elegans. Methods and Results In this study, a total number of 3105 differentially expressed genes were identified in C. elegans. Among them, 1398 genes were significantly upregulated and 1707 genes were notably downregulated in C. elegans. Gene ontology analysis revealed that the significant change of gene functional categories triggered by SiNPs was focused on locomotion, determination of adult lifespan, reproduction, body morphogenesis, multicellular organism development, endoplasmic reticulum unfolded protein response, oocyte development, and nematode larval development. Meanwhile, we explored the regulated effects between microRNA and genes or signaling pathways. Pathway enrichment analysis and miRNA-gene-pathway-network displayed that 23 differential expression microRNA including cel-miR-85-3p, cel-miR-793, cel-miR-241-5p, and cel-miR-5549-5p could regulate the longevity-related pathways and inflammation signaling pathways, etc. Additionally, our data confirmed that SiNPs could disrupt the locomotion behavior and reduce the longevity by activating ins-7, daf-16, ftt-2, fat-5, and rho-1 genes in C. elegans. Conclusion Our study showed that SiNPs induced the change of the whole transcriptome in C. elegans, and triggered negative effects on longevity, development, reproduction, and body morphogenesis. These data provide abundant clues to understand the molecular mechanisms of SiNPs in C. elegans.
Collapse
Affiliation(s)
- Shuang Liang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China
| | - Hejing Hu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China
| | - Jingyi Zhang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China
| | - Shan Gao
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control/Beijing Center of Preventive Medicine Research, Beijing 100013, People's Republic of China
| | - Haiming Jing
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control/Beijing Center of Preventive Medicine Research, Beijing 100013, People's Republic of China
| | - Guojun Li
- Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control/Beijing Center of Preventive Medicine Research, Beijing 100013, People's Republic of China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, People's Republic of China
| |
Collapse
|
24
|
Yin J, Qian Z, Chen Y, Li Y, Zhou X. MicroRNA regulatory networks in the pathogenesis of sarcopenia. J Cell Mol Med 2020; 24:4900-4912. [PMID: 32281300 PMCID: PMC7205827 DOI: 10.1111/jcmm.15197] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/25/2020] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Sarcopenia is an age‐related disease characterized by disturbed homeostasis of skeletal muscle, leading to a decline in muscle mass and function. Loss of muscle mass and strength leads to falls and fracture, and is often accompanied by other geriatric diseases, including osteoporosis, frailty and cachexia, resulting in a general decrease in quality of life and an increase in mortality. Although the underlying mechanisms of sarcopenia are still not completely understood, there has been a marked improvement in the understanding of the pathophysiological changes leading to sarcopenia in recent years. The role of microRNAs (miRNAs), especially, has been clearer in skeletal muscle development and homeostasis. miRNAs form part of a gene regulatory network and have numerous activities in many biological processes. Intervention based on miRNAs may develop into an innovative treatment strategy to conquer sarcopenia. This review is divided into three sections: firstly, the latest understanding of the pathogenesis of sarcopenia is summarized; secondly, increasing evidence for the involvement of miRNAs in the regulation of muscle quantity or quality and muscle homeostasis is highlighted; and thirdly, the possibilities and limitations of miRNAs as a treatment for sarcopenia are explored.
Collapse
Affiliation(s)
- Jiayu Yin
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhiyuan Qian
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuqi Chen
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Li
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
25
|
Nehammer C, Ejlerskov P, Gopal S, Handley A, Ng L, Moreira P, Lee H, Issazadeh-Navikas S, Rubinsztein DC, Pocock R. Interferon-β-induced miR-1 alleviates toxic protein accumulation by controlling autophagy. eLife 2019; 8:49930. [PMID: 31799933 PMCID: PMC6914338 DOI: 10.7554/elife.49930] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
Appropriate regulation of autophagy is crucial for clearing toxic proteins from cells. Defective autophagy results in accumulation of toxic protein aggregates that detrimentally affect cellular function and organismal survival. Here, we report that the microRNA miR-1 regulates the autophagy pathway through conserved targeting of the orthologous Tre-2/Bub2/CDC16 (TBC) Rab GTPase-activating proteins TBC-7 and TBC1D15 in Caenorhabditis elegans and mammalian cells, respectively. Loss of miR-1 causes TBC-7/TBC1D15 overexpression, leading to a block on autophagy. Further, we found that the cytokine interferon-β (IFN-β) can induce miR-1 expression in mammalian cells, reducing TBC1D15 levels, and safeguarding against proteotoxic challenges. Therefore, this work provides a potential therapeutic strategy for protein aggregation disorders.
Collapse
Affiliation(s)
- Camilla Nehammer
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Ejlerskov
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Ava Handley
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Leelee Ng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Pedro Moreira
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Huikyong Lee
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Shohreh Issazadeh-Navikas
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David C Rubinsztein
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom.,UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
26
|
Liu H, Nichols RL, Qiu L, Sun R, Zhang B, Pan X. Small RNA Sequencing Reveals Regulatory Roles of MicroRNAs in the Development of Meloidogyne incognita. Int J Mol Sci 2019; 20:ijms20215466. [PMID: 31684025 PMCID: PMC6862286 DOI: 10.3390/ijms20215466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/27/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are an extensive class of small regulatory RNAs. Knowing the specific expression and functions of miRNAs during root-knot nematode (RKN) (Meloidogyne incognita) development could provide fundamental information about RKN development as well as a means to design new strategies to control RKN infection, a major problem of many important crops. Employing high throughput deep sequencing, we identified a total of 45 conserved and novel miRNAs from two developmental stages of RKN, eggs and J2 juveniles, during their infection of cotton (Gossypium hirsutum L.). Twenty-one of the miRNAs were differentially expressed between the two stages. Compared with their expression in eggs, two miRNAs were upregulated (miR252 and miRN19), whereas 19 miRNAs were downregulated in J2 juveniles. Nine miRNAs were expressed at high levels, with >1000 reads per mapped million (RPM) sequenced reads in both eggs and J2 juveniles (miR1, miR124, miR2-3p, miR252, miR279, miR57-5p, miR7904, miR87, and miR92). Three miRNAs were only expressed in eggs (miR4738, miRN3, and miRN5). These differentially expressed miRNAs may control RKN development by regulating specific protein-coding genes in pathways associated with RKN growth and development.
Collapse
Affiliation(s)
- Huawei Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | | | - Li Qiu
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
| | - Runrun Sun
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
- Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| |
Collapse
|
27
|
Eivani M, Alijanpour S, Arefian E, Rezayof A. Corticolimbic analysis of microRNAs and protein expressions in scopolamine-induced memory loss under stress. Neurobiol Learn Mem 2019; 164:107065. [PMID: 31400468 DOI: 10.1016/j.nlm.2019.107065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/18/2019] [Accepted: 08/06/2019] [Indexed: 11/19/2022]
Abstract
The aim of the present study was to assess thealterations of corticolimbic microRNAs and protein expressions in the effect of scopolamine with or without stress on passive-avoidance memory in male Wistar rats. The expressions of miR-1, miR-10 and miR-26 and also the levels of p-CREB, CREB, C-FOS and BDNF in the prefrontal cortex (PFC), the hippocampus and the amygdala were evaluated using RT-qPCR and Western blotting techniques. The data showed that the administration of a muscarinic receptor antagonist, scopolamine or the exposure to 30 min stress significantly induced memory loss. Interestingly, the injection of an ineffective dose of scopolamine (0.5 mg/kg) alongside with exposure to an ineffective time of stress (10 min) impaired memory formation, suggesting a potentiative effect of stress on scopolamine response. Our results showed that memory formation was associated with the down-regulated expression of miR-1, miR-10 and miR-26 in the PFC and the hippocampus, but not the amygdala. The relative expression increase of miR-1 and miR-10 in the PFC and the hippocampus was shown in memory loss induced by scopolamine administration or 30-min stress. The PFC level of miR-10 and also hippocampal level of miR-1 and miR-10 were significantly up-regulated, while amygdala miR-1 and miR-26 were down-regulated in scopolamine-induced memory loss under stress. Memory formation increased BDNF, C-FOS and p-CREB/CREB in the PFC, the hippocampus and the amygdala. In contrast, the PFC, hippocampal and amygdala protein expressions were significantly decreased in memory loss induced by scopolamine administration (2 mg/kg), stress exposure (for 30 min) or scopolamine (0.5 mg/kg) plus stress (10 min). One of the most significant findings to emerge from this study is that the stress exposure potentiated the amnesic effect of scopolamine may via affecting the expressions of miRs and proteins in the PFC, the hippocampus and the amygdala. It is possible to hypothesis that corticolimbic signaling pathways play a critical role in relationship between stress and Alzheimer's disease.
Collapse
Affiliation(s)
- Mehdi Eivani
- Neuroscience Lab, Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Sakineh Alijanpour
- Department of Biology, Faculty of Science, Gonbad Kavous University, Gonbad Kavous, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ameneh Rezayof
- Neuroscience Lab, Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| |
Collapse
|
28
|
Nawaz M, Malik MI, Hameed M, Zhou J. Research progress on the composition and function of parasite-derived exosomes. Acta Trop 2019; 196:30-36. [PMID: 31071298 DOI: 10.1016/j.actatropica.2019.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/04/2019] [Indexed: 12/20/2022]
Abstract
Parasites use excretory-secretory pathways to communicate with the host. Characterization of exosomes within the excretory-secretory products reveal by which parasites manipulate their hosts. Parasite derived exosomes provide a mechanistic framework for protein and miRNAs transfer. Transcriptomics and proteomics of parasite exosomes identified a large number of miRNAs and proteins being utilized by parasites in their survival, reproduction and development. Characterization of proteins and miRNAs in parasite secreted exosomes provide important information on host-parasite communication and forms the basis for future studies. In this review, we summarize recent advances in isolation and molecular characterization (protein and miRNAs) of parasite derived exosomes.
Collapse
Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Muhammad Irfan Malik
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Muddassar Hameed
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| |
Collapse
|
29
|
mir-234 controls neuropeptide release at the Caenorhabditis elegans neuromuscular junction. Mol Cell Neurosci 2019; 98:70-81. [PMID: 31200102 DOI: 10.1016/j.mcn.2019.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/16/2023] Open
Abstract
miR-137 is a highly conserved microRNA (miRNA) that is associated with the control of brain function and the etiology of psychiatric disorders including schizophrenia and bipolar disorder. The Caenorhabditis elegans genome encodes a single miR-137 ortholog called mir-234, the function of which is unknown. Here we show that mir-234 is expressed in a subset of sensory, motor and interneurons in C. elegans. Using a mir-234 deletion strain, we systematically examined the development and function of these neurons in addition to global C. elegans behaviors. We were however unable to detect phenotypes associated with loss of mir-234, possibly due to genetic redundancy. To circumvent this issue, we overexpressed mir-234 in mir-234-expressing neurons to uncover possible phenotypes. We found that mir-234-overexpression endows resistance to the acetylcholinesterase inhibitor aldicarb, suggesting modification of neuromuscular junction (NMJ) function. Further analysis revealed that mir-234 controls neuropeptide levels, therefore positing a cause of NMJ dysfunction. Together, our data suggest that mir-234 functions to control the expression of target genes that are important for neuropeptide maturation and/or transport in C. elegans. SIGNIFICANCE STATEMENT: The miR-137 family of miRNAs is linked to the control of brain function in humans. Defective regulation of miR-137 is associated with psychiatric disorders that include schizophrenia and bipolar disorder. Previous studies have revealed that miR-137 is required for the development of dendrites and for controlling the release of fast-acting neurotransmitters. Here, we analyzed the function a miR-137 family member (called mir-234) in the nematode animal model using anatomical, behavioral, electrophysiological and neuropeptide analysis. We reveal for the first time that mir-234/miR-137 is required for the release of slow-acting neuropeptides, which may also be of relevance for controlling human brain function.
Collapse
|
30
|
Tao C, Sun H, Sang W, Li S. miRNA-99a inhibits cell invasion and migration in liver cancer by directly targeting HOXA1. Oncol Lett 2019; 17:5108-5114. [PMID: 31186723 PMCID: PMC6507307 DOI: 10.3892/ol.2019.10199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/14/2019] [Indexed: 12/18/2022] Open
Abstract
Liver cancer is a malignant tumor that threatens human health worldwide. It has poor prognosis rates and ineffective therapeutic options. Recently, various miRNAs have been proven to exert promoting or inhibiting functions in different malignancies. However, the definitive mechanisms of miR-99a in liver cancer remain unclear. In the current study, we explored the relationships between the expression of miR-99a and HOXA1 in liver cancer tissues and cells to explore their combined effects on the occurrence and metastasis of liver cancer. The expression of miR-99a and HOXA1 in liver cancer tissue samples and cells was measured by RT-qPCR. Following transfection, transwell assays were conducted to assess the invasion and migration capacities of liver cancer cells. Subsequently, western blots and luciferase reporter assays were performed in liver cancer cells to identify the target of miR-99a. The data indicated that miRNA-99a expression was significantly reduced in both liver cancer tissue samples and cells compared with normal tissues and normal liver cells respectively. By contrast, the HOXA1 expression levels in liver cancer tissues and cells were significantly increased in contrast to the control group. The findings also revealed that the miR-99a expression was negatively correlated with HOXA1 expression in liver cancer tissue samples and miR-99a could suppress cell invasion and migration by targeting HOXA1 in liver cancer.
Collapse
Affiliation(s)
- Changming Tao
- Department of Hepatology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Huiling Sun
- Department of Gastroenterology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Weiwei Sang
- Department of Gastroenterology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Shanshan Li
- Department of Gastroenterology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| |
Collapse
|
31
|
Furtado LFV, de Aguiar PHN, Zuccherato LW, Teixeira TTG, Alves WP, da Silva VJ, Gasser RB, Rabelo ÉML. Albendazole resistance induced in Ancylostoma ceylanicum is not due to single-nucleotide polymorphisms (SNPs) at codons 167, 198, or 200 of the beta-tubulin gene, indicating another resistance mechanism. Parasitol Res 2019; 118:837-849. [PMID: 30697644 DOI: 10.1007/s00436-019-06218-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 01/17/2019] [Indexed: 12/12/2022]
Abstract
Mass drug administration has been implicated as the major cause of drug resistance in nematodes of ruminants. Single-nucleotide polymorphisms (SNPs) at codons 167, 198, and 200 of the beta-tubulin isotype 1 gene are associated with albendazole resistance mechanisms. Although drug resistance is suspected to occur in nematodes of the same order, at present, there is no evidence of a strong correlation between these canonical SNPs and albendazole resistance in hookworms. In the absence of a hookworm strain that is naturally resistant to albendazole, we produced an albendazole-resistant Ancylostoma ceylanicum strain by selective drug pressure. Restriction fragment length polymorphism-PCR (RFLP-PCR) was employed to identify the presence of SNPs previously associated with drug resistance in other nematodes. However, none of the benzimidazole resistance-associated SNPs known in other nematodes were found. A beta-tubulin isotype 1 gene mini-cDNA library was constructed to obtain the complete cDNA gene sequence for the analysis of the entire gene to identify distinct SNPs associated with resistance. Some SNPs were found, but the resulting sequences were not reproducibly detected among the different clones, preventing their association with the resistance mechanism. The parasitological and hematological parameters of the albendazole-resistant strain were characterized and compared to those of the sensitive strain. Although the albendazole-resistant strain was less adapted to its host, with fewer worms recovered, all other parameters analyzed were similar between both strains. The results of the present study indicate that the mechanism of albendazole resistance of the resistant strain described herein must differ from those that have previously been characterized. Thus, new mechanistic studies are needed in the future.
Collapse
Affiliation(s)
- Luis Fernando Viana Furtado
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro Henrique Nascimento de Aguiar
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Luciana Werneck Zuccherato
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Tatiana Guimarães Teixeira
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - William Pereira Alves
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Vivian Jordania da Silva
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Élida Mara Leite Rabelo
- Departamento de Parasitologia, L4 237, Laboratório de Parasitologia Molecular, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Avenida Presidente Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
| |
Collapse
|
32
|
Weigelt CM, Hahn O, Arlt K, Gruhn M, Jahn AJ, Eßer J, Werner JA, Klein C, Büschges A, Grönke S, Partridge L. Loss of miR-210 leads to progressive retinal degeneration in Drosophila melanogaster. Life Sci Alliance 2019; 2:2/1/e201800149. [PMID: 30670478 PMCID: PMC6343102 DOI: 10.26508/lsa.201800149] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 12/22/2022] Open
Abstract
Depletion of miRNA-210 disrupts photoreceptor integrity and visual function in Drosophila melanogaster. miRNAs are small, non-coding RNAs that regulate gene expression post-transcriptionally. We used small RNA sequencing to identify tissue-specific miRNAs in the adult brain, thorax, gut, and fat body of Drosophila melanogaster. One of the most brain-specific miRNAs that we identified was miR-210, an evolutionarily highly conserved miRNA implicated in the regulation of hypoxia in mammals. In Drosophila, we show that miR-210 is specifically expressed in sensory organs, including photoreceptors. miR-210 knockout mutants are not sensitive toward hypoxia but show progressive degradation of photoreceptor cells, accompanied by decreased photoreceptor potential, demonstrating an important function of miR-210 in photoreceptor maintenance and survival.
Collapse
Affiliation(s)
| | - Oliver Hahn
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Katharina Arlt
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Matthias Gruhn
- Department for Animal Physiology, Biocenter Cologne, Institute of Zoology, Cologne, Germany
| | - Annika J Jahn
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Jacqueline Eßer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Corinna Klein
- Cluster of Excellence-Cellular Stress Responses in Aging-Associated Diseases Research Centre, University of Cologne, Cologne, Germany
| | - Ansgar Büschges
- Department for Animal Physiology, Biocenter Cologne, Institute of Zoology, Cologne, Germany
| | | | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany .,Institute of Healthy Ageing, Genetics, Evolution and Environment, University College London, London, UK
| |
Collapse
|
33
|
Liu YP, Xu P, Guo CX, Luo ZR, Zhu J, Mou FF, Cai H, Wang C, Ye XC, Shao SJ, Guo HD. miR-1b overexpression suppressed proliferation and migration of RSC96 and increased cell apoptosis. Neurosci Lett 2018; 687:137-145. [PMID: 30261232 DOI: 10.1016/j.neulet.2018.09.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 08/31/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
Abstract
Peripheral nerve injury (PNI) is a global problem that leads to severe disability and high healthcare expenditure. Accumulating evidence suggested that the phenotypes of Schwann cells (SCs) could be regulated by microRNAs (miRNAs) and expressions of various miRNAs are altered after PNI. In this study, the expression of miR-1b in the injured nerve and hypoxia-treated SCs was detected through qRT-PCR. The target genes of miR-1b were predicted by bioinformatics prediction and dual-luciferase reporter assay and verified through qRT-PCR and western blot. The effects of miR-1b and its specific target gene on the proliferation, migration and apoptosis of SCs were determined and the regulation of miR-1b on peripheral nerve regeneration after PNI was further investigated in vivo. We found that miR-1b was obviously downregulated in the injured nerve in a rat sciatic nerve transection model and directly targeted N-myc downstream-regulated gene 3 (NDRG3) by binding to its 3'-UTR and caused both mRNA degradation and translation suppression of NDRG3. Overexpression of miR-1b or knockdown of NDRG3 decreased the proliferation and migration as well as increased the apoptosis of SCs. NDRG3 reversed the effects of miR-1b overexpression on proliferation/migration/apoptosis of RSC96. In addition, injection of miR-1b antagomir promoted the expression of NDRG3 in the injured nerve following sciatic nerve injury. Compared to the model group, the rats treated with miR-1b agomir had lower functional recovery rate, and downregulation of miR-1b through injection of specific antagomir improved the functional recovery rate according to the results of sciatic functional index and nerve conduction velocity. Overall, our results will contribute to the development of novel targets for promoting nerve regeneration after PNI.
Collapse
Affiliation(s)
- Yu-Pu Liu
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Peng Xu
- Affiliated Hospital of JiNing Medical College, Jining, Shandong, 272000, China
| | - Chun-Xia Guo
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhi-Rong Luo
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jing Zhu
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Fang-Fang Mou
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hao Cai
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chang Wang
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiao-Chun Ye
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shui-Jin Shao
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Hai-Dong Guo
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| |
Collapse
|
34
|
Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
Collapse
|
35
|
The Claudin-like Protein HPO-30 Is Required to Maintain LAChRs at the C. elegans Neuromuscular Junction. J Neurosci 2018; 38:7072-7087. [PMID: 29950505 PMCID: PMC6083452 DOI: 10.1523/jneurosci.3487-17.2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 06/07/2018] [Accepted: 06/07/2018] [Indexed: 12/22/2022] Open
Abstract
Communications across chemical synapses are primarily mediated by neurotransmitters and their postsynaptic receptors. There are diverse molecular systems to localize and regulate the receptors at the synapse. Here, we identify HPO-30, a member of the claudin superfamily of membrane proteins, as a positive regulator for synaptic localization of levamisole-dependent AChRs (LAChRs) at the Caenorhabditis elegans neuromuscular junction (NMJ). The HPO-30 protein localizes at the NMJ and shows genetic and physical association with the LAChR subunits LEV-8, UNC-29, and UNC-38. Using genetic and electrophysiological assays in the hermaphrodite C. elegans, we demonstrate that HPO-30 functions through Neuroligin at the NMJ to maintain postsynaptic LAChR levels at the synapse. Together, this work suggests a novel function for a tight junction protein in maintaining normal receptor levels at the NMJ. SIGNIFICANCE STATEMENT Claudins are a large superfamily of membrane proteins. Their role in maintaining the functional integrity of tight junctions has been widely explored. Our experiments suggest a critical role for the claudin-like protein, HPO-30, in maintaining synaptic levamisole-dependent AChR (LAChR) levels. LAChRs contribute to <20% of the acetylcholine-mediated conductance in adult Caenorhabditis elegans; however, they play a significant functional role in worm locomotion. This study provides a new perspective in the study of LAChR physiology.
Collapse
|
36
|
Rauthan M, Gong J, Liu J, Li Z, Wescott SA, Liu J, Xu XZS. MicroRNA Regulation of nAChR Expression and Nicotine-Dependent Behavior in C. elegans. Cell Rep 2018; 21:1434-1441. [PMID: 29117550 DOI: 10.1016/j.celrep.2017.10.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 05/14/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022] Open
Abstract
Chronic exposure to nicotine upregulates nicotinic acetylcholine receptors (nAChRs), and such upregulation is critical for the development of nicotine dependence in humans and animal models. However, how nicotine upregulates nAChRs is not well understood. Here, we identify a key role for microRNA in regulating nicotine-dependent behavior by modulating nAChR expression in C. elegans. We show that the nAChR gene acr-19 and alg-1, a key Argonaute-family member in the microRNA machinery, are specifically required for nicotine withdrawal response following chronic nicotine treatment. Chronic exposure to nicotine downregulates alg-1, leading to upregulation of acr-19. This effect is mediated by the microRNA miR-238 that recognizes the 3' UTR of acr-19 transcript. Our results unveil a previously unrecognized role for microRNA in nicotine signaling, providing insights into how chronic nicotine administration leads to upregulation of nAChR and ultimately nicotine dependence.
Collapse
Affiliation(s)
- Manish Rauthan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianke Gong
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jinzhi Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhaoyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seth A Wescott
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianfeng Liu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - X Z Shawn Xu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
37
|
Lin CY, He JY, Zeng CW, Loo MR, Chang WY, Zhang PH, Tsai HJ. microRNA-206 modulates an Rtn4a/Cxcr4a/Thbs3a axis in newly forming somites to maintain and stabilize the somite boundary formation of zebrafish embryos. Open Biol 2018; 7:rsob.170009. [PMID: 28701377 PMCID: PMC5541343 DOI: 10.1098/rsob.170009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022] Open
Abstract
Although microRNA-206 (miR-206) is known to regulate proliferation and differentiation of muscle fibroblasts, the role of miR-206 in early-stage somite development is still unknown. During somitogenesis of zebrafish embryos, reticulon4a (rtn4a) is specifically repressed by miR-206. The somite boundary was defective, and actin filaments were crossing over the boundary in either miR-206-knockdown or rtn4a-overexpressed embryos. In these treated embryos, C-X-C motif chemokine receptor 4a (cxcr4a) was reduced, while thrombospondin 3a (thbs3a) was increased. The defective boundary was phenocopied in either cxcr4a-knockdown or thbs3a-overexpressed embryos. Repression of thbs3a expression by cxcr4a reduced the occurrence of the boundary defect. We demonstrated that cxcr4a is an upstream regulator of thbs3a and that defective boundary cells could not process epithelialization in the absence of intracellular accumulation of the phosphorylated focal adhesion kinase (p-FAK) in boundary cells. Therefore, in the newly forming somites, miR-206-mediated downregulation of rtn4a increases cxcr4a. This activity largely decreases thbs3a expression in the epithelial cells of the somite boundary, which causes epithelialization of boundary cells through mesenchymal-epithelial transition (MET) and eventually leads to somite boundary formation. Collectively, we suggest that miR-206 mediates a novel pathway, the Rtn4a/Cxcr4a/Thbs3a axis, that allows boundary cells to undergo MET and form somite boundaries in the newly forming somites of zebrafish embryos.
Collapse
Affiliation(s)
- Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
| | - Jun-Yu He
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Chih-Wei Zeng
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Moo-Rumg Loo
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Wen-Yen Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, Republic of China
| | - Po-Hsiang Zhang
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, No. 46, Section 3 Zhongzhen Road, Sanzhi Dist., New Taipei City 252, Taiwan, Republic of China
| |
Collapse
|
38
|
Zhang S, Fan Z, Qiao P, Zhao Y, Wang Y, Jiang D, Wang X, Zhu X, Zhang Y, Huang B, Lu J, Li X. miR-51 regulates GABAergic synapses by targeting Rab GEF GLO-4 and lysosomal trafficking-related GLO/AP-3 pathway in Caenorhabditis elegans. Dev Biol 2018; 436:66-74. [DOI: 10.1016/j.ydbio.2018.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/30/2018] [Accepted: 02/17/2018] [Indexed: 01/22/2023]
|
39
|
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L. Cell-type specific sequencing of microRNAs from complex animal tissues. Nat Methods 2018; 15:283-289. [PMID: 29481550 PMCID: PMC5886366 DOI: 10.1038/nmeth.4610] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals. The method combines cell-type-specific 3'-terminal 2'-O-methylation of animal miRNAs by a genetically encoded, plant-specific methyltransferase (HEN1), with chemoselective small-RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of specific cells within Caenorhabditis elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes current challenges in cell-type-specific small-RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.
Collapse
Affiliation(s)
- Chiara Alberti
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | | | - Ivica Sowemimo
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Thomas R Burkard
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Katharina Mahofsky
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| |
Collapse
|
40
|
|
41
|
Wang BG, Li JS, Liu YF, Xu Q. MicroRNA-200b suppresses the invasion and migration of hepatocellular carcinoma by downregulating RhoA and circRNA_000839. Tumour Biol 2017; 39:1010428317719577. [PMID: 28695771 DOI: 10.1177/1010428317719577] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs could mediate the targeted coding gene and the targeted non-coding RNA to form endogenous competition, which have an important regulatory role in tumorigenesis of many types of cancer, including hepatocellular carcinoma. The goal of this study was to characterize the role of miR-200b in the pathogenesis of hepatocellular carcinoma. We identified miR-200b that was predicted to regulate RhoA and circ_000839. Our data establish that miR-200b is expressed at a relatively low level in hepatocellular carcinoma ( p < 0.001). RhoA and circ_000839 are expressed at a relatively high level in hepatocellular carcinoma ( p < 0.001, respectively). Our mechanistic data indicate that RhoA is a direct target of miR-200b ( p < 0.001), binding of which affects the expression of invasion and migration in hepatocellular carcinoma cell lines ( p < 0.05). And correlation analysis showed that miR-200b was inversely correlated with RhoA and circ_000839 ( p = 0.012, p = 0.002, respectively), while RhoA was positively correlated with circ_000839 ( p < 0.001). Taken together, our data suggest that miR-200b could mediate RhoA gene and circ_000839 to form endogenous competition. And this is a direction for the association study of miR-200b and RhoA in the future.
Collapse
Affiliation(s)
- Ben-Gang Wang
- 1 Hepatobiliary Surgery Department of General Surgery Institute, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jun-Shuai Li
- 1 Hepatobiliary Surgery Department of General Surgery Institute, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yong-Feng Liu
- 1 Hepatobiliary Surgery Department of General Surgery Institute, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qian Xu
- 2 Tumor Etiology and Screening Department of General Surgery Institute, The First Affiliated Hospital of China Medical University, Shenyang, China
| |
Collapse
|
42
|
Dynamic Partitioning of Synaptic Vesicle Pools by the SNARE-Binding Protein Tomosyn. J Neurosci 2017; 36:11208-11222. [PMID: 27807164 DOI: 10.1523/jneurosci.1297-16.2016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022] Open
Abstract
Neural networks engaged in high-frequency activity rely on sustained synaptic vesicle recycling and coordinated recruitment from functionally distinct synaptic vesicle (SV) pools. However, the molecular pathways matching neural activity to SV dynamics and release requirements remain unclear. Here we identify unique roles of SNARE-binding Tomosyn1 (Tomo1) proteins as activity-dependent substrates that regulate dynamics of SV pool partitioning at rat hippocampal synapses. Our analysis is based on monitoring changes in distinct functionally defined SV pools via V-Glut1-pHluorin fluorescence in cultured hippocampal neurons in response to alterations in presynaptic protein expression. Specifically, we find knockdown of Tomo1 facilitates release efficacy from the Readily Releasable Pool (RRP), and regulates SV distribution to the Total Recycling Pool (TRP), which is matched by a decrease in the SV Resting Pool. Notably, these effects were reversed by Tomo1 rescue and overexpression. Further, we identify that these actions of Tomo1 are regulated via activity-dependent phosphorylation by cyclin-dependent kinase 5 (Cdk5). Assessment of molecular interactions that may contribute to these actions identified Tomo1 interaction with the GTP-bound state of Rab3A, an SV GTPase involved in SV targeting and presynaptic membrane tethering. In addition, Tomo1 via Rab3A-GTP was also observed to interact with Synapsin 1a/b cytoskeletal interacting proteins. Finally, our data indicate that Tomo1 regulation of SV pool sizes serves to adapt presynaptic neurotransmitter release to chronic silencing of network activity. Overall, the results establish Tomo1 proteins as central mediators in neural activity-dependent changes in SV distribution among SV pools. SIGNIFICANCE STATEMENT Although information transfer at central synapses via sustained high-frequency neural activity requires coordinated synaptic vesicle (SV) recycling, the mechanism(s) by which synapses sense and dynamically modify SV pools to match network demands remains poorly defined. To advance understanding, we quantified SV pool sizes and their sensitivity to neural activity while altering Tomo1 expression, a putative regulator of the presynaptic Readily Releasable Pool. Remarkably, we find Tomo1 actions to extend beyond the Readily Releasable Pool to mediate the Total Recycling Pool and SV Resting Pool distribution, and this action is sensitive to neural activity through Cdk5 phosphorylation of Tomo1. Moreover, Tomo1 appears to exert these actions through interaction with Rab3A-GTP and synapsin proteins. Together, our results argue that Tomo1 is a central mediator of SV availability for neurotransmission.
Collapse
|
43
|
Tong XJ, López-Soto EJ, Li L, Liu H, Nedelcu D, Lipscombe D, Hu Z, Kaplan JM. Retrograde Synaptic Inhibition Is Mediated by α-Neurexin Binding to the α2δ Subunits of N-Type Calcium Channels. Neuron 2017; 95:326-340.e5. [PMID: 28669545 DOI: 10.1016/j.neuron.2017.06.018] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/20/2017] [Accepted: 06/08/2017] [Indexed: 12/31/2022]
Abstract
The synaptic adhesion molecules Neurexin and Neuroligin alter the development and function of synapses and are linked to autism in humans. In C. elegans, post-synaptic Neurexin (NRX-1) and pre-synaptic Neuroligin (NLG-1) mediate a retrograde synaptic signal that inhibits acetylcholine (ACh) release at neuromuscular junctions. Here, we show that the retrograde signal decreases ACh release by inhibiting the function of pre-synaptic UNC-2/CaV2 calcium channels. Post-synaptic NRX-1 binds to an auxiliary subunit of pre-synaptic UNC-2/CaV2 channels (UNC-36/α2δ), decreasing UNC-36 abundance at pre-synaptic elements. Retrograde inhibition is mediated by a soluble form of NRX-1's ectodomain, which is released from the post-synaptic membrane by the SUP-17/ADAM10 protease. Mammalian Neurexin-1α binds α2δ-3 and decreases CaV2.2 current in transfected cells, whereas Neurexin-1α has no effect on CaV2.2 reconstituted with α2δ-1 and α2δ-2. Collectively, these results suggest that α-Neurexin binding to α2δ is a conserved mechanism for regulating synaptic transmission.
Collapse
Affiliation(s)
- Xia-Jing Tong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Eduardo Javier López-Soto
- Department of Neuroscience and Brown Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Lei Li
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Haowen Liu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Nedelcu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Diane Lipscombe
- Department of Neuroscience and Brown Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Zhitao Hu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
44
|
Cecchetelli AD, Cram EJ. Regulating distal tip cell migration in space and time. Mech Dev 2017; 148:11-17. [PMID: 28442366 DOI: 10.1016/j.mod.2017.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/26/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022]
Abstract
Gonad morphogenesis in the nematode C. elegans is guided by two leader cells, the distal tip cells (DTC). The DTCs migrate along a stereotyped path, executing two 90° turns before stopping at the midpoint of the animal. This migratory path determines the double-U shape of the adult gonad, therefore, the path taken by the DTCs can be inferred from the final shape of the organ. In this review, we focus on the mechanism by which the DTC executes the first 90° turn from the ventral to dorsal side of the animal, and how it finds its correct stopping place at the midpoint of the animal. We discuss the role of heterochronic genes in coordinating DTC migration with larval development, the role of feedback loops and miRNA regulation in phenotypic robustness, and the role of RNA binding proteins in the cessation of DTC migration.
Collapse
Affiliation(s)
- Alyssa D Cecchetelli
- Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Hall, Boston, MA 02115, United States
| | - Erin J Cram
- Department of Biology, Northeastern University, 360 Huntington Avenue, 134 Mugar Hall, Boston, MA 02115, United States.
| |
Collapse
|
45
|
Simchovitz A, Heneka MT, Soreq H. Personalized genetics of the cholinergic blockade of neuroinflammation. J Neurochem 2017; 142 Suppl 2:178-187. [PMID: 28326544 PMCID: PMC5600134 DOI: 10.1111/jnc.13928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/27/2016] [Accepted: 12/05/2016] [Indexed: 01/09/2023]
Abstract
Acetylcholine signaling is essential for cognitive functioning and blocks inflammation. To maintain homeostasis, cholinergic signaling is subjected to multi‐leveled and bidirectional regulation by both proteins and non‐coding microRNAs (‘CholinomiRs’). CholinomiRs coordinate the cognitive and inflammatory aspects of cholinergic signaling by targeting major cholinergic transcripts including the acetylcholine hydrolyzing enzyme acetylcholinesterase (AChE). Notably, AChE inhibitors are the only currently approved line of treatment for Alzheimer's disease patients. Since cholinergic signaling blocks neuroinflammation which is inherent to Alzheimer's disease, genomic changes modifying AChE's properties and its susceptibility to inhibitors and/or to CholinomiRs regulation may affect the levels and properties of inflammasome components such as NLRP3. This calls for genomic‐based medicine approaches based on genotyping of both coding and non‐coding single nucleotide polymorphisms (SNPs) in the genes involved in cholinergic signaling. An example is a SNP in a recognition element for the primate‐specific microRNA‐608 within the 3′ untranslated region of the AChE transcript. Carriers of the minor allele of that SNP present massively elevated brain AChE levels, increased trait anxiety and inflammation, accompanied by perturbed CholinomiR‐608 regulatory networks and elevated prefrontal activity under exposure to stressful insults. Several additional SNPs in the AChE and other cholinergic genes await further studies, and might likewise involve different CholinomiRs and pathways including those modulating the initiation and progression of neurodegenerative diseases. CholinomiRs regulation of the cholinergic system thus merits in‐depth interrogation and is likely to lead to personalized medicine approaches for achieving better homeostasis in health and disease. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. ![]()
Collapse
Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | | | - Hermona Soreq
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| |
Collapse
|
46
|
Andachi Y, Kohara Y. A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2016; 22:1099-1106. [PMID: 27154969 PMCID: PMC4911917 DOI: 10.1261/rna.054239.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
Whole-mount in situ hybridization (WISH) is an outstanding method to decipher the spatiotemporal expression patterns of microRNAs (miRNAs) and provides important clues for elucidating their functions. The first WISH method for miRNA detection was developed in zebrafish. Although this method was quickly adapted for other vertebrates and fruit flies, WISH analysis has not been successfully used to detect miRNAs in Caenorhabditis elegans Here, we show a novel WISH method for miRNA detection in C. elegans Using this method, mir-1 miRNA was detected in the body-wall muscle where the expression and roles of mir-1 miRNA have been previously elucidated. Application of the method to let-7 family miRNAs, let-7, mir-48, mir-84, and mir-241, revealed their distinct but partially overlapping expression patterns, indicating that miRNAs sharing a short common sequence were distinguishably detected. In pash-1 mutants that were depleted of mature miRNAs, signals of mir-48 miRNA were greatly reduced, suggesting that mature miRNAs were detected by the method. These results demonstrate the validity of WISH to detect mature miRNAs in C. elegans.
Collapse
Affiliation(s)
- Yoshiki Andachi
- Genetic Strains Research Center, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima 411-8540, Japan
| | - Yuji Kohara
- Genetic Strains Research Center, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima 411-8540, Japan
| |
Collapse
|
47
|
Neumann E, Brandenburger T, Santana-Varela S, Deenen R, Köhrer K, Bauer I, Hermanns H, Wood JN, Zhao J, Werdehausen R. MicroRNA-1-associated effects of neuron-specific brain-derived neurotrophic factor gene deletion in dorsal root ganglia. Mol Cell Neurosci 2016; 75:36-43. [PMID: 27346077 DOI: 10.1016/j.mcn.2016.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 06/08/2016] [Accepted: 06/20/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) regulate gene expression in physiological as well as in pathological processes, including chronic pain. Whether deletion of a gene can affect expression of the miRNAs that associate with the deleted gene mRNA remains elusive. We investigated the effects of brain-derived neurotrophic factor (Bdnf) gene deletion on the expression of miR-1 in dorsal root ganglion (DRG) neurons and its pain-associated downstream targets heat shock protein 60 (Hsp60) and connexin 43 (Cx43) in tamoxifen-inducible conditional knockout mice, Bdnf(fl/fl); Advillin-CreER(T2) (Bdnf cKO). RESULTS Efficient Bdnf gene deletion was confirmed in DRG of Bdnf cKO mice by Real-Time qRT-PCR and ELISA 10days after completed tamoxifen treatment. In DRG, miR-1 expression was reduced 0.44-fold (p<0.05; Real-time qRT-PCR) in Bdnf cKO compared to floxed wildtype littermate control Bdnf(fl/fl) mice (WT). While Hsp60 protein expression was increased 1.85-fold (p<0.05; Western blot analysis), expression levels of Cx43 and the miR-1-associated transcription factors MEF2a and SRF remained unchanged. When analyzing Bdnf cKO mice 32days after complete tamoxifen treatment to investigate whether observed expression alterations remain permanently, we found no significant differences between Bdnf cKO and WT mice. However, miRNA microarray analysis revealed that 167 miRNAs altered (p<0.05) in DRG of these mice following Bdnf gene deletion. CONCLUSIONS Our results indicate that deletion of Bdnf in DRG neurons leads to a temporary dysregulation of miR-1, suggesting an impairment of a presumable feedback loop between BDNF protein and its targeting miR-1. This appears to affect its downstream protein Hsp60 and as a consequence might influence the phenotype after inducible Bdnf gene deletion. While this appears to be a MEF2a-/SRF-independent and transient effect, expression levels of various other miRNAs may remain permanently altered.
Collapse
Affiliation(s)
- Elena Neumann
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, Düsseldorf 40225, Germany.
| | - Timo Brandenburger
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, Düsseldorf 40225, Germany.
| | - Sonia Santana-Varela
- Molecular Nociception Group, Wolfson Institute for Biomedical Research (WIBR), Cruciform Building, University College London (UCL), London WC1E 6BT, UK.
| | - René Deenen
- Biological and Medical Research Center (BMFZ), Medical Faculty, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf 40225, Germany.
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Medical Faculty, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, Düsseldorf 40225, Germany.
| | - Inge Bauer
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, Düsseldorf 40225, Germany.
| | - Henning Hermanns
- Department of Anesthesiology, Academic Medical Center, Meibergdreef 9, Amsterdam 1100 DD, The Netherlands.
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research (WIBR), Cruciform Building, University College London (UCL), London WC1E 6BT, UK.
| | - Jing Zhao
- Molecular Nociception Group, Wolfson Institute for Biomedical Research (WIBR), Cruciform Building, University College London (UCL), London WC1E 6BT, UK.
| | - Robert Werdehausen
- Department of Anesthesiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Moorenstr. 5, Düsseldorf 40225, Germany.
| |
Collapse
|
48
|
Hollins SL, Cairns MJ. MicroRNA: Small RNA mediators of the brains genomic response to environmental stress. Prog Neurobiol 2016; 143:61-81. [PMID: 27317386 DOI: 10.1016/j.pneurobio.2016.06.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/24/2016] [Accepted: 06/11/2016] [Indexed: 01/09/2023]
Abstract
The developmental processes that establish the synaptic architecture of the brain while retaining capacity for activity-dependent remodeling, are complex and involve a combination of genetic and epigenetic influences. Dysregulation of these processes can lead to problems with neural circuitry which manifest in humans as a range of neurodevelopmental syndromes, such as schizophrenia, bipolar disorder and fragile X mental retardation. Recent studies suggest that prenatal, postnatal and intergenerational environmental factors play an important role in the aetiology of stress-related psychopathology. A number of these disorders have been shown to display epigenetic changes in the postmortem brain that reflect early life experience. These changes affect the regulation of gene expression though chromatin remodeling (transcriptional) and post-transcriptional influences, especially small noncoding microRNA (miRNA). These dynamic and influential molecules appear to play an important function in both brain development and its adaption to stress. In this review, we examine the role of miRNA in mediating the brain's response to both prenatal and postnatal environmental perturbations and explore how stress- induced alterations in miRNA expression can regulate the stress response via modulation of the immune system. Given the close relationship between environmental stress, miRNA, and brain development/function, we assert that miRNA hold a significant position at the molecular crossroads between neural development and adaptations to environmental stress. A greater understanding of the dynamics that mediate an individual's predisposition to stress-induced neuropathology has major human health benefits and is an important area of research.
Collapse
Affiliation(s)
- Sharon L Hollins
- School of Biomedical Sciences and Pharmacy and the Hunter Medical Research Institute, the University of Newcastle, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy and the Hunter Medical Research Institute, the University of Newcastle, Callaghan, NSW 2308, Australia; Schizophrenia Research Institute, Sydney, NSW, Australia.
| |
Collapse
|
49
|
Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing. Funct Integr Genomics 2016; 16:127-42. [PMID: 26743520 DOI: 10.1007/s10142-015-0472-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/21/2015] [Accepted: 12/21/2015] [Indexed: 10/22/2022]
Abstract
The root-knot nematode Meloidogyne incognita is among the most damaging plant-parasitic pests of several crops including cotton (Gossypium hirsutum) and tomato (Lycopersicon escultentum). Recently, a genome has become available for M. incognita, which greatly facilitates investigation of the interactions between M. incognita and its plant hosts at the molecular level and enables formation of hypotheses concerning development at the cellular level. MicroRNAs (miRNAs) are a class of small RNA molecules that serve as endogenous gene regulators. They regulate many biological processes including reproduction, the sequencing of morphological development, and potentially of parasitism as well. Certain miRNAs regulate fundamental metabolism pathways and stress responses in M. incognita. Since a list of miRNAs has not been generated for M. incognita, we employed a bioinformatics tool called mirDeepFinder to identify miRNAs from the small RNA database of M. incognita (GSM611102) that was generated from deep sequencing. A total of 254 conserved miRNAs belonging to 161 miRNA families were identified, as were 35 novel miRNAs belonging to 31 families. The 16 most commonly found miRNAs in order of abundance were min-miR-100a, min-miR-124, min-miR-71a, min-miR-1, min-miR-228, min-miR-92, min-miR-72, min-miR-49b, min-miR-58, min-miR-252, min-miR-lin-4, min-miR-87, min-miR-2a, min-miR-34a, min-miR-50a, and min-miR-279a. The length of the pre-miRNAs varied greatly from 50 to 197 nt, with an average of 88 ± 39 nt. The average minimal folding free energy (MFE) and MFE index (MFEI) of the identified miRNAs were -30.3 Kcal/mol and 0.92, respectively, indicating that these miRNAs can readily fold into a typical hairpin secondary structure.
Collapse
|
50
|
Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1. Proc Natl Acad Sci U S A 2015; 112:E7213-22. [PMID: 26669440 DOI: 10.1073/pnas.1509499112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) play essential, conserved roles in diverse developmental processes through association with the miRNA-induced silencing complex (miRISC). Whereas fundamental insights into the mechanistic framework of miRNA biogenesis and target gene silencing have been established, posttranslational modifications that affect miRISC function are less well understood. Here we report that the conserved serine/threonine kinase, casein kinase II (CK2), promotes miRISC function in Caenorhabditis elegans. CK2 inactivation results in developmental defects that phenocopy loss of miRISC cofactors and enhances the loss of miRNA function in diverse cellular contexts. Whereas CK2 is dispensable for miRNA biogenesis and the stability of miRISC cofactors, it is required for efficient miRISC target mRNA binding and silencing. Importantly, we identify the conserved DEAD-box RNA helicase, CGH-1/DDX6, as a key CK2 substrate within miRISC and demonstrate phosphorylation of a conserved N-terminal serine is required for CGH-1 function in the miRNA pathway.
Collapse
|