1
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Li X, Mills WT, Jin DS, Meffert MK. Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. CELL REPORTS METHODS 2024:100836. [PMID: 39127045 DOI: 10.1016/j.crmeth.2024.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024]
Abstract
Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T Mills
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel S Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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2
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Wang W, Ji L, Jing X, Zhao P, Xia Q. MicroRNA let-7 targets BmCDK1 to regulate cell proliferation and endomitosis of silk gland in the silkworm, Bombyx mori. INSECT SCIENCE 2024; 31:1026-1040. [PMID: 38053466 DOI: 10.1111/1744-7917.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/17/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023]
Abstract
MicroRNAs play critical roles in multiple developmental processes in insects. Our previous study showed that CRISPR/Cas9-mediated knock down of the microRNA let-7 in silkworms increased the size of larvae and silk glands, thereby improving the silk production capacity. In this study, we elucidate the molecular mechanism underlying of let-7 regulates growth. Identification of differentially expressed genes in response to let-7 knock down revealed enrichment of pathways associated with cell proliferation and DNA replication. let-7 dysregulation affected the cell cycle and proliferation of the Bombyx mori cell line BmN. Dual-luciferase and target site mutation assays showed that BmCDK1 is a direct target gene of let-7, with only 1 binding site on its 3'-untranslated region. RNA interference of BmCDK1 inhibited cell proliferation, but this effect was counteracted by co-transfection with let-7 antagomir. Moreover, let-7 knock down induced BmCDK1 expression and promoted cell proliferation in multiple tissues, and further induced endomitosis in the silk gland in vivo. Knock down of BmCDK1 resulted in abnormal formation of a new epidermis, and larval development was arrested at the 2nd or 3rd molt stage. Taken together, our results demonstrated that BmCDK1 is a novel target of let-7 in cell fate determination, possessing potential for improving silk yield in silkworm.
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Affiliation(s)
- Wei Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing, China
| | - Linshengzhe Ji
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Xinyuan Jing
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
| | - Ping Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Biological Science Research Center, Southwest University, China
- Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Chongqing, China
- Engineering Laboratory of Sericultural and Functional Genome and Biotechnology, Development and Reform Commission, Chongqing, China
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3
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Huang KY, Upadhyay G, Ahn Y, Sakakura M, Pagan-Diaz GJ, Cho Y, Weiss AC, Huang C, Mitchell JW, Li J, Tan Y, Deng YH, Ellis-Mohr A, Dou Z, Zhang X, Kang S, Chen Q, Sweedler JV, Im SG, Bashir R, Chung HJ, Popescu G, Gillette MU, Gazzola M, Kong H. Neuronal innervation regulates the secretion of neurotrophic myokines and exosomes from skeletal muscle. Proc Natl Acad Sci U S A 2024; 121:e2313590121. [PMID: 38683978 PMCID: PMC11087749 DOI: 10.1073/pnas.2313590121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 05/02/2024] Open
Abstract
Myokines and exosomes, originating from skeletal muscle, are shown to play a significant role in maintaining brain homeostasis. While exercise has been reported to promote muscle secretion, little is known about the effects of neuronal innervation and activity on the yield and molecular composition of biologically active molecules from muscle. As neuromuscular diseases and disabilities associated with denervation impact muscle metabolism, we hypothesize that neuronal innervation and firing may play a pivotal role in regulating secretion activities of skeletal muscles. We examined this hypothesis using an engineered neuromuscular tissue model consisting of skeletal muscles innervated by motor neurons. The innervated muscles displayed elevated expression of mRNAs encoding neurotrophic myokines, such as interleukin-6, brain-derived neurotrophic factor, and FDNC5, as well as the mRNA of peroxisome-proliferator-activated receptor γ coactivator 1α, a key regulator of muscle metabolism. Upon glutamate stimulation, the innervated muscles secreted higher levels of irisin and exosomes containing more diverse neurotrophic microRNAs than neuron-free muscles. Consequently, biological factors secreted by innervated muscles enhanced branching, axonal transport, and, ultimately, spontaneous network activities of primary hippocampal neurons in vitro. Overall, these results reveal the importance of neuronal innervation in modulating muscle-derived factors that promote neuronal function and suggest that the engineered neuromuscular tissue model holds significant promise as a platform for producing neurotrophic molecules.
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Affiliation(s)
- Kai-Yu Huang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gaurav Upadhyay
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yujin Ahn
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
| | - Masayoshoi Sakakura
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gelson J. Pagan-Diaz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Younghak Cho
- Department of Chemical and Biomolecular Engineering and KI for the Nano Century, Korea Advanced Institute of Science and Technology, Daejeon305-701, Republic of Korea
| | - Amanda C. Weiss
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Chen Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jennifer W. Mitchell
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jiahui Li
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yanqi Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yu-Heng Deng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Austin Ellis-Mohr
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Zhi Dou
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Xiaotain Zhang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Sehong Kang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jonathan V. Sweedler
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering and KI for the Nano Century, Korea Advanced Institute of Science and Technology, Daejeon305-701, Republic of Korea
| | - Rashid Bashir
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gabriel Popescu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Martha U. Gillette
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Mattia Gazzola
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Hyunjoon Kong
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Korea University-Korea Institute of Science and Technology Graduate School of Converging Science and Technology, Korea University, Seoul02841, Republic of Korea
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4
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Karpagavalli M, Sivagurunathan S, Panda TS, Srikakulam N, Arora R, Dohadwala L, Tiwary BK, Sadras SR, Arunachalam JP, Pandi G, Chidambaram S. piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress. Mol Omics 2024; 20:248-264. [PMID: 38314503 DOI: 10.1039/d3mo00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-hsa-26131 and the sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina-enriched piR-hsa-26131 was positively correlated with miR-182 in HIWI2-silenced Y79 cells. In addition, the lnc-ZNF169 sequence matched with two miRNAs of the let-7 family, and piRNAs, piR-hsa-11361 and piR-hsa-11360, which could modulate the regulatory network of retinal differentiation. Interestingly, we annotated four enriched motifs among the piRNAs and found that the piRNAs containing CACAATG and CTCATCAKYG motifs were snoRNA-derived piRNAs, which are significantly associated with developmental functions. However, piRNAs consisting of ACCACTANACCAC and AKCACGYTCSC motifs were mainly tRNA-derived fragments linked to stress response and sensory perception. Additionally, co-expression network analysis revealed cell cycle control, intracellular transport and stress response as the important biological functions regulated by piRNAs in the retina. Moreover, loss of piRNAs in HIWI2 knockdown ARPE19 confirmed altered expression of targets implicated in intracellular transport, circadian clock, and retinal degeneration. Moreover, piRNAs were dysregulated under oxidative stress conditions, indicating their potential role in retinal pathology. Therefore, we postulate that piRNAs, miRNAs, and lncRNAs might have a functional interplay during retinal development and functions to regulate retinal homeostasis.
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Affiliation(s)
| | - Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India
| | - T Sayamsmruti Panda
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Reety Arora
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
| | - Jayamuruga Pandian Arunachalam
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry-607402, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Subbulakshmi Chidambaram
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
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5
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Salama RM, Eissa N, Doghish AS, Abulsoud AI, Abdelmaksoud NM, Mohammed OA, Abdel Mageed SS, Darwish SF. Decoding the secrets of longevity: unraveling nutraceutical and miRNA-Mediated aging pathways and therapeutic strategies. FRONTIERS IN AGING 2024; 5:1373741. [PMID: 38605867 PMCID: PMC11007187 DOI: 10.3389/fragi.2024.1373741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
MicroRNAs (miRNAs) are short RNA molecules that are not involved in coding for proteins. They have a significant function in regulating gene expression after the process of transcription. Their participation in several biological processes has rendered them appealing subjects for investigating age-related disorders. Increasing data indicates that miRNAs can be influenced by dietary variables, such as macronutrients, micronutrients, trace minerals, and nutraceuticals. This review examines the influence of dietary factors and nutraceuticals on the regulation of miRNA in relation to the process of aging. We examine the present comprehension of miRNA disruption in age-related illnesses and emphasize the possibility of dietary manipulation as a means of prevention or treatment. Consolidating animal and human research is essential to validate the significance of dietary miRNA control in living organisms, despite the abundance of information already provided by several studies. This review elucidates the complex interaction among miRNAs, nutrition, and aging, offering valuable insights into promising areas for further research and potential therapies for age-related disorders.
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Affiliation(s)
- Rania M. Salama
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Nermin Eissa
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Ahmed S. Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Egypt
| | - Ahmed I. Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Egypt
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo, Egypt
| | | | - Osama A. Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha, Saudi Arabia
| | - Sherif S. Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
| | - Samar F. Darwish
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
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6
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Hewitt T, Alural B, Tilak M, Wang J, Becke N, Chartley E, Perreault M, Haggarty SJ, Sheridan SD, Perlis RH, Jones N, Mellios N, Lalonde J. Bipolar disorder-iPSC derived neural progenitor cells exhibit dysregulation of store-operated Ca 2+ entry and accelerated differentiation. Mol Psychiatry 2023; 28:5237-5250. [PMID: 37402854 DOI: 10.1038/s41380-023-02152-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
While most of the efforts to uncover mechanisms contributing to bipolar disorder (BD) focused on phenotypes at the mature neuron stage, little research has considered events that may occur during earlier timepoints of neurodevelopment. Further, although aberrant calcium (Ca2+) signaling has been implicated in the etiology of this condition, the possible contribution of store-operated Ca2+ entry (SOCE) is not well understood. Here, we report Ca2+ and developmental dysregulations related to SOCE in BD patient induced pluripotent stem cell (iPSC)-derived neural progenitor cells (BD-NPCs) and cortical-like glutamatergic neurons. First, using a Ca2+ re-addition assay we found that BD-NPCs and neurons had attenuated SOCE. Intrigued by this finding, we then performed RNA-sequencing and uncovered a unique transcriptome profile in BD-NPCs suggesting accelerated neurodifferentiation. Consistent with these results, we measured a slower rate of proliferation, increased neurite outgrowth, and decreased size in neurosphere formations with BD-NPCs. Also, we observed decreased subventricular areas in developing BD cerebral organoids. Finally, BD NPCs demonstrated high expression of the let-7 family while BD neurons had increased miR-34a, both being microRNAs previously implicated in neurodevelopmental deviations and BD etiology. In summary, we present evidence supporting an accelerated transition towards the neuronal stage in BD-NPCs that may be indicative of early pathophysiological features of the disorder.
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Affiliation(s)
- Tristen Hewitt
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- Neuroscience Center, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Begüm Alural
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Manali Tilak
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Jennifer Wang
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Natalina Becke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Ellis Chartley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Melissa Perreault
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Stephen J Haggarty
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steven D Sheridan
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Roy H Perlis
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nikolaos Mellios
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jasmin Lalonde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
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7
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Gialeli G, Panagopoulou O, Liosis G, Siahanidou T. Potential Epigenetic Effects of Human Milk on Infants' Neurodevelopment. Nutrients 2023; 15:3614. [PMID: 37630804 PMCID: PMC10460013 DOI: 10.3390/nu15163614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The advantages of human milk feeding, especially in preterm babies, are well recognized. Infants' feeding with breast milk lowers the likelihood of developing a diverse range of non-communicable diseases later in life and it is also associated with improved neurodevelopmental outcomes. Although the precise mechanisms through which human milk feeding is linked with infants' neurodevelopment are still unknown, potential epigenetic effects of breast milk through its bioactive components, including non-coding RNAs, stem cells and microbiome, could at least partly explain this association. Micro- and long-non-coding RNAs, enclosed in milk exosomes, as well as breast milk stem cells, survive digestion, reach the circulation and can cross the blood-brain barrier. Certain non-coding RNAs potentially regulate genes implicated in brain development and function, whereas nestin-positive stem cells can possibly differentiate into neural cells or/and act as epigenetic regulators in the brain. Furthermore, breast milk microbiota contributes to the establishment of infant's gut microbiome, which is implicated in brain development via epigenetic modifications and key molecules' regulation. This narrative review provides an updated analysis of the relationship between breast milk feeding and infants' neurodevelopment via epigenetics, pointing out how breast milk's bioactive components could have an impact on the neurodevelopment of both full-term and preterm babies.
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Affiliation(s)
- Giannoula Gialeli
- First Department of Pediatrics, Medical School, National & Kapodistrian University of Athens, 11527 Athens, Greece; (G.G.); (O.P.)
| | - Ourania Panagopoulou
- First Department of Pediatrics, Medical School, National & Kapodistrian University of Athens, 11527 Athens, Greece; (G.G.); (O.P.)
| | - Georgios Liosis
- Neonatal Intensive Care Unit, “Elena Venizelou” General and Maternal Hospital, 11521 Athens, Greece;
| | - Tania Siahanidou
- First Department of Pediatrics, Medical School, National & Kapodistrian University of Athens, 11527 Athens, Greece; (G.G.); (O.P.)
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8
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Wang Y, Su X, Leung GHD, Ren B, Zhang Q, Xiong Z, Zhou J, Yang L, Lu G, Chan WY, Ren L. Circulating microRNAs as diagnostic biomarkers for ischemic stroke: evidence from comprehensive analysis and real-world validation. Int J Med Sci 2023; 20:1009-1023. [PMID: 37484808 PMCID: PMC10357437 DOI: 10.7150/ijms.83963] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/16/2023] [Indexed: 07/25/2023] Open
Abstract
Ischemic stroke (IS) is the majority of strokes which remain the second leading cause of deaths in the last two decades. Circulating microRNAs (miRNAs) have been suggested as potential diagnostic and therapeutic tools for IS by previous studies analyzing their differential expression. However, inconclusive and controversial conclusions of these results have to be addressed. In this study, comprehensive analysis and real-world validation were performed to assess the associations between circulating miRNAs and IS. 29 studies with 112 miRNAs were extracted after manual selection and filtering, 12 differentially expressed miRNAs were obtained from our results of meta-analysis. These miRNAs were evaluated in 20 IS patients, compared to 20 healthy subjects. 4 miRNAs (hsa-let-7e-5p, hsa-miR-124-3p, hsa-miR-17-5p, hsa-miR-185-5p) exhibited the significant expression level in IS patient plasma samples. Pathway and biological process enrichment analysis for the target genes of the 4 validated miRNAs identified cellular senescence and neuroinflammation as key post-IS response pathways. The results of our analyses closely correlated with the pathogenesis and implicated pathways observed in IS subjects suggested by the literature, which may provide aid in the development of circulating diagnostic or therapeutic targets for IS patients.
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Affiliation(s)
- Yang Wang
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518000, China
| | - Xianwei Su
- Research and Development Unit, Shenzhen GenDo Medical Technology Co., Ltd., Dapeng, Shenzhen 518000, China
| | | | - Bohua Ren
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Medical University, Dongguan 523808, China
- Faculty of Education, Health and Wellbeing, University of Wolverhampton, Wolverhampton WV1 1QU, UK
| | - Qiang Zhang
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518000, China
| | - Zhiqiang Xiong
- SDIVF R&D Centre, 209,12W, HKSTP, Shatin, Hong Kong, China
| | - Jingye Zhou
- Research and Development Unit, Shenzhen GenDo Medical Technology Co., Ltd., Dapeng, Shenzhen 518000, China
| | - Ling Yang
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518000, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wai-Yee Chan
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lijie Ren
- Department of Neurology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518000, China
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9
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Exosomes induce neurogenesis of pluripotent P19 cells. Stem Cell Rev Rep 2023:10.1007/s12015-023-10512-6. [PMID: 36811747 PMCID: PMC10366297 DOI: 10.1007/s12015-023-10512-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 02/24/2023]
Abstract
Exosomes play a role in tissue/organ development and differentiation. Retinoic acid induces differentiation of P19 cells (UD-P19) to P19 neurons (P19N) that behave like cortical neurons and express characteristic neuronal genes such as NMDA receptor subunits. Here we report P19N exosome-mediated differentiation of UD-P19 to P19N. Both UD-P19 and P19N released exosomes with characteristic exosome morphology, size, and common protein markers. P19N internalized significantly higher number of Dil-P19N exosomes as compared to UD-P19 with accumulation in the perinuclear region. Continuous exposure of UD-P19 to P19N exosomes for six days induced formation of small-sized embryoid bodies that differentiated into MAP2-/GluN2B-positive neurons recapitulating RA-induction of neurogenesis. Incubation with UD-P19 exosomes for six days did not affect UD-P19. Small RNA-seq identified enrichment of P19N exosomes with pro-neurogenic non-coding RNAs (ncRNAs) such as miR-9, let-7, MALAT1 and depleted with ncRNAs involved in maintenance of stem cell characteristics. UD-P19 exosomes were rich with ncRNAs required for maintenance of stemness. P19N exosomes provide an alternative method to genetic modifications for cellular differentiation of neurons. Our novel findings on exosomes-mediated differentiation of UD-P19 to P19 neurons provide tools to study pathways directing neuron development/differentiation and develop novel therapeutic strategies in neuroscience.
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Navarro-Calvo J, Esquiva G, Gómez-Vicente V, Valor LM. MicroRNAs in the Mouse Developing Retina. Int J Mol Sci 2023; 24:ijms24032992. [PMID: 36769311 PMCID: PMC9918188 DOI: 10.3390/ijms24032992] [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: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The retina is among the highest organized tissues of the central nervous system. To achieve such organization, a finely tuned regulation of developmental processes is required to form the retinal layers that contain the specialized neurons and supporting glial cells to allow precise phototransduction. MicroRNAs are a class of small RNAs with undoubtful roles in fundamental biological processes, including neurodevelopment of the brain and the retina. This review provides a short overview of the most important findings regarding microRNAs in the regulation of retinal development, from the developmental-dependent rearrangement of the microRNA expression program to the key roles of particular microRNAs in the differentiation and maintenance of retinal cell subtypes.
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Affiliation(s)
- Jorge Navarro-Calvo
- Unidad de Investigación, Hospital General Universitario Dr. Balmis, ISABIAL, 03010 Alicante, Spain
| | - Gema Esquiva
- Department of Optics, Pharmacology and Anatomy, University of Alicante, 03690 Alicante, Spain
| | - Violeta Gómez-Vicente
- Department of Optics, Pharmacology and Anatomy, University of Alicante, 03690 Alicante, Spain
| | - Luis M. Valor
- Unidad de Investigación, Hospital General Universitario Dr. Balmis, ISABIAL, 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-913-988
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11
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Nedel F, Ferrúa CP, do Amaral CC, Corrêa GP, Silveira RG, Trettim JP, da Cunha GK, Klug AB, Ardais AP, Fogaça TB, Pinheiro KA, Bast RK, Ghisleni G, de M Souza LD, de Matos MB, Quevedo LDA, Pinheiro RT. Maternal expression of miR-let-7d-3p and miR-451a during gestation influences the neuropsychomotor development of 90 days old babies: "Pregnancy care, healthy baby" study. J Psychiatr Res 2023; 158:185-191. [PMID: 36587497 PMCID: PMC9907453 DOI: 10.1016/j.jpsychires.2022.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Studies on maternal microRNA expression have emerged to better understand regulatory mechanisms during the gestational period, since microRNA expression has been associated with pregnancy disorders. OBJECTIVES This study aims to investigate the association between the expression of the maternal microRNAs miR-let-7d-3p and miR-451a during the second gestational trimester and neuropsychomotor development at 90 days of life of infants. METHODS This is a case-control study nested within a cohort, with the groups being divided into dyads in which pregnant women presented Major Depressive Episode (MDE) (n = 64), these being the cases, and their respective controls (no MDE; n = 64). The Bayley Scale III was used to assess the outcome of child development, and MDE was assessed through the Mini International Neuropsychiatric Interview Plus. The analysis of miR-let-7d-3p and miR-451a was done via serum from the pregnant women, utilizing the qRT-PCR (n = 128). RESULTS The results indicated a negative association between expression levels of miR-451a (β -3.3 CI95% -6.4;-0.3) and a positive associated of the miR-let-7d-3p with the cognitive development domain (β 1.7 CI95% 0.1; 3.0), and a positive association between expression of miR-let-7d-3p with motor development of the infants (β 1.6 CI95% 0.3; 2.9). CONCLUSION This is a pioneering study on the topic that indicates a biological interrelationship between the miRNAs miR-let-7d-3p and miR-451a evaluated during the pregnancy and the motor and cognitive domains of infant development at 90 days postpartum.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tatiane B. Fogaça
- San Francisco de Paula University Hospital – Fetal Medicine Service, Pelotas, RS, Brazil
| | - Karen A.T. Pinheiro
- University of Rio Grande Foundation (FURG), FAMED, Department of Specialized Surgery, Rio Grande/RS, Brazil
| | - Rachel K.S.S. Bast
- Graduate Program in Biological Sciences: Biochemistry, Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul. Porto Alegre/RS, Brazil
| | | | | | | | | | - Ricardo T. Pinheiro
- Catholic University of Pelotas, Pelotas, RS, Brazil,Corresponding author. Post-Graduate Program in Health and Behavior, Catholic University of Pelotas, Gonçalves Chaves, 373, Centro – Pelotas, Rio Grande do Sul, 96015-560, Brazil.
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12
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Suzuki N, Zou Y, Sun H, Eichel K, Shao M, Shih M, Shen K, Chang C. Two intrinsic timing mechanisms set start and end times for dendritic arborization of a nociceptive neuron. Proc Natl Acad Sci U S A 2022; 119:e2210053119. [PMID: 36322763 PMCID: PMC9659368 DOI: 10.1073/pnas.2210053119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
Choreographic dendritic arborization takes place within a defined time frame, but the timing mechanism is currently not known. Here, we report that the precisely timed lin-4-lin-14 regulatory circuit triggers an initial dendritic growth activity, whereas the precisely timed lin-28-let-7-lin-41 regulatory circuit signals a subsequent developmental decline in dendritic growth ability, hence restricting dendritic arborization within a set time frame. Loss-of-function mutations in the lin-4 microRNA gene cause limited dendritic outgrowth, whereas loss-of-function mutations in its direct target, the lin-14 transcription factor gene, cause precocious and excessive outgrowth. In contrast, loss-of-function mutations in the let-7 microRNA gene prevent a developmental decline in dendritic growth ability, whereas loss-of-function mutations in its direct target, the lin-41 tripartite motif protein gene, cause further decline. lin-4 and let-7 regulatory circuits are expressed in the right place at the right time to set start and end times for dendritic arborization. Replacing the lin-4 upstream cis-regulatory sequence at the lin-4 locus with a late-onset let-7 upstream cis-regulatory sequence delays dendrite arborization, whereas replacing the let-7 upstream cis-regulatory sequence at the let-7 locus with an early-onset lin-4 upstream cis-regulatory sequence causes a precocious decline in dendritic growth ability. Our results indicate that the lin-4-lin-14 and the lin-28-let-7-lin-41 regulatory circuits control the timing of dendrite arborization through antagonistic regulation of the DMA-1 receptor level on dendrites. The LIN-14 transcription factor likely directly represses dma-1 gene expression through a transcriptional means, whereas the LIN-41 tripartite motif protein likely indirectly promotes dma-1 gene expression through a posttranscriptional means.
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Affiliation(s)
- Nobuko Suzuki
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Yan Zou
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - HaoSheng Sun
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Kelsie Eichel
- HHMI, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Meiyu Shao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mushaine Shih
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Kang Shen
- HHMI, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Chieh Chang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607
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13
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Blount GS, Coursey L, Kocerha J. MicroRNA Networks in Cognition and Dementia. Cells 2022; 11:cells11121882. [PMID: 35741010 PMCID: PMC9221254 DOI: 10.3390/cells11121882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
The change from viewing noncoding RNA as “junk” in the genome to seeing it as a critical epigenetic regulator in almost every human condition or disease has forced a paradigm shift in biomedical and clinical research. Small and long noncoding RNA transcripts are now routinely evaluated as putative diagnostic or therapeutic agents. A prominent role for noncoding microRNAs in the central nervous system has uncovered promising new clinical candidates for dementia-related disorders, treatments for which currently remain elusive even as the percentage of diagnosed patients increases significantly. Cognitive decline is a core neurodegenerative process in Alzheimer’s Disease, Frontotemporal Dementia, Lewy body dementia, vascular dementia, Huntington’s Disease, Creutzfeldt–Jakob disease, and a significant portion of Parkinson’s Disease patients. This review will discuss the microRNA-associated networks which influence these pathologies, including inflammatory and viral-mediated pathways (such as the novel SARS-CoV-2 virus implicated in COVID-19), and their current status in clinical trials.
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Fishman ES, Han JS, La Torre A. Oscillatory Behaviors of microRNA Networks: Emerging Roles in Retinal Development. Front Cell Dev Biol 2022; 10:831750. [PMID: 35186936 PMCID: PMC8847441 DOI: 10.3389/fcell.2022.831750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/07/2022] [Indexed: 01/02/2023] Open
Abstract
A broad repertoire of transcription factors and other genes display oscillatory patterns of expression, typically ranging from 30 min to 24 h. These oscillations are associated with a variety of biological processes, including the circadian cycle, somite segmentation, cell cycle, and metabolism. These rhythmic behaviors are often prompted by transcriptional feedback loops in which transcriptional activities are inhibited by their corresponding gene target products. Oscillatory transcriptional patterns have been proposed as a mechanism to drive biological clocks, the molecular machinery that transforms temporal information into accurate spatial patterning during development. Notably, several microRNAs (miRNAs) -small non-coding RNA molecules-have been recently shown to both exhibit rhythmic expression patterns and regulate oscillatory activities. Here, we discuss some of these new findings in the context of the developing retina. We propose that miRNA oscillations are a powerful mechanism to coordinate signaling pathways and gene expression, and that addressing the dynamic interplay between miRNA expression and their target genes could be key for a more complete understanding of many developmental processes.
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Affiliation(s)
| | | | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
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15
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Identification of let-7f and miR-338 as plasma-based biomarkers for sporadic amyotrophic lateral sclerosis using meta-analysis and empirical validation. Sci Rep 2022; 12:1373. [PMID: 35082326 PMCID: PMC8791978 DOI: 10.1038/s41598-022-05067-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/06/2022] [Indexed: 12/11/2022] Open
Abstract
AbstractAmyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that in most cases occurs sporadic (sALS). The disease is not curable, and its pathogenesis mechanisms are not well understood yet. Given the intricacy of underlying molecular interactions and heterogeneity of ALS, the discovery of molecules contributing to disease onset and progression will open a new avenue for advancement in early diagnosis and therapeutic intervention. Here we conducted a meta-analysis of 12 circulating miRNA profiling studies using the robust rank aggregation (RRA) method, followed by enrichment analysis and experimental verification. We identified miR-451a and let-7f-5p as meta-signature miRNAs whose targets are involved in critical pathogenic pathways underlying ALS, including ‘FoxO signaling pathway’, ‘MAPK signaling pathway’, and ‘apoptosis’. A systematic review of 7 circulating gene profiling studies elucidated that 241 genes up-regulated in sALS circulation with concomitant being targets of the meta-signature miRNAs. Protein–protein interaction (PPI) network analysis of the candidate targets using MCODE algorithm revealed the main subcluster is involved in multiple cascades eventually leads apoptosis, including ‘positive regulation of neuron apoptosis. Besides, we validated the meta-analysis results using RT-qPCR. Indeed, relative expression analysis verified let-7f-5p and miR-338-3p as significantly down-regulated and up-regulated biomarkers in the plasma of sALS patients, respectively. Receiver operating characteristic (ROC) analysis also highlighted the let-7f-5p and miR-338-3p potential as robustness plasma biomarkers for diagnosis and potential therapeutic targets of sALS disease.
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Prodromidou K, Matsas R. Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. Cell Mol Life Sci 2021; 79:56. [PMID: 34921638 PMCID: PMC11071749 DOI: 10.1007/s00018-021-04063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The human cerebral cortex is a uniquely complex structure encompassing an unparalleled diversity of neuronal types and subtypes. These arise during development through a series of evolutionary conserved processes, such as progenitor cell proliferation, migration and differentiation, incorporating human-associated adaptations including a protracted neurogenesis and the emergence of novel highly heterogeneous progenitor populations. Disentangling the unique features of human cortical development involves elucidation of the intricate developmental cell transitions orchestrated by progressive molecular events. Crucially, developmental timing controls the fine balance between cell cycle progression/exit and the neurogenic competence of precursor cells, which undergo morphological transitions coupled to transcriptome-defined temporal states. Recent advances in bulk and single-cell transcriptomic technologies suggest that alongside protein-coding genes, non-coding RNAs exert important regulatory roles in these processes. Interestingly, a considerable number of novel long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have appeared in human and non-human primates suggesting an evolutionary role in shaping cortical development. Here, we present an overview of human cortical development and highlight the marked diversification and complexity of human neuronal progenitors. We further discuss how lncRNAs and miRNAs constitute critical components of the extended epigenetic regulatory network defining intermediate states of progenitors and controlling cell cycle dynamics and fate choices with spatiotemporal precision, during human neurodevelopment.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece
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Rajool Dezfuly A, Safaee A, Salehi H. Therapeutic effects of mesenchymal stem cells-derived extracellular vesicles' miRNAs on retinal regeneration: a review. Stem Cell Res Ther 2021; 12:530. [PMID: 34620234 PMCID: PMC8499475 DOI: 10.1186/s13287-021-02588-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs), which consist of microvesicles and exosomes, are secreted from all cells to transform vital information in the form of lipids, proteins, mRNAs and small RNAs such as microRNAs (miRNAs). Many studies demonstrated that EVs' miRNAs have effects on target cells. Numerous people suffer from the blindness caused by retinal degenerations. The death of retinal neurons is irreversible and creates permanent damage to the retina. In the absence of acceptable cures for retinal degenerative diseases, stem cells and their paracrine agents including EVs have become a promising therapeutic approach. Several studies showed that the therapeutic effects of stem cells are due to the miRNAs of their EVs. Considering the effects of microRNAs in retinal cells development and function and studies which provide the possible roles of mesenchymal stem cells-derived EVs miRNA content on retinal diseases, we focused on the similarities between these two groups of miRNAs that could be helpful for promoting new therapeutic techniques for retinal degenerative diseases.
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Affiliation(s)
- Ali Rajool Dezfuly
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Azadeh Safaee
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Salehi
- Department of Anatomical and Molecular Biology Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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18
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Yuen SC, Liang X, Zhu H, Jia Y, Leung SW. Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer's disease by meta-analysis and adaptive boosting ensemble learning. Alzheimers Res Ther 2021; 13:126. [PMID: 34243793 PMCID: PMC8272278 DOI: 10.1186/s13195-021-00862-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/17/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Blood circulating microRNAs that are specific for Alzheimer's disease (AD) can be identified from differentially expressed microRNAs (DEmiRNAs). However, non-reproducible and inconsistent reports of DEmiRNAs hinder biomarker development. The most reliable DEmiRNAs can be identified by meta-analysis. To enrich the pool of DEmiRNAs for potential AD biomarkers, we used a machine learning method called adaptive boosting for miRNA disease association (ABMDA) to identify eligible candidates that share similar characteristics with the DEmiRNAs identified from meta-analysis. This study aimed to identify blood circulating DEmiRNAs as potential AD biomarkers by augmenting meta-analysis with the ABMDA ensemble learning method. METHODS Studies on DEmiRNAs and their dysregulation states were corroborated with one another by meta-analysis based on a random-effects model. DEmiRNAs identified by meta-analysis were collected as positive examples of miRNA-AD pairs for ABMDA ensemble learning. ABMDA identified similar DEmiRNAs according to a set of predefined criteria. The biological significance of all resulting DEmiRNAs was determined by their target genes according to pathway enrichment analyses. The target genes common to both meta-analysis- and ABMDA-identified DEmiRNAs were collected to construct a network to investigate their biological functions. RESULTS A systematic database search found 7841 studies for an extensive meta-analysis, covering 54 independent comparisons of 47 differential miRNA expression studies, and identified 18 reliable DEmiRNAs. ABMDA ensemble learning was conducted based on the meta-analysis results and the Human MicroRNA Disease Database, which identified 10 additional AD-related DEmiRNAs. These 28 DEmiRNAs and their dysregulated pathways were related to neuroinflammation. The dysregulated pathway related to neuronal cell cycle re-entry (CCR) was the only statistically significant pathway of the ABMDA-identified DEmiRNAs. In the biological network constructed from 1865 common target genes of the identified DEmiRNAs, the multiple core ubiquitin-proteasome system, that is involved in neuroinflammation and CCR, was highly connected. CONCLUSION This study identified 28 DEmiRNAs as potential AD biomarkers in blood, by meta-analysis and ABMDA ensemble learning in tandem. The DEmiRNAs identified by meta-analysis and ABMDA were significantly related to neuroinflammation, and the ABMDA-identified DEmiRNAs were related to neuronal CCR.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Xiaonan Liang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Yongliang Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan China
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Siu-wai Leung
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, China
- Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Edinburgh, Scotland, UK
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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Ghosh S, Kumar V, Mukherjee H, Lahiri D, Roy P. Nutraceutical regulation of miRNAs involved in neurodegenerative diseases and brain cancers. Heliyon 2021; 7:e07262. [PMID: 34195404 PMCID: PMC8225984 DOI: 10.1016/j.heliyon.2021.e07262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/24/2021] [Accepted: 06/05/2021] [Indexed: 12/12/2022] Open
Abstract
The human brain is a well-connected, intricate network of neurons and supporting glial cells. Neurodegenerative diseases arise as a consequence of extensive loss of neuronal cells leading to disruption of their natural structure and function. On the contrary, rapid proliferation and growth of glial as well as neuronal cells account for the occurrence of malignancy in brain. In both cases, the molecular microenvironment holds pivotal importance in the progression of the disease. MicroRNAs (miRNA) are one of the major components of the molecular microenvironment. miRNAs are small, noncoding RNAs that control gene expression post-transcriptionally. As compared to other tissues, the brain expresses a substantially high number of miRNAs. In the early stage of neurodegeneration, miRNA expression upregulates, while in oncogenesis, miRNA expression is gradually lost. Neurodegeneration and brain cancer is presumed to be under the influence of identical pathways of cell proliferation, differentiation and cell death which are tightly regulated by miRNAs. It has been confirmed experimentally that miRNA expression can be regulated by nutraceuticals - macronutrients, micronutrients or natural products derived from food; thereby making dietary supplements immensely significant for targeting miRNAs having altered expression patterns during neurodegeneration or oncogenesis. In this review, we will discuss in detail, about the common miRNAs involved in brain cancers and neurodegenerative diseases along with the comprehensive list of miRNAs involved separately in both pathological conditions. We will also discuss the role of nutraceuticals in the regulation of those miRNAs which are involved in both of these pathological conditions.
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Affiliation(s)
- Souvik Ghosh
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Biomaterials and Multiscale Mechanics Laboratory, Department of Metallurgical and Materials Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Centre of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Viney Kumar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Haimanti Mukherjee
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Debrupa Lahiri
- Biomaterials and Multiscale Mechanics Laboratory, Department of Metallurgical and Materials Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Centre of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Partha Roy
- Molecular Endocrinology Laboratory, Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
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let-7 microRNAs: Their Role in Cerebral and Cardiovascular Diseases, Inflammation, Cancer, and Their Regulation. Biomedicines 2021; 9:biomedicines9060606. [PMID: 34073513 PMCID: PMC8227213 DOI: 10.3390/biomedicines9060606] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
The let-7 family is among the first microRNAs found. Recent investigations have indicated that it is highly expressed in many systems, including cerebral and cardiovascular systems. Numerous studies have implicated the aberrant expression of let-7 members in cardiovascular diseases, such as stroke, myocardial infarction (MI), cardiac fibrosis, and atherosclerosis as well as in the inflammation related to these diseases. Furthermore, the let-7 microRNAs are involved in development and differentiation of embryonic stem cells in the cardiovascular system. Numerous genes have been identified as target genes of let-7, as well as a number of the let-7’ regulators. Further studies are necessary to identify the gene targets and signaling pathways of let-7 in cardiovascular diseases and inflammatory processes. The bulk of the let-7’ regulatory proteins are well studied in development, proliferation, differentiation, and cancer, but their roles in inflammation, cardiovascular diseases, and/or stroke are not well understood. Further knowledge on the regulation of let-7 is crucial for therapeutic advances. This review focuses on research progress regarding the roles of let-7 and their regulation in cerebral and cardiovascular diseases and associated inflammation.
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22
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Prieto-Colomina A, Fernández V, Chinnappa K, Borrell V. MiRNAs in early brain development and pediatric cancer: At the intersection between healthy and diseased embryonic development. Bioessays 2021; 43:e2100073. [PMID: 33998002 DOI: 10.1002/bies.202100073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022]
Abstract
The size and organization of the brain are determined by the activity of progenitor cells early in development. Key mechanisms regulating progenitor cell biology involve miRNAs. These small noncoding RNA molecules bind mRNAs with high specificity, controlling their abundance and expression. The role of miRNAs in brain development has been studied extensively, but their involvement at early stages remained unknown until recently. Here, recent findings showing the important role of miRNAs in the earliest phases of brain development are reviewed, and it is discussed how loss of specific miRNAs leads to pathological conditions, particularly adult and pediatric brain tumors. Let-7 miRNA downregulation and the initiation of embryonal tumors with multilayered rosettes (ETMR), a novel link recently discovered by the laboratory, are focused upon. Finally, it is discussed how miRNAs may be used for the diagnosis and therapeutic treatment of pediatric brain tumors, with the hope of improving the prognosis of these devastating diseases.
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Affiliation(s)
- Anna Prieto-Colomina
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Virginia Fernández
- Neurobiology of miRNA, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Kaviya Chinnappa
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
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Ahmed SH, Espinoza-Sánchez NA, El-Damen A, Fahim SA, Badawy MA, Greve B, El-Shinawi M, Götte M, Ibrahim SA. Small extracellular vesicle-encapsulated miR-181b-5p, miR-222-3p and let-7a-5p: Next generation plasma biopsy-based diagnostic biomarkers for inflammatory breast cancer. PLoS One 2021; 16:e0250642. [PMID: 33901254 PMCID: PMC8075236 DOI: 10.1371/journal.pone.0250642] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory breast cancer (IBC) is a rare, but aggressive entity of breast carcinoma with rapid dermal lymphatic invasion in young females. It is either poorly or misdiagnosed as mastitis because of the absence of a distinct lump. Small extracellular vesicles (sEVs) circulating in liquid biopsies are a novel class of minimally invasive diagnostic alternative to invasive tissue biopsies. They modulate cancer progression via shuttling their encapsulated cargo including microRNAs (miRNAs) into recipient cells to either trigger signaling or induce malignant transformation of targeted cells. Plasma sEVs < 200 nm were isolated using a modified cost-effective polyethylene glycol (PEG)-based precipitation method and compared to standard methods, namely ultracentrifugation and a commercial kit, where the successful isolation was verified by different approaches. We evaluated the expression levels of selected sEV-derived miR-181b-5p, miR-222-3p and let-7a-5p using quantitative real PCR (qPCR). Relative to non-IBC, our qPCR data showed that sEV-derived miR-181b-5p and miR-222-3p were significantly upregulated, whereas let-7a-5p was downregulated in IBC patients. Interestingly, receiver operating characteristic (ROC) curves analysis revealed that diagnostic accuracy of let-7a-5p alone was the highest for IBC with an area under curve (AUC) value of 0.9188, and when combined with miR-222-3p the AUC was improved to 0.973. Further, 38 hub genes were identified using bioinformatics analysis. Together, circulating sEV-derived miR-181b-5p, miR-222-3p and let-7a-5p serve as promising non-invasive diagnostic biomarkers for IBC.
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Affiliation(s)
- Sarah Hamdy Ahmed
- Biotechnology/Biomolecular Chemistry Program, Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Nancy A Espinoza-Sánchez
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany.,Department of Radiotherapy-Radiooncology, University Hospital Münster, Münster, Germany
| | - Ahmed El-Damen
- Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt
| | - Sarah Atef Fahim
- Biochemistry Program, Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed A Badawy
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Burkhard Greve
- Department of Radiotherapy-Radiooncology, University Hospital Münster, Münster, Germany
| | - Mohamed El-Shinawi
- Galala University, Suez, Egypt.,Department of General Surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster, Germany
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24
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Fishman ES, Louie M, Miltner AM, Cheema SK, Wong J, Schlaeger NM, Moshiri A, Simó S, Tarantal AF, La Torre A. MicroRNA Signatures of the Developing Primate Fovea. Front Cell Dev Biol 2021; 9:654385. [PMID: 33898453 PMCID: PMC8060505 DOI: 10.3389/fcell.2021.654385] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/16/2021] [Indexed: 11/22/2022] Open
Abstract
Rod and cone photoreceptors differ in their shape, photopigment expression, synaptic connection patterns, light sensitivity, and distribution across the retina. Although rods greatly outnumber cones, human vision is mostly dependent on cone photoreceptors since cones are essential for our sharp visual acuity and color discrimination. In humans and other primates, the fovea centralis (fovea), a specialized region of the central retina, contains the highest density of cones. Despite the vast importance of the fovea for human vision, the molecular mechanisms guiding the development of this region are largely unknown. MicroRNAs (miRNAs) are small post-transcriptional regulators known to orchestrate developmental transitions and cell fate specification in the retina. Here, we have characterized the transcriptional landscape of the developing rhesus monkey retina. Our data indicates that non-human primate fovea development is significantly accelerated compared to the equivalent retinal region at the other side of the optic nerve head, as described previously. Notably, we also identify several miRNAs differentially expressed in the presumptive fovea, including miR-15b-5p, miR-342-5p, miR-30b-5p, miR-103-3p, miR-93-5p as well as the miRNA cluster miR-183/-96/-182. Interestingly, miR-342-5p is enriched in the nasal primate retina and in the peripheral developing mouse retina, while miR-15b is enriched in the temporal primate retina and increases over time in the mouse retina in a central-to-periphery gradient. Together our data constitutes the first characterization of the developing rhesus monkey retinal miRNome and provides novel datasets to attain a more comprehensive understanding of foveal development.
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Affiliation(s)
- Elizabeth S Fishman
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Mikaela Louie
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Adam M Miltner
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Simranjeet K Cheema
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Joanna Wong
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Nicholas M Schlaeger
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Ala Moshiri
- Department of Ophthalmology, University of California, Davis, Davis, CA, United States
| | - Sergi Simó
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | - Alice F Tarantal
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States.,Department of Pediatrics, University of California, Davis, Davis, CA, United States.,California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Anna La Torre
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
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25
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Findeiss E, Schwarz SC, Evsyukov V, Rösler TW, Höllerhage M, Chakroun T, Nykänen NP, Shen Y, Wurst W, Kohl M, Tost J, Höglinger GU. Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle Genes. Front Cell Dev Biol 2021; 9:561086. [PMID: 33748099 PMCID: PMC7969723 DOI: 10.3389/fcell.2021.561086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Growing evidence suggests that epigenetic mechanisms like microRNA-mediated transcriptional regulation contribute to the pathogenesis of parkinsonism. In order to study the influence of microRNAs (miRNAs), we analyzed the miRNome 2 days prior to major cell death in α-synuclein-overexpressing Lund human mesencephalic neurons, a well-established cell model of Parkinson’s disease (PD), by next-generation sequencing. The expression levels of 23 miRNAs were significantly altered in α-synuclein-overexpressing cells, 11 were down- and 12 upregulated (P < 0.01; non-adjusted). The in silico analysis of known target genes of these miRNAs was complemented by the inclusion of a transcriptome dataset (BeadChip) of the same cellular system, revealing the G0/G1 cell cycle transition to be markedly enriched. Out of 124 KEGG-annotated cell cycle genes, 15 were present in the miRNA target gene dataset and six G0/G1 cell cycle genes were found to be significantly altered upon α-synuclein overexpression, with five genes up- (CCND1, CCND2, and CDK4 at P < 0.01; E2F3, MYC at P < 0.05) and one gene downregulated (CDKN1C at P < 0.001). Additionally, several of these altered genes are targeted by miRNAs hsa-miR-34a-5p and hsa-miR-34c-5p, which also modulate α-synuclein expression levels. Functional intervention by siRNA-mediated knockdown of the cell cycle gene cyclin D1 (CCND1) confirmed that silencing of cell cycle initiation is able to substantially reduce α-synuclein-mediated cytotoxicity. The present findings suggest that α-synuclein accumulation induces microRNA-mediated aberrant cell cycle activation in post-mitotic dopaminergic neurons. Thus, the mitotic cell cycle pathway at the level of miRNAs might offer interesting novel therapeutic targets for PD.
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Affiliation(s)
- Elisabeth Findeiss
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sigrid C Schwarz
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany
| | - Valentin Evsyukov
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Thomas W Rösler
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matthias Höllerhage
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
| | - Tasnim Chakroun
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Niko-Petteri Nykänen
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Yimin Shen
- Laboratory for Epigenetics and Environment, Center National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, Munich, Germany.,Genome Engineering, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Michael Kohl
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Center National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Günter U Höglinger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases, Munich, Germany.,Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Neurology, Hannover Medical School, Hanover, Germany
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26
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Konar GJ, Ferguson C, Flickinger Z, Kent MR, Patton JG. miRNAs and Müller Glia Reprogramming During Retina Regeneration. Front Cell Dev Biol 2021; 8:632632. [PMID: 33537319 PMCID: PMC7848101 DOI: 10.3389/fcell.2020.632632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
The use of model systems that are capable of robust, spontaneous retina regeneration has allowed for the identification of genetic pathways and components that are required for retina regeneration. Complemented by mouse models in which retina regeneration can be induced after forced expression of key factors, altered chromatin accessibility, or inhibition of kinase/signaling cascades, a clearer picture of the key regulatory events that control retina regeneration is emerging. In all cases, Müller glia (MG) serve as an adult retinal stem cell that must be reprogrammed to allow for regeneration, with the end goal being to understand why regenerative pathways are blocked in mammals, but spontaneous in other vertebrates such as zebrafish. miRNAs have emerged as key gene regulatory molecules that control both development and regeneration in vertebrates. Here, we focus on a small subset of miRNAs that control MG reprogramming during retina regeneration and have the potential to serve as therapeutic targets for treatment of visual disorders and damage.
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Affiliation(s)
- Gregory J Konar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Claire Ferguson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Zachary Flickinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Matthew R Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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27
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Age-related increase of let-7 family microRNA in rat retina and vitreous. Exp Eye Res 2021; 204:108434. [PMID: 33412132 DOI: 10.1016/j.exer.2020.108434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/01/2020] [Accepted: 12/28/2020] [Indexed: 11/21/2022]
Abstract
Vitreous alterations occur from early stages and continue through the normal aging, with gradual lamellae formation and the appearance of liquefied spaces, which eventually leads to complications, such as retinal tear, retinal detachment, and intravitreal hemorrhage. The aim of the present study was to investigate the expression of let-7 miRNA family in the vitreous and retina in newborn (1-3- day-old), young adult (2-month-old), and aging (12-month-old) rats, as well as their role as regulators of vitreous components. MicroRNAs are small, non-coding RNAs that post-transcriptionally regulate gene expression. Our results showed detection of all investigated let-7 isoforms (let-7a, let-7b, let-7c, let-7d, let-7e, let-7f and let-7i) in the retina and vitreous. Although most let-7 members were significantly upregulated in the vitreous during development, only let-7b, let-7c, and let-7e followed this same expression pattern in the retina. Let-7b and -7c increased in aging vitreous as well, and were expressed in vitro by Müller glial cells and their extracellular vesicles. Moreover, let-7 targeted hyaluronan synthase 2 (Has2) mRNA, a synthesizing enzyme of hyaluronan. These observations indicate that let-7 function is important during retina and vitreous development, and that isoforms of let-7 increased with aging, potentially modulating hyaluronan content.
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