1
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. Nat Commun 2024; 15:5270. [PMID: 38902233 PMCID: PMC11190236 DOI: 10.1038/s41467-024-48344-8] [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: 08/10/2023] [Accepted: 04/25/2024] [Indexed: 06/22/2024] Open
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.
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Affiliation(s)
- Rebeccah K Stewart
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Patrick Nguyen
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jessica K Sawyer
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA.
- Duke Regeneration Center, Duke University, Durham, NC, USA.
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2
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Shang Z, Wanyan P, Wang M, Zhang B, Cui X, Wang X. Stem cell-derived exosomes for traumatic spinal cord injury: a systematic review and network meta-analysis based on a rat model. Cytotherapy 2024; 26:1-10. [PMID: 37804282 DOI: 10.1016/j.jcyt.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/06/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND AIMS Exosome therapy for traumatic spinal cord injury (TSCI) is a current research hotspot, but its therapeutic effect and the best source of stem cells for exosomes are unclear. METHODS The Web of Science, PubMed, Embase, Cochrane, and Scopus databases were searched from inception to March 28, 2023. Literature screening, data extraction and risk of bias assessment were performed independently by two investigators. RESULTS A total of 40 studies were included for data analysis. The findings of our traditional meta-analysis indicate that exosomes derived from stem cells significantly improve the motor function of TSCI at various time points (1 week: weighted mean difference [WMD] = 1.58, 95% confidence interval [CI] 0.87-2.30] 2 weeks: WMD = 3.12, 95% CI 2.64-3.61; 3 weeks: WMD = 4.44, 95% CI 3.27-5.60; 4 weeks: WMD = 4.54, 95% CI 3.42-5.66). Four kinds of stem cell-derived exosomes have been studied: bone marrow mesenchymal stem cells, adipose mesenchymal stem cells, umbilical cord mesenchymal stem cells and neural stem cells. The results of the network meta-analysis showed that there was no significant statistical difference in the therapeutic effect among the exosomes derived from four kinds of stem cells at different treatment time points. Although exosomes derived from bone marrow mesenchymal stem cells are the current research focus, exosomes derived from neural stem cells have the most therapeutic potential and should become the focus of future attention. CONCLUSIONS The exosomes derived from stem cells can significantly improve the motor function of TSCI rats, and the exosomes derived from neural stem cells have the most therapeutic potential. However, the lower evidence quality of animal studies limits the reliability of experimental results, emphasizing the need for more high-quality, direct comparative studies to explore the therapeutic efficacy of exosomes and the best source of stem cells.
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Affiliation(s)
- Zhizhong Shang
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Pingping Wanyan
- Department of Pathology and Pathophysiology, School of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China; The Second Hospital of Lanzhou University, Lanzhou, China
| | - Mingchuan Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Baolin Zhang
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xiaoqian Cui
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Xin Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, China; Chengren Institute of Traditional Chinese Medicine, Gansu Province, China; Department of Spine, Changzheng Hospital, Naval Medical University, Shanghai, China.
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3
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Amirbekyan M, Adhikarla V, Cheng JP, Moschonas EH, Bondi CO, Rockne RC, Kline AE, Gutova M. Neuroprotective potential of intranasally delivered L-myc immortalized human neural stem cells in female rats after a controlled cortical impact injury. Sci Rep 2023; 13:17874. [PMID: 37857701 PMCID: PMC10587115 DOI: 10.1038/s41598-023-44426-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023] Open
Abstract
Efficacious stem cell-based therapies for traumatic brain injury (TBI) depend on successful delivery, migration, and engraftment of stem cells to induce neuroprotection. L-myc expressing human neural stem cells (LMNSC008) demonstrate an inherent tropism to injury sites after intranasal (IN) administration. We hypothesize that IN delivered LMNSC008 cells migrate to primary and secondary injury sites and modulate biomarkers associated with neuroprotection and tissue regeneration. To test this hypothesis, immunocompetent adult female rats received either controlled cortical impact injury or sham surgery. LMNSC008 cells or a vehicle were administered IN on postoperative days 7, 9, 11, 13, 15, and 17. The distribution and migration of eGFP-expressing LMNSC008 cells were quantified over 1 mm-thick optically cleared (CLARITY) coronal brain sections from TBI and SHAM controls. NSC migration was observed along white matter tracts projecting toward the hippocampus and regions of TBI. ELISA and Nanostring assays revealed a shift in tissue gene expression in LMNSC008 treated rats relative to controls. LMNSC008 treatment reduced expression of genes and pathways involved in inflammatory response, microglial function, and various cytokines and receptors. Our proof-of-concept studies, although preliminary, support the rationale of using intranasal delivery of LMNSC008 cells for functional studies in preclinical models of TBI and provide support for potential translatability in TBI patients.
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Affiliation(s)
- Mari Amirbekyan
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Vikram Adhikarla
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jeffrey P Cheng
- Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eleni H Moschonas
- Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Corina O Bondi
- Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Russell C Rockne
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Anthony E Kline
- Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA.
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA.
- Critical Care Medicine, and Psychology, University of Pittsburgh, Pittsburgh, PA, USA.
- Psychology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Margarita Gutova
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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4
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Salamon I, Park Y, Miškić T, Kopić J, Matteson P, Page NF, Roque A, McAuliffe GW, Favate J, Garcia-Forn M, Shah P, Judaš M, Millonig JH, Kostović I, De Rubeis S, Hart RP, Krsnik Ž, Rasin MR. Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex. Nat Commun 2023; 14:6025. [PMID: 37758766 PMCID: PMC10533865 DOI: 10.1038/s41467-023-41730-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Abnormalities in neocortical and synaptic development are linked to neurodevelopmental disorders. However, the molecular and cellular mechanisms governing initial synapse formation in the prenatal neocortex remain poorly understood. Using polysome profiling coupled with snRNAseq on human cortical samples at various fetal phases, we identify human mRNAs, including those encoding synaptic proteins, with finely controlled translation in distinct cell populations of developing frontal neocortices. Examination of murine and human neocortex reveals that the RNA binding protein and translational regulator, CELF4, is expressed in compartments enriched in initial synaptogenesis: the marginal zone and the subplate. We also find that Celf4/CELF4-target mRNAs are encoded by risk genes for adverse neurodevelopmental outcomes translating into synaptic proteins. Surprisingly, deleting Celf4 in the forebrain disrupts the balance of subplate synapses in a sex-specific fashion. This highlights the significance of RNA binding proteins and mRNA translation in evolutionarily advanced synaptic development, potentially contributing to sex differences.
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Affiliation(s)
- Iva Salamon
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Rutgers University, School of Graduate Studies, New Brunswick, NJ, 08854, USA
| | - Yongkyu Park
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Terezija Miškić
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Janja Kopić
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Nicholas F Page
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Alfonso Roque
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Geoffrey W McAuliffe
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - John Favate
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Miloš Judaš
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - James H Millonig
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Ivica Kostović
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Željka Krsnik
- Croatian Institute for Brain Research, Center of Research Excellence for Basic, Clinical and Translational Neuroscience, University of Zagreb, School of Medicine, Zagreb, 10000, Croatia.
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
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5
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Amirbekyan M, Cheng JP, Adhikarla V, Moschonas EH, Bondi CO, Rockne RC, Kline AE, Gutova M. Neuroprotective potential of intranasally delivered L-myc immortalized human neural stem cells in female rats after a controlled cortical impact injury. RESEARCH SQUARE 2023:rs.3.rs-3242570. [PMID: 37720043 PMCID: PMC10503851 DOI: 10.21203/rs.3.rs-3242570/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Efficacious stem cell-based therapies for traumatic brain injury (TBI) depend on successful delivery, migration, and engraftment of stem cells to induce neuroprotection. L-myc expressing human neural stem cells (LMNSC008) demonstrate an inherent tropism to injury sites after intranasal (IN) administration. We hypothesize that IN delivered LMNSC008 cells migrate to primary and secondary injury sites and modulate biomarkers associated with neuroprotection and tissue regeneration. To test this, immunocompetent adult female rats received a controlled cortical impact injury (CCI) or sham surgery. LMNSC008 cells or a vehicle (VEH) were administered IN on postoperative days 7, 9, 11, 13, 15, and 17. The distribution and migration of eGFP-expressing LMNSC008 cells were quantified over 1 mm-thick optically cleared (CLARITY) coronal brain sections from TBI and SHAM controls. NSC migration was observed along white matter tracts projecting toward the hippocampus and regions of TBI. ELISA and Nanostring assays revealed a shift in tissue gene expression in LMNSC008 treated rats relative to controls. LMNSC008 treatment reduced expression of genes and pathways involved in inflammatory response, microglial function, and various cytokines and receptors. The data demonstrate a robust proof-of-concept for LMNSC008 therapy for TBI and provides a strong rationale for IN delivery for translation in TBI patients.
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Affiliation(s)
| | - Jeffrey P Cheng
- University of Pittsburgh School of Medicine Children's Hospital of Pittsburgh John G. Rangos Research Center - Room 6126
| | | | - Eleni H Moschonas
- University of Pittsburgh School of Medicine Children's Hospital of Pittsburgh John G. Rangos Research Center - Room 6126
| | - Corina O Bondi
- University of Pittsburgh School of Medicine Children's Hospital of Pittsburgh John G. Rangos Research Center - Room 6126
| | | | - Anthony E Kline
- University of Pittsburgh School of Medicine Children's Hospital of Pittsburgh John G. Rangos Research Center - Room 6126
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6
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Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550700. [PMID: 37546801 PMCID: PMC10402044 DOI: 10.1101/2023.07.26.550700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent expression in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for expression control and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA and protein expression.
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7
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Wang C, Zhang H, Fan J, Li Q, Guo R, Pan J, Liu Y, Peng J, Zhu Q, Feng Y, Wu C, Luo P, Qiu X, Shi J, Deng Y, Qi S, Liu Y. Inhibition of integrated stress response protects against lipid-induced senescence in hypothalamic neural stem cells in adamantinomatous craniopharyngioma. Neuro Oncol 2023; 25:720-732. [PMID: 36454228 PMCID: PMC10076952 DOI: 10.1093/neuonc/noac261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Adamantinomatous craniopharyngioma (ACP) is a benign tumor with malignant clinical manifestations. ACP adjacent to the hypothalamus often presents with more severe symptoms and higher incidence of hypothalamic dysfunction. However, the mechanism underlying hypothalamic dysfunction remains unclear. METHODS Immunostaining was performed to determine the nerve damage to the floor of the third ventricle (3VF) adjacent to ACP and to examine the recruitment and senescence of hypothalamic neural stem cells (htNSCs). The accumulation of lipid droplets (LDs) in htNSCs was evaluated via BODIPY staining, oil red O staining, and transmission electron microscopy. In vitro and in vivo assays were used to evaluate the effect of cystic fluid or oxidized low-density lipoprotein and that of oxytocin (OXT) on htNSC senescence and the hypothalamic function. The protein expression levels were analyzed using western blotting. RESULTS htNSCs with massive LD accumulation were recruited to the damaged 3VF adjacent to ACP. The LDs in htNSCs induced senescence and reduced neuronal differentiation; however, htNSC senescence was effectively prevented by inhibiting either CD36 or integrated stress response (ISR) signaling. Furthermore, OXT pretreatment reduced lipotoxicity via the inhibition of ISR signaling and the repair of the blood-brain barrier. CONCLUSIONS Reduced LD aggregation or ISR signaling inhibition prevented senescence in htNSCs and identified molecular pathways and potential therapeutic targets that may improve hypothalamic dysfunction in ACP patients.
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Affiliation(s)
- Chaohu Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Huarong Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jun Fan
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Qing Li
- Department of Dietetics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Rongrong Guo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jun Pan
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yawei Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Junxiang Peng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Qianchao Zhu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yiwen Feng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Chengdong Wu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Peng Luo
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xiaoyu Qiu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jin Shi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yingying Deng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yi Liu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
- Central Laboratory, Shunde Hospital, Southern Medical University, Foshan 528300, Guangdong, China
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8
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Sidhaye J, Trepte P, Sepke N, Novatchkova M, Schutzbier M, Dürnberger G, Mechtler K, Knoblich JA. Integrated transcriptome and proteome analysis reveals posttranscriptional regulation of ribosomal genes in human brain organoids. eLife 2023; 12:85135. [PMID: 36989136 PMCID: PMC10059687 DOI: 10.7554/elife.85135] [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: 11/24/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. Investigations of the transcriptome and epigenome have revealed important gene regulatory networks underlying this crucial developmental event. However, the posttranscriptional control of gene expression and protein abundance during human corticogenesis remains poorly understood. We addressed this issue by using human telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons and performed cell class and developmental stage-specific transcriptome and proteome analysis. Integrating the two datasets revealed modules of gene expression during human corticogenesis. Investigation of one such module uncovered mTOR-mediated regulation of translation of the 5'TOP element-enriched translation machinery in early progenitor cells. We show that in early progenitors partial inhibition of the translation of ribosomal genes prevents precocious translation of differentiation markers. Overall, our multiomics approach proposes novel posttranscriptional regulatory mechanisms crucial for the fidelity of cortical development.
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Affiliation(s)
- Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Philipp Trepte
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Natalie Sepke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | | | | | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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9
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The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool. Cell Rep 2023; 42:112242. [PMID: 36924490 DOI: 10.1016/j.celrep.2023.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/19/2023] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that these NPCs are transcriptionally primed to differentiate and that the primed mRNAs are associated with the translational repressor 4E-T. 4E-T also broadly associates with other NPC mRNAs encoding transcriptional regulators, and these are preferentially depleted from ribosomes, consistent with repression. By contrast, a second translational regulator, Cpeb4, associates with diverse target mRNAs that are largely ribosome associated. The 4E-T-dependent mRNA association is functionally important because 4E-T knockdown or conditional knockout derepresses proneurogenic mRNA translation and perturbs maintenance versus differentiation of early postnatal NPCs in culture and in vivo. Thus, early postnatal NPCs are primed to differentiate, and 4E-T regulates the balance between cell genesis and stem cell expansion by sequestering and repressing mRNAs encoding transcriptional regulators.
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10
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Patterning the cerebral cortex into distinct functional domains during development. Curr Opin Neurobiol 2023; 80:102698. [PMID: 36893490 DOI: 10.1016/j.conb.2023.102698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023]
Abstract
The cerebral cortex is compartmentalized into multiple regions, including the newly evolved neocortex and evolutionarily older paleocortex and archicortex. These broad cortical regions can be further subdivided into different functional domains, each with its own unique cytoarchitecture and distinct set of input and output projections to perform specific functions. While many excitatory projection neurons show region-specific gene expression profiles, the cells are derived from the seemingly uniform progenitors in the dorsal telencephalon. Much progress has been made in defining the genetic mechanisms involved in generating the morphological and functional diversity of the central nervous system. In this review, we summarize the current knowledge of mouse corticogenesis and discuss key events involved in cortical patterning during early developmental stages.
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11
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Mufteev M, Rodrigues DC, Yuki KE, Narula A, Wei W, Piekna A, Liu J, Pasceri P, Rissland OS, Wilson MD, Ellis J. Transcriptional buffering and 3'UTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530249. [PMID: 36909614 PMCID: PMC10002768 DOI: 10.1101/2023.03.01.530249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The contribution of mRNA half-life is commonly overlooked when examining changes in mRNA abundance during development. mRNA levels of some genes are regulated by transcription rate only, but others may be regulated by mRNA half-life only shifts. Furthermore, transcriptional buffering is predicted when changes in transcription rates have compensating shifts in mRNA half-life resulting in no change to steady-state levels. Likewise, transcriptional boosting should result when changes in transcription rate are accompanied by amplifying half-life shifts. During neurodevelopment there is widespread 3'UTR lengthening that could be shaped by differential shifts in the stability of existing short or long 3'UTR transcript isoforms. We measured transcription rate and mRNA half-life changes during induced human Pluripotent Stem Cell (iPSC)-derived neuronal development using RATE-seq. During transitions to progenitor and neuron stages, transcriptional buffering occurred in up to 50%, and transcriptional boosting in up to 15%, of genes with changed transcription rates. The remaining changes occurred by transcription rate only or mRNA half-life only shifts. Average mRNA half-life decreased two-fold in neurons relative to iPSCs. Short gene isoforms were more destabilized in neurons and thereby increased the average 3'UTR length. Small RNA sequencing captured an increase in microRNA copy number per cell during neurodevelopment. We propose that mRNA destabilization and 3'UTR lengthening are driven in part by an increase in microRNA load in neurons. Our findings identify mRNA stability mechanisms in human neurodevelopment that regulate gene and isoform level abundance and provide a precedent for similar post-transcriptional regulatory events as other tissues develop.
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Affiliation(s)
- Marat Mufteev
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Kyoko E Yuki
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Ashrut Narula
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Wei Wei
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Alina Piekna
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Jiajie Liu
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Peter Pasceri
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Olivia S Rissland
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- RNA Bioscience Initiative and Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Genetics & Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - James Ellis
- Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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12
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Kołosowska KA, Schratt G, Winterer J. microRNA-dependent regulation of gene expression in GABAergic interneurons. Front Cell Neurosci 2023; 17:1188574. [PMID: 37213213 PMCID: PMC10196030 DOI: 10.3389/fncel.2023.1188574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/20/2023] [Indexed: 05/23/2023] Open
Abstract
Information processing within neuronal circuits relies on their proper development and a balanced interplay between principal and local inhibitory interneurons within those circuits. Gamma-aminobutyric acid (GABA)ergic inhibitory interneurons are a remarkably heterogeneous population, comprising subclasses based on their morphological, electrophysiological, and molecular features, with differential connectivity and activity patterns. microRNA (miRNA)-dependent post-transcriptional control of gene expression represents an important regulatory mechanism for neuronal development and plasticity. miRNAs are a large group of small non-coding RNAs (21-24 nucleotides) acting as negative regulators of mRNA translation and stability. However, while miRNA-dependent gene regulation in principal neurons has been described heretofore in several studies, an understanding of the role of miRNAs in inhibitory interneurons is only beginning to emerge. Recent research demonstrated that miRNAs are differentially expressed in interneuron subclasses, are vitally important for migration, maturation, and survival of interneurons during embryonic development and are crucial for cognitive function and memory formation. In this review, we discuss recent progress in understanding miRNA-dependent regulation of gene expression in interneuron development and function. We aim to shed light onto mechanisms by which miRNAs in GABAergic interneurons contribute to sculpting neuronal circuits, and how their dysregulation may underlie the emergence of numerous neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Jochen Winterer
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
- *Correspondence: Jochen Winterer,
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13
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Jiang X, Zhou R, Zhang Y, Zhu T, Li Q, Zhang W. Interleukin-17 as a potential therapeutic target for chronic pain. Front Immunol 2022; 13:999407. [PMID: 36248896 PMCID: PMC9556763 DOI: 10.3389/fimmu.2022.999407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic pain remains to be a clinical challenge and is recognized as a major health problem with varying impacts on quality of life. Currently, the first-line therapy for chronic pain is opioids, which are often accompanied by unwanted psychoactive side effects. Thus, new and effective treatments for chronic pain are urgently needed and eagerly pursued. Inflammatory cytokines, especially interleukin-17 (IL-17), are reportedly potential therapeutic targets owing to their pivotal role in chronic pain from the neuroinflammation perspective. Recently, substantial evidence confirmed that IL-17 and IL-17 receptors (IL-17Rs) were increased in neuropathic, inflammatory, and cancer pain models. Notably, IL-17/IL-17R antibodies also reportedly relieve or cure inflammatory- and pain-related diseases. However, existing studies have reported controversial results regarding IL-17/IL-17Rs as potential therapeutic targets in diverse animal models of chronic pain. In this review, we present a summary of published studies and discuss the evidence, from basic to clinical to research, regarding the role and mechanism of action between IL-17 and diverse kinds of chronic pain in animal models and clinical patients. Furthermore, we evaluated IL-17-based therapy as a potential therapeutic strategy for inflammatory- and pain-related disease. Importantly, we also discussed clinical trials of IL-17/IL-17R targeting monoclonal antibodies. Overall, we found that IL-17 is a potential therapeutic target for chronic pain from the perspective of neuroinflammation.
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Affiliation(s)
- Xiaojuan Jiang
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Ruihao Zhou
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Yujun Zhang
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Zhu
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Li
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Qian Li, ; Weiyi Zhang,
| | - Weiyi Zhang
- Department of Anesthesiology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Qian Li, ; Weiyi Zhang,
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14
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Kedia S, Aghanoori MR, Burns KML, Subha M, Williams L, Wen P, Kopp D, Erickson SL, Harvey EM, Chen X, Hua M, Perez JU, Ishraque F, Yang G. Ubiquitination and deubiquitination of 4E-T regulate neural progenitor cell maintenance and neurogenesis by controlling P-body formation. Cell Rep 2022; 40:111070. [PMID: 35830814 DOI: 10.1016/j.celrep.2022.111070] [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: 09/13/2021] [Revised: 05/17/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
During embryogenesis, neural stem/progenitor cells (NPCs) proliferate and differentiate to form brain tissues. Here, we show that in the developing murine cerebral cortex, the balance between the NPC maintenance and differentiation is coordinated by ubiquitin signals that control the formation of processing bodies (P-bodies), cytoplasmic membraneless organelles critical for cell state regulation. We find that the deubiquitinase Otud4 and the E3 ligase Trim56 counter-regulate the ubiquitination status of a core P-body protein 4E-T to orchestrate the assembly of P-bodies in NPCs. Aberrant induction of 4E-T ubiquitination promotes P-body assembly in NPCs and causes a delay in their cell cycle progression and differentiation. In contrast, loss of 4E-T ubiquitination abrogates P-bodies and results in premature neurogenesis. Thus, our results reveal a critical role of ubiquitin-dependent regulation of P-body formation in NPC maintenance and neurogenesis during brain development.
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Affiliation(s)
- Shreeya Kedia
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Mohamad-Reza Aghanoori
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kaylan M L Burns
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Maneesha Subha
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Laura Williams
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Pengqiang Wen
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Drayden Kopp
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Sarah L Erickson
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Emily M Harvey
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Xin Chen
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michelle Hua
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jose Uriel Perez
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Fatin Ishraque
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Guang Yang
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Owerko Centre, ACHRI, Calgary, AB T2N 4N1, Canada.
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15
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Lins ÉM, Oliveira NCM, Reis O, Ferrasa A, Herai R, Muotri AR, Massirer KB, Bengtson MH. Genome-wide translation control analysis of developing human neurons. Mol Brain 2022; 15:55. [PMID: 35706057 PMCID: PMC9199153 DOI: 10.1186/s13041-022-00940-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/29/2022] [Indexed: 11/25/2022] Open
Abstract
During neuronal differentiation, neuroprogenitor cells become polarized, change shape, extend axons, and form complex dendritic trees. While growing, axons are guided by molecular cues to their final destination, where they establish synaptic connections with other neuronal cells. Several layers of regulation are integrated to control neuronal development properly. Although control of mRNA translation plays an essential role in mammalian gene expression, how it contributes temporarily to the modulation of later stages of neuronal differentiation remains poorly understood. Here, we investigated how translation control affects pathways and processes essential for neuronal maturation, using H9-derived human neuro progenitor cells differentiated into neurons as a model. Through Ribosome Profiling (Riboseq) combined with RNA sequencing (RNAseq) analysis, we found that translation control regulates the expression of critical hub genes. Fundamental synaptic vesicle secretion genes belonging to SNARE complex, Rab family members, and vesicle acidification ATPases are strongly translationally regulated in developing neurons. Translational control also participates in neuronal metabolism modulation, particularly affecting genes involved in the TCA cycle and glutamate synthesis/catabolism. Importantly, we found translation regulation of several critical genes with fundamental roles regulating actin and microtubule cytoskeleton pathways, critical to neurite generation, spine formation, axon guidance, and circuit formation. Our results show that translational control dynamically integrates important signals in neurons, regulating several aspects of its development and biology.
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Affiliation(s)
- Érico Moreto Lins
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, 13083-970, Brazil.,Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas, SP, 13083-886, Brazil
| | - Natássia Cristina Martins Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, 13083-970, Brazil.,Center of Medicinal Chemistry-CQMED, Structural Genomics Consortium-SGC, University of Campinas-UNICAMP, Campinas, SP, 13083-886, Brazil
| | - Osvaldo Reis
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, 13083-970, Brazil
| | - Adriano Ferrasa
- School of Medicine, Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, 80215-901, Brazil.,Department of Computer Science, State University of Ponta Grossa-UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Roberto Herai
- School of Medicine, Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, 80215-901, Brazil
| | - Alysson R Muotri
- Department of Pediatrics and Cellular and Molecular Medicine, School of Medicine, UC San Diego, La Jolla, CA, 92037, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering-CBMEG, University of Campinas-UNICAMP, Campinas, SP, 13083-875, Brazil.,Center of Medicinal Chemistry-CQMED, Structural Genomics Consortium-SGC, University of Campinas-UNICAMP, Campinas, SP, 13083-886, Brazil
| | - Mário Henrique Bengtson
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas-UNICAMP, Campinas, SP, 13083-970, Brazil. .,Center of Medicinal Chemistry-CQMED, Structural Genomics Consortium-SGC, University of Campinas-UNICAMP, Campinas, SP, 13083-886, Brazil.
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16
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Derkus B, Isik M, Eylem CC, Ergin I, Camci CB, Bilgin S, Elbuken C, Arslan YE, Akkulak M, Adali O, Kiran F, Okesola BO, Nemutlu E, Emregul E. Xenogenic Neural Stem Cell-Derived Extracellular Nanovesicles Modulate Human Mesenchymal Stem Cell Fate and Reconstruct Metabolomic Structure. Adv Biol (Weinh) 2022; 6:e2101317. [PMID: 35347890 DOI: 10.1002/adbi.202101317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/02/2022] [Indexed: 01/27/2023]
Abstract
Extracellular nanovesicles, particularly exosomes, can deliver their diverse bioactive biomolecular content, including miRNAs, proteins, and lipids, thus providing a context for investigating the capability of exosomes to induce stem cells toward lineage-specific cells and tissue regeneration. In this study, it is demonstrated that rat subventricular zone neural stem cell-derived exosomes (rSVZ-NSCExo) can control neural-lineage specification of human mesenchymal stem cells (hMSCs). Microarray analysis shows that the miRNA content of rSVZ-NSCExo is a faithful representation of rSVZ tissue. Through immunocytochemistry, gene expression, and multi-omics analyses, the capability to use rSVZ-NSCExo to induce hMSCs into a neuroglial or neural stem cell phenotype and genotype in a temporal and dose-dependent manner via multiple signaling pathways is demonstrated. The current study presents a new and innovative strategy to modulate hMSCs fate by harnessing the molecular content of exosomes, thus suggesting future opportunities for rSVZ-NSCExo in nerve tissue regeneration.
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Affiliation(s)
- Burak Derkus
- Stem Cell Research Lab, Department of ChemistryFaculty of Science, Ankara University, Ankara, 06560, Turkey.,Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Melis Isik
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Cemil Can Eylem
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey
| | - Irem Ergin
- Department of Surgery, Faculty of Veterinary Medicine, Ankara University, Turkey
| | - Can Berk Camci
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Sila Bilgin
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Caglar Elbuken
- UNAM-National Nanotechnology Research Center, Institute of Materials Science and Nanotechnology, Bilkent University, Ankara, 06800, Turkey.,Faculty of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Oulu, Oulu, 90014, Finland
| | - Yavuz Emre Arslan
- Regenerative Biomaterials Laboratory, Department of Bioengineering, Engineering Faculty, Canakkale Onsekiz Mart University, Canakkale, 17100, Turkey
| | - Merve Akkulak
- Department of Biological Sciences, Faculty of Science, Middle East Technical University, Ankara, 06800, Turkey
| | - Orhan Adali
- Department of Biological Sciences, Faculty of Science, Middle East Technical University, Ankara, 06800, Turkey
| | - Fadime Kiran
- Department of Biology, Faculty of Science, Ankara University, Ankara, 06560, Turkey
| | - Babatunde O Okesola
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, Faculty of Medicine, University of Liverpool, Liverpool, L7 8TX, UK
| | - Emirhan Nemutlu
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey.,Bioanalytic and Omics Laboratory, Faculty of Pharmacy, Hacettepe University, Ankara, 06530, Turkey
| | - Emel Emregul
- Interdisciplinary Research Unit for Advanced Materials (INTRAM) Department of Chemistry, Faculty of Science, Ankara University, Ankara, 06560, Turkey
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17
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Beyrampour-Basmenj H, Rahmati M, Moghamddam MP, Kalan ME, Alivand M, Aliyari-Serej Z, Nastarin P, Omrani M, Khodakarimi S, Ebrahimi-Kalan A. Association between miRNAs expression and multiple sclerosis pathogenesis: A novel therapeutic approach. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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19
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A critical period of translational control during brain development at codon resolution. Nat Struct Mol Biol 2022; 29:1277-1290. [PMID: 36482253 PMCID: PMC9758057 DOI: 10.1038/s41594-022-00882-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 10/19/2022] [Indexed: 12/13/2022]
Abstract
Translation modulates the timing and amplification of gene expression after transcription. Brain development requires uniquely complex gene expression patterns, but large-scale measurements of translation directly in the prenatal brain are lacking. We measure the reactants, synthesis and products of mRNA translation spanning mouse neocortex neurogenesis, and discover a transient window of dynamic regulation at mid-gestation. Timed translation upregulation of chromatin-binding proteins like Satb2, which is essential for neuronal subtype differentiation, restricts protein expression in neuronal lineages despite broad transcriptional priming in progenitors. In contrast, translation downregulation of ribosomal proteins sharply decreases ribosome biogenesis, coinciding with a major shift in protein synthesis dynamics at mid-gestation. Changing activity of eIF4EBP1, a direct inhibitor of ribosome biogenesis, is concurrent with ribosome downregulation and affects neurogenesis of the Satb2 lineage. Thus, the molecular logic of brain development includes the refinement of transcriptional programs by translation. Modeling of the developmental neocortex translatome is provided as an open-source searchable resource at https://shiny.mdc-berlin.de/cortexomics .
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20
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Salamon I, Palsule G, Luo X, Roque A, Tucai S, Khosla I, Volk N, Liu W, Cui H, Pozzo VD, Zalamea P, Jiao X, D'Arcangelo G, Hart RP, Rasin MR, Kiledjian M. mRNA-Decapping Associated DcpS Enzyme Controls Critical Steps of Neuronal Development. Cereb Cortex 2021; 32:1494-1507. [PMID: 34467373 DOI: 10.1093/cercor/bhab302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Homozygous mutations in the gene encoding the scavenger mRNA-decapping enzyme, DcpS, have been shown to underlie developmental delay and intellectual disability. Intellectual disability is associated with both abnormal neocortical development and mRNA metabolism. However, the role of DcpS and its scavenger decapping activity in neuronal development is unknown. Here, we show that human neurons derived from patients with a DcpS mutation have compromised differentiation and neurite outgrowth. Moreover, in the developing mouse neocortex, DcpS is required for the radial migration, polarity, neurite outgrowth, and identity of developing glutamatergic neurons. Collectively, these findings demonstrate that the scavenger mRNA decapping activity contributes to multiple pivotal roles in neural development and further corroborate that mRNA metabolism and neocortical pathologies are associated with intellectual disability.
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Affiliation(s)
- Iva Salamon
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Geeta Palsule
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaobing Luo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alfonso Roque
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shawn Tucai
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ishan Khosla
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Nicole Volk
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wendy Liu
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huijuan Cui
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Valentina Dal Pozzo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Petronio Zalamea
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gabriella D'Arcangelo
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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21
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Park Y, Page N, Salamon I, Li D, Rasin MR. Making sense of mRNA landscapes: Translation control in neurodevelopment. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1674. [PMID: 34137510 DOI: 10.1002/wrna.1674] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/27/2022]
Abstract
Like all other parts of the central nervous system, the mammalian neocortex undergoes temporally ordered set of developmental events, including proliferation, differentiation, migration, cellular identity, synaptogenesis, connectivity formation, and plasticity changes. These neurodevelopmental mechanisms have been characterized by studies focused on transcriptional control. Recent findings, however, have shown that the spatiotemporal regulation of post-transcriptional steps like alternative splicing, mRNA traffic/localization, mRNA stability/decay, and finally repression/derepression of protein synthesis (mRNA translation) have become just as central to the neurodevelopment as transcriptional control. A number of dynamic players act post-transcriptionally in the neocortex to regulate these steps, as RNA binding proteins (RBPs), ribosomal proteins (RPs), long non-coding RNAs, and/or microRNA. Remarkably, mutations in these post-transcriptional regulators have been associated with neurodevelopmental, neurodegenerative, inherited, or often co-morbid disorders, such as microcephaly, autism, epilepsy, intellectual disability, white matter diseases, Rett-syndrome like phenotype, spinocerebellar ataxia, and amyotrophic lateral sclerosis. Here, we focus on the current state, advanced methodologies and pitfalls of this exciting and upcoming field of RNA metabolism with vast potential in understanding fundamental neurodevelopmental processes and pathologies. This article is categorized under: Translation > Translation Regulation RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yongkyu Park
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Nicholas Page
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Iva Salamon
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | | | - Mladen-Roko Rasin
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
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22
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Martins M, Galfrè S, Terrigno M, Pandolfini L, Appolloni I, Dunville K, Marranci A, Rizzo M, Mercatanti A, Poliseno L, Morandin F, Pietrosanto M, Helmer-Citterich M, Malatesta P, Vignali R, Cremisi F. A eutherian-specific microRNA controls the translation of Satb2 in a model of cortical differentiation. Stem Cell Reports 2021; 16:1496-1509. [PMID: 34019815 PMCID: PMC8190598 DOI: 10.1016/j.stemcr.2021.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 10/25/2022] Open
Abstract
Cerebral cortical development is controlled by key transcription factors that specify the neuronal identities in the different layers. The mechanisms controlling their expression in distinct cells are only partially known. We investigated the expression and stability of Tbr1, Bcl11b, Fezf2, Satb2, and Cux1 mRNAs in single developing mouse cortical cells. We observe that Satb2 mRNA appears much earlier than its protein and in a set of cells broader than expected, suggesting an initial inhibition of its translation, subsequently released during development. Mechanistically, Satb2 3'UTR modulates protein translation of GFP reporters during mouse corticogenesis. We select miR-541, a eutherian-specific miRNA, and miR-92a/b as the best candidates responsible for SATB2 inhibition, being strongly expressed in early and reduced in late progenitor cells. Their inactivation triggers robust and premature SATB2 translation in both mouse and human cortical cells. Our findings indicate RNA interference as a major mechanism in timing cortical cell identities.
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Affiliation(s)
- Manuella Martins
- Scuola Normale, Pisa, Italy; Istituto di Biofisica CNR, Pisa, Italy
| | - Silvia Galfrè
- Scuola Normale, Pisa, Italy; Dipartimento di Biologia, Università Roma Tor Vergata, Roma, Italy
| | - Marco Terrigno
- Scuola Normale, Pisa, Italy; Istituto di Biofisica CNR, Pisa, Italy
| | | | - Irene Appolloni
- Dipartimento di Medicina Sperimentale, Università di Genova, Genova, Italy; Ospedale Policlinico San Martino, IRCCS per l'Oncologia, Genova, Italy
| | - Keagan Dunville
- Scuola Normale, Pisa, Italy; Istituto di Biofisica CNR, Pisa, Italy
| | - Andrea Marranci
- Istituto di Fisiologia Clinica CNR, Pisa, Italy; Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
| | | | | | - Laura Poliseno
- Istituto di Fisiologia Clinica CNR, Pisa, Italy; Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
| | - Francesco Morandin
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | | | | | - Paolo Malatesta
- Dipartimento di Medicina Sperimentale, Università di Genova, Genova, Italy; Ospedale Policlinico San Martino, IRCCS per l'Oncologia, Genova, Italy
| | - Robert Vignali
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Federico Cremisi
- Scuola Normale, Pisa, Italy; Istituto di Biofisica CNR, Pisa, Italy.
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23
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Gutova M, Cheng JP, Adhikarla V, Tsaturyan L, Barish ME, Rockne RC, Moschonas EH, Bondi CO, Kline AE. Intranasally Administered L-Myc-Immortalized Human Neural Stem Cells Migrate to Primary and Distal Sites of Damage after Cortical Impact and Enhance Spatial Learning. Stem Cells Int 2021; 2021:5549381. [PMID: 34122556 PMCID: PMC8166475 DOI: 10.1155/2021/5549381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
As the success of stem cell-based therapies is contingent on efficient cell delivery to damaged areas, neural stem cells (NSCs) have promising therapeutic potential because they inherently migrate to sites of central nervous system (CNS) damage. To explore the possibility of NSC-based therapy after traumatic brain injury (TBI), isoflurane-anesthetized adult male rats received a controlled cortical impact (CCI) of moderate severity (2.8 mm deformation at 4 m/s) or sham injury (i.e., no cortical impact). Beginning 1-week post-injury, the rats were immunosuppressed and 1 × 106 human NSCs (LM-NS008.GFP.fLuc) or vehicle (VEH) (2% human serum albumen) were administered intranasally (IN) on post-operative days 7, 9, 11, 13, 15, and 17. To evaluate the spatial distributions of the LM-NSC008 cells, half of the rats were euthanized on day 25, one day after completion of the cognitive task, and the other half were euthanized on day 46. 1 mm thick brain sections were optically cleared (CLARITY), and volumes were imaged by confocal microscopy. In addition, LM-NSC008 cell migration to the TBI site by immunohistochemistry for human-specific Nestin was observed at day 39. Acquisition of spatial learning was assessed in a well-established Morris water maze task on six successive days beginning on post-injury day 18. IN administration of LM-NSC008 cells after TBI (TBI + NSC) significantly facilitated spatial learning relative to TBI + VEH rats (p < 0.05) and had no effect on sham + NSC rats. Overall, these data indicate that IN-administered LM-NSC008 cells migrate to sites of TBI damage and that their presence correlates with cognitive improvement. Future studies will expand on these preliminary findings by evaluating other LM-NSC008 cell dosing paradigms and evaluating mechanisms by which LM-NSC008 cells contribute to cognitive recovery.
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Affiliation(s)
- Margarita Gutova
- Department of Developmental & Stem Cell Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jeffrey P. Cheng
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vikram Adhikarla
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lusine Tsaturyan
- Department of Developmental & Stem Cell Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Michael E. Barish
- Department of Developmental & Stem Cell Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Russell C. Rockne
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Eleni H. Moschonas
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Corina O. Bondi
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anthony E. Kline
- Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
- Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Psychology, University of Pittsburgh, Pittsburgh, PA, USA
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24
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Oproescu AM, Han S, Schuurmans C. New Insights Into the Intricacies of Proneural Gene Regulation in the Embryonic and Adult Cerebral Cortex. Front Mol Neurosci 2021; 14:642016. [PMID: 33658912 PMCID: PMC7917194 DOI: 10.3389/fnmol.2021.642016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Historically, the mammalian brain was thought to lack stem cells as no new neurons were found to be made in adulthood. That dogma changed ∼25 years ago with the identification of neural stem cells (NSCs) in the adult rodent forebrain. However, unlike rapidly self-renewing mature tissues (e.g., blood, intestinal crypts, skin), the majority of adult NSCs are quiescent, and those that become 'activated' are restricted to a few neurogenic zones that repopulate specific brain regions. Conversely, embryonic NSCs are actively proliferating and neurogenic. Investigations into the molecular control of the quiescence-to-proliferation-to-differentiation continuum in the embryonic and adult brain have identified proneural genes encoding basic-helix-loop-helix (bHLH) transcription factors (TFs) as critical regulators. These bHLH TFs initiate genetic programs that remove NSCs from quiescence and drive daughter neural progenitor cells (NPCs) to differentiate into specific neural cell subtypes, thereby contributing to the enormous cellular diversity of the adult brain. However, new insights have revealed that proneural gene activities are context-dependent and tightly regulated. Here we review how proneural bHLH TFs are regulated, with a focus on the murine cerebral cortex, drawing parallels where appropriate to other organisms and neural tissues. We discuss upstream regulatory events, post-translational modifications (phosphorylation, ubiquitinylation), protein-protein interactions, epigenetic and metabolic mechanisms that govern bHLH TF expression, stability, localization, and consequent transactivation of downstream target genes. These tight regulatory controls help to explain paradoxical findings of changes to bHLH activity in different cellular contexts.
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Affiliation(s)
- Ana-Maria Oproescu
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sisu Han
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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25
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Hoye ML, Silver DL. Decoding mixed messages in the developing cortex: translational regulation of neural progenitor fate. Curr Opin Neurobiol 2021; 66:93-102. [PMID: 33130411 PMCID: PMC8058166 DOI: 10.1016/j.conb.2020.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/10/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022]
Abstract
Regulation of stem cell fate decisions is elemental to faithful development, homeostasis, and organismal fitness. Emerging data demonstrate pluripotent stem cells exhibit a vast transcriptional landscape, which is refined as cells differentiate. In the developing neocortex, transcriptional priming of neural progenitors, coupled with post-transcriptional control, is critical for defining cell fates of projection neurons. In particular, radial glial progenitors exhibit dynamic post-transcriptional regulation, including subcellular mRNA localization, RNA decay, and translation. These processes involve both cis-regulatory and trans-regulatory factors, many of which are implicated in neurodevelopmental disease. This review highlights emerging post-transcriptional mechanisms which govern cortical development, with a particular focus on translational control of neuronal fates, including those relevant for disease.
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Affiliation(s)
- Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, United States; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, United States; Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, United States.
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26
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Extrinsic Regulators of mRNA Translation in Developing Brain: Story of WNTs. Cells 2021; 10:cells10020253. [PMID: 33525513 PMCID: PMC7911671 DOI: 10.3390/cells10020253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
Extrinsic molecules such as morphogens can regulate timed mRNA translation events in developing neurons. In particular, Wingless-type MMTV integration site family, member 3 (Wnt3), was shown to regulate the translation of Foxp2 mRNA encoding a Forkhead transcription factor P2 in the neocortex. However, the Wnt receptor that possibly mediates these translation events remains unknown. Here, we report Frizzled member 7 (Fzd7) as the Wnt3 receptor that lays downstream in Wnt3-regulated mRNA translation. Fzd7 proteins co-localize with Wnt3 ligands in developing neocortices. In addition, the Fzd7 proteins overlap in layer-specific neuronal subpopulations expressing different transcription factors, Foxp1 and Foxp2. When Fzd7 was silenced, we found decreased Foxp2 protein expression and increased Foxp1 protein expression, respectively. The Fzd7 silencing also disrupted the migration of neocortical glutamatergic neurons. In contrast, Fzd7 overexpression reversed the pattern of migratory defects and Foxp protein expression that we found in the Fzd7 silencing. We further discovered that Fzd7 is required for Wnt3-induced Foxp2 mRNA translation. Surprisingly, we also determined that the Fzd7 suppression of Foxp1 protein expression is not Wnt3 dependent. In conclusion, it is exhibited that the interaction between Wnt3 and Fzd7 regulates neuronal identity and the Fzd7 receptor functions as a downstream factor in ligand Wnt3 signaling for mRNA translation. In particular, the Wnt3-Fzd7 signaling axis determines the deep layer Foxp2-expressing neurons of developing neocortices. Our findings also suggest that Fzd7 controls the balance of the expression for Foxp transcription factors in developing neocortical neurons. These discoveries are presented in our manuscript within a larger framework of this review on the role of extrinsic factors in regulating mRNA translation.
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27
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Sjöqvist M, Antfolk D, Suarez-Rodriguez F, Sahlgren C. From structural resilience to cell specification - Intermediate filaments as regulators of cell fate. FASEB J 2020; 35:e21182. [PMID: 33205514 PMCID: PMC7839487 DOI: 10.1096/fj.202001627r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022]
Abstract
During the last decades intermediate filaments (IFs) have emerged as important regulators of cellular signaling events, ascribing IFs with functions beyond the structural support they provide. The organ and developmental stage‐specific expression of IFs regulate cell differentiation within developing or remodeling tissues. Lack of IFs causes perturbed stem cell differentiation in vasculature, intestine, nervous system, and mammary gland, in transgenic mouse models. The aberrant cell fate decisions are caused by deregulation of different stem cell signaling pathways, such as Notch, Wnt, YAP/TAZ, and TGFβ. Mutations in genes coding for IFs cause an array of different diseases, many related to stem cell dysfunction, but the molecular mechanisms remain unresolved. Here, we provide a comprehensive overview of how IFs interact with and regulate the activity, localization and function of different signaling proteins in stem cells, and how the assembly state and PTM profile of IFs may affect these processes. Identifying when, where and how IFs and cell signaling congregate, will expand our understanding of IF‐linked stem cell dysfunction during development and disease.
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Affiliation(s)
- Marika Sjöqvist
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.,Turku Bioscience, Åbo Akademi University and University of Turku, Turku, Finland
| | - Daniel Antfolk
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.,Turku Bioscience, Åbo Akademi University and University of Turku, Turku, Finland
| | - Freddy Suarez-Rodriguez
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.,Turku Bioscience, Åbo Akademi University and University of Turku, Turku, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.,Turku Bioscience, Åbo Akademi University and University of Turku, Turku, Finland.,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
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28
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Oliveira NCM, Lins ÉM, Massirer KB, Bengtson MH. Translational Control during Mammalian Neocortex Development and Postembryonic Neuronal Function. Semin Cell Dev Biol 2020; 114:36-46. [PMID: 33020045 DOI: 10.1016/j.semcdb.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022]
Abstract
The control of mRNA translation has key roles in the regulation of gene expression and biological processes such as mammalian cellular differentiation and identity. Methodological advances in the last decade have resulted in considerable progress towards understanding how translational control contributes to the regulation of diverse biological phenomena. In this review, we discuss recent findings in the involvement of translational control in the mammalian neocortex development and neuronal biology. We focus on regulatory mechanisms that modulate translational efficiency during neural stem cells self-renewal and differentiation, as well as in neuronal-related processes such as synapse, plasticity, and memory.
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Affiliation(s)
- Natássia Cristina Martins Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Érico Moreto Lins
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; PhD Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas, SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Mário Henrique Bengtson
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil.
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29
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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30
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The roles of MicroRNAs in neural regenerative medicine. Exp Neurol 2020; 332:113394. [DOI: 10.1016/j.expneurol.2020.113394] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/15/2020] [Accepted: 06/25/2020] [Indexed: 12/22/2022]
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31
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Channakkar AS, Singh T, Pattnaik B, Gupta K, Seth P, Adlakha YK. MiRNA-137-mediated modulation of mitochondrial dynamics regulates human neural stem cell fate. Stem Cells 2020; 38:683-697. [PMID: 32012382 PMCID: PMC7217206 DOI: 10.1002/stem.3155] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/23/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022]
Abstract
The role of miRNAs in determining human neural stem cell (NSC) fate remains elusive despite their high expression in the developing nervous system. In this study, we investigate the role of miR‐137, a brain‐enriched miRNA, in determining the fate of human induced pluripotent stem cells‐derived NSCs (hiNSCs). We show that ectopic expression of miR‐137 in hiNSCs reduces proliferation and accelerates neuronal differentiation and migration. TargetScan and MicroT‐CDS predict myocyte enhancer factor‐2A (MEF2A), a transcription factor that regulates peroxisome proliferator‐activated receptor‐gamma coactivator (PGC1α) transcription, as a target of miR‐137. Using a reporter assay, we validate MEF2A as a downstream target of miR‐137. Our results indicate that reduced levels of MEF2A reduce the transcription of PGC1α, which in turn impacts mitochondrial dynamics. Notably, miR‐137 accelerates mitochondrial biogenesis in a PGC1α independent manner by upregulating nuclear factor erythroid 2 (NFE2)‐related factor 2 (NRF2) and transcription factor A of mitochondria (TFAM). In addition, miR‐137 modulates mitochondrial dynamics by inducing mitochondrial fusion and fission events, resulting in increased mitochondrial content and activation of oxidative phosphorylation (OXPHOS) and oxygen consumption rate. Pluripotency transcription factors OCT4 and SOX2 are known to have binding sites in the promoter region of miR‐137 gene. Ectopic expression of miR‐137 elevates the expression levels of OCT4 and SOX2 in hiNSCs which establishes a feed‐forward self‐regulatory loop between miR‐137 and OCT4/SOX2. Our study provides novel molecular insights into NSC fate determination by miR‐137.
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Affiliation(s)
- Asha S Channakkar
- Molecular and Cellular Neuroscience, National Brain Research Centre, Manesar, India
| | - Tanya Singh
- Molecular and Cellular Neuroscience, National Brain Research Centre, Manesar, India.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Bijay Pattnaik
- Centre of Excellence in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Karnika Gupta
- Molecular and Cellular Neuroscience, National Brain Research Centre, Manesar, India
| | - Pankaj Seth
- Molecular and Cellular Neuroscience, National Brain Research Centre, Manesar, India
| | - Yogita K Adlakha
- Molecular and Cellular Neuroscience, National Brain Research Centre, Manesar, India
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