1
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Dominguez D, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. Regulation by the RNA-binding protein Unkempt at its effector interface. Nat Commun 2024; 15:3159. [PMID: 38605040 PMCID: PMC11009413 DOI: 10.1038/s41467-024-47449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here, we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for the reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
| | - David J Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 5 Cutcombe Road, SE5 9RX, London, UK
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076, Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA.
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA, 92521, USA.
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2
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Yun HM, Hyun B, Song X, Hyun S. Piwi expressed in Drosophila adipose tissues regulates systemic IGF signaling and growth via IGF-binding protein. Biochem Biophys Res Commun 2024; 695:149495. [PMID: 38211532 DOI: 10.1016/j.bbrc.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
Piwi and its partner, Piwi-interacting RNA (piRNA), are pivotal in suppressing the harmful effects of transposable elements (TEs) linked to genomic insertional mutagenesis. While primarily active in Drosophila's adult gonadal tissues, causing sterility in its absence, Piwi's role in post-embryonic development remains unclear. Our study reveals Piwi's functional presence in the larval fat body, where it governs developmental growth through systemic insulin/insulin-like growth factor (IGF) signaling (IIS). Piwi knockdown in the fat body resulted in dysregulated TE expression, reduced developmental rate and body growth, and diminished systemic IIS activity. Notably, Piwi knockdown increased Imaginal Morphogenic Protein Late 2 (Imp-L2) expression, akin to insulin-like growth factor-binding protein 7 (IGFBP7), reducing systemic IIS and inhibiting body growth. This unveils a novel role for Piwi in larval adipose tissues, emphasizing its importance in regulating systemic IIS and overall organismal growth.
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Affiliation(s)
- Hyun Myoung Yun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Bom Hyun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Xinge Song
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seogang Hyun
- Department of Life Science, Chung-Ang University, Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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3
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Yin C, Morita T, Parrish JZ. A cell atlas of the larval Aedes aegypti ventral nerve cord. Neural Dev 2024; 19:2. [PMID: 38297398 PMCID: PMC10829479 DOI: 10.1186/s13064-023-00178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024] Open
Abstract
Mosquito-borne diseases account for nearly 1 million human deaths annually, yet we have a limited understanding of developmental events that influence host-seeking behavior and pathogen transmission in mosquitoes. Mosquito-borne pathogens are transmitted during blood meals, hence adult mosquito behavior and physiology have been intensely studied. However, events during larval development shape adult traits, larvae respond to many of the same sensory cues as adults, and larvae are susceptible to infection by many of the same disease-causing agents as adults. Hence, a better understanding of larval physiology will directly inform our understanding of physiological processes in adults. Here, we use single cell RNA sequencing (scRNA-seq) to provide a comprehensive view of cellular composition in the Aedes aegypti larval ventral nerve cord (VNC), a central hub of sensory inputs and motor outputs which additionally controls multiple aspects of larval physiology. We identify more than 35 VNC cell types defined in part by neurotransmitter and neuropeptide expression. We also explore diversity among monoaminergic and peptidergic neurons that likely control key elements of larval physiology and developmental timing, and identify neuroblasts and immature neurons, providing a view of neuronal differentiation in the VNC. Finally, we find that larval cell composition, number, and position are preserved in the adult abdominal VNC, suggesting studies of larval VNC form and function will likely directly inform our understanding adult mosquito physiology. Altogether, these studies provide a framework for targeted analysis of VNC development and neuronal function in Aedes aegypti larvae.
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Affiliation(s)
- Chang Yin
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Takeshi Morita
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, New York, NY, 10065, USA
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.
- Division of Education, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA.
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4
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Shah K, He S, Turner DJ, Corbo J, Rebbani K, Bateman JM, Cheloufi S, Igreja C, Valkov E, Murn J. A paradigm for regulation at the effector interface with RNA-binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558714. [PMID: 37790431 PMCID: PMC10542489 DOI: 10.1101/2023.09.20.558714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.
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Affiliation(s)
- Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- These authors contributed equally
| | - David J. Turner
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- These authors contributed equally
| | - Joshua Corbo
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, U.S.A
| | - Khadija Rebbani
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Joseph M. Bateman
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, 5 Cutcombe Road, London, SE5 9RX, U.K
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA 92521, U.S.A
| | - Cátia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, D-72076 Tübingen, Germany
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, U.S.A
- Center for RNA Biology and Medicine, 900 University Ave, Riverside, CA 92521, U.S.A
- Lead contact
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5
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Geben LC, Brockman AA, Chalkley MBL, Sweet SR, Gallagher JE, Scheuing AL, Simerly RB, Ess KC, Irish JM, Ihrie RA. Dephosphorylation of 4EBP1/2 Induces Prenatal Neural Stem Cell Quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528513. [PMID: 36824760 PMCID: PMC9948964 DOI: 10.1101/2023.02.14.528513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A limiting factor in the regenerative capacity of the adult brain is the abundance and proliferative ability of neural stem cells (NSCs). Adult NSCs are derived from a subpopulation of embryonic NSCs that temporarily enter quiescence during mid-gestation and remain quiescent until postnatal reactivation. Here we present evidence that the mechanistic/mammalian target of rapamycin (mTOR) pathway regulates quiescence entry in embryonic NSCs of the developing forebrain. Throughout embryogenesis, two downstream effectors of mTOR, p-4EBP1/2 T37/46 and p-S6 S240/244, were mutually exclusive in NSCs, rarely occurring in the same cell. While 4EBP1/2 was phosphorylated in stem cells undergoing mitosis at the ventricular surface, S6 was phosphorylated in more differentiated cells migrating away from the ventricle. Phosphorylation of 4EBP1/2, but not S6, was responsive to quiescence induction in cultured embryonic NSCs. Further, inhibition of p-4EBP1/2, but not p-S6, was sufficient to induce quiescence. Collectively, this work offers new insight into the regulation of quiescence entry in embryonic NSCs and, thereby, correct patterning of the adult brain. These data suggest unique biological functions of specific posttranslational modifications and indicate that the preferential inhibition of such modifications may be a useful therapeutic approach in neurodevelopmental diseases where NSC numbers, proliferation, and differentiation are altered.
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Affiliation(s)
- Laura C. Geben
- Program in Pharmacology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Asa A. Brockman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | | | - Serena R. Sweet
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Julia E. Gallagher
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Alexandra L. Scheuing
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Richard B. Simerly
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
| | - Kevin C. Ess
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Rebecca A. Ihrie
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN 37235, USA
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6
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Baskaran P, Mihaylov SR, Vinsland E, Shah K, Granat L, Ultanir SK, Tee AR, Murn J, Bateman JM. Phosphorylation of the novel mTOR substrate Unkempt regulates cellular morphogenesis. J Biol Chem 2023; 299:102788. [PMID: 36509146 PMCID: PMC9852543 DOI: 10.1016/j.jbc.2022.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) is a protein kinase that integrates multiple inputs to regulate anabolic cellular processes. For example, mTOR complex 1 (mTORC1) has key functions in growth control, autophagy, and metabolism. However, much less is known about the signaling components that act downstream of mTORC1 to regulate cellular morphogenesis. Here, we show that the RNA-binding protein Unkempt, a key regulator of cellular morphogenesis, is a novel substrate of mTORC1. We show that Unkempt phosphorylation is regulated by nutrient levels and growth factors via mTORC1. To analyze Unkempt phosphorylation, we immunoprecipitated Unkempt from cells in the presence or the absence of the mTORC1 inhibitor rapamycin and used mass spectrometry to identify mTORC1-dependent phosphorylated residues. This analysis showed that mTORC1-dependent phosphorylation is concentrated in a serine-rich intrinsically disordered region in the C-terminal half of Unkempt. We also found that Unkempt physically interacts with and is directly phosphorylated by mTORC1 through binding to the regulatory-associated protein of mTOR, Raptor. Furthermore, analysis in the developing brain of mice lacking TSC1 expression showed that phosphorylation of Unkempt is mTORC1 dependent in vivo. Finally, mutation analysis of key serine/threonine residues in the serine-rich region indicates that phosphorylation inhibits the ability of Unkempt to induce a bipolar morphology. Phosphorylation within this serine-rich region thus profoundly affects the ability of Unkempt to regulate cellular morphogenesis. Taken together, our findings reveal a novel molecular link between mTORC1 signaling and cellular morphogenesis.
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Affiliation(s)
- Pranetha Baskaran
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Simeon R Mihaylov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Elin Vinsland
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK; Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Kriti Shah
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Lucy Granat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, London, UK
| | - Andrew R Tee
- Cancer and Genetics Building, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park Way, Cardiff, UK
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, California, USA.
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
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7
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Zinc in Cognitive Impairment and Aging. Biomolecules 2022; 12:biom12071000. [PMID: 35883555 PMCID: PMC9312494 DOI: 10.3390/biom12071000] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
Zinc, an essential micronutrient for life, was first discovered in 1869 and later found to be indispensable for the normal development of plants and for the normal growth of rats and birds. Zinc plays an important role in many physiological and pathological processes in normal mammalian brain development, especially in the development of the central nervous system. Zinc deficiency can lead to neurodegenerative diseases, mental abnormalities, sleep disorders, tumors, vascular diseases, and other pathological conditions, which can cause cognitive impairment and premature aging. This study aimed to review the important effects of zinc and zinc-associated proteins in cognitive impairment and aging, to reveal its molecular mechanism, and to highlight potential interventions for zinc-associated aging and cognitive impairments.
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8
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Serra I, Stravs A, Osório C, Oyaga MR, Schonewille M, Tudorache C, Badura A. Tsc1 Haploinsufficiency Leads to Pax2 Dysregulation in the Developing Murine Cerebellum. Front Mol Neurosci 2022; 15:831687. [PMID: 35645731 PMCID: PMC9137405 DOI: 10.3389/fnmol.2022.831687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/04/2022] [Indexed: 12/03/2022] Open
Abstract
Tuberous sclerosis complex 1 (TSC1) is a tumor suppressor that promotes the inhibition of mechanistic target of rapamycin (mTOR) pathway, and mutations in TSC1 lead to a rare complex disorder of the same name. Despite phenotype heterogeneity, up to 50% of TSC patients present with autism spectrum disorder (ASD). Consequently, TSC models are often used to probe molecular and behavioral mechanisms of ASD development. Amongst the different brain areas proposed to play a role in the development of ASD, the cerebellum is commonly reported to be altered, and cerebellar-specific deletion of Tsc1 in mice is sufficient to induce ASD-like phenotypes. However, despite these functional changes, whether Tsc1 haploinsufficiency affects cerebellar development is still largely unknown. Given that the mTOR pathway is a master regulator of cell replication and migration, we hypothesized that dysregulation of this pathway would also disrupt the development of cell populations during critical periods of cerebellar development. Here, we used a mouse model of TSC to investigate gene and protein expression during embryonic and early postnatal periods of cerebellar development. We found that, at E18 and P7, mRNA levels of the cerebellar inhibitory interneuron marker paired box gene 2 (Pax2) were dysregulated. This dysregulation was accompanied by changes in the expression of mTOR pathway-related genes and downstream phosphorylation of S6. Differential gene correlation analysis revealed dynamic changes in correlated gene pairs across development, with an overall loss of correlation between mTOR- and cerebellar-related genes in Tsc1 mutants compared to controls. We corroborated the genetic findings by characterizing the mTOR pathway and cerebellar development on protein and cellular levels with Western blot and immunohistochemistry. We found that Pax2-expressing cells were largely unchanged at E18 and P1, while at P7, their number was increased and maturation into parvalbumin-expressing cells delayed. Our findings indicate that, in mice, Tsc1 haploinsufficiency leads to altered cerebellar development and that cerebellar interneuron precursors are particularly susceptible to mTOR pathway dysregulation.
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Affiliation(s)
- Ines Serra
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | - Ana Stravs
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Catarina Osório
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | - Maria Roa Oyaga
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | | | | | - Aleksandra Badura
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- *Correspondence: Aleksandra Badura,
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9
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Chen X, Bai X, Liu H, Zhao B, Yan Z, Hou Y, Chu Q. Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken. Front Genet 2022; 13:830393. [PMID: 35391799 PMCID: PMC8980806 DOI: 10.3389/fgene.2022.830393] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3, NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.
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Affiliation(s)
- Xia Chen
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xue Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Binbin Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yali Hou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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10
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Girodengo M, Ultanir SK, Bateman JM. Mechanistic target of rapamycin signaling in human nervous system development and disease. Front Mol Neurosci 2022; 15:1005631. [PMID: 36226315 PMCID: PMC9549271 DOI: 10.3389/fnmol.2022.1005631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that regulates fundamental cellular processes including growth control, autophagy and metabolism. mTOR has key functions in nervous system development and mis-regulation of mTOR signaling causes aberrant neurodevelopment and neurological diseases, collectively called mTORopathies. In this mini review we discuss recent studies that have deepened our understanding of the key roles of the mTOR pathway in human nervous system development and disease. Recent advances in single-cell transcriptomics have been exploited to reveal specific roles for mTOR signaling in human cortical development that may have contributed to the evolutionary divergence from our primate ancestors. Cerebral organoid technology has been utilized to show that mTOR signaling is active in and regulates outer radial glial cells (RGCs), a population of neural stem cells that distinguish the human developing cortex. mTOR signaling has a well-established role in hamartoma syndromes such as tuberous sclerosis complex (TSC) and other mTORopathies. New ultra-sensitive techniques for identification of somatic mTOR pathway mutations have shed light on the neurodevelopmental origin and phenotypic heterogeneity seen in mTORopathy patients. These emerging studies suggest that mTOR signaling may facilitate developmental processes specific to human cortical development but also, when mis-regulated, cause cortical malformations and neurological disease.
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Affiliation(s)
- Marie Girodengo
- Kinases and Brain Development Lab, The Francis Crick Institute, London, United Kingdom.,King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
| | - Joseph M Bateman
- King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
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11
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Wang G, Yang Y, Yi D, Yuan L, Yin PH, Ke X, Jun-Jie W, Tao MF. Eudragit S100 prepared pH-responsive liposomes-loaded betulinic acid against colorectal cancer in vitro and in vivo. J Liposome Res 2021; 32:250-264. [PMID: 34895013 DOI: 10.1080/08982104.2021.1999974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This study aimed to develop polymer Eudragit S100 for preparing pH-responsive liposomes-loaded betulinic acid (pH-BA-LP) to improve the therapeutic index of chemotherapy for colorectal cancer. BA-loaded liposomes were coated with Eudragit S100 by a thin film dispersion and easily scalable pH-driven method. The prepared liposomes were evaluated for size, surface morphology, entrapment efficiency, stability, in vitro drug release, and antitumor activity. In particular, pH-BA-LP showed advantages such as lower size (<100 nm), encapsulation efficiency of 90%, high stability, and stably cumulative release. By detecting the antitumor effects of pH-BA-LP in vivo, it showed that the tumor proliferation and cell migration were significantly inhibited in colorectal cancer. The pH-BA-LP also inhibited tumor growth via the regulation of Akt/TLR-mediated signalling and significantly down-regulated the expression of NFAT1 and NFAT4 proteins. It was found that pH-BA-LP can increase NK cells and CD3+ cells in tumor tissues, and the proportion of CD8+ cells in CD3+ cells was also increased, which proved that pH-BA-LP can play an antitumor effect by enhancing the autoimmunity level in tumor-bearing mice. The positive infiltration rates of CD8 and CD68 were increased and CD163 was relatively decreased by using pH-BA-LP, which proved that pH-BA-LP can regulate the immune infiltration levels in tumor-bearing mice. Therefore, the present work provides an effective method to prepare pH-responsive polymer-coated liposomes for colonic delivery with biologically active compounds.
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Affiliation(s)
- Gang Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Yu Yang
- Jiangsu University School of Pharmacy, Zhenjiang City, China
| | - Du Yi
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Lu Yuan
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Pei-Hao Yin
- Interventional Cancer Institute of Chinese Integrative Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Ke
- Interventional Cancer Institute of Chinese Integrative Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wang Jun-Jie
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Min-Fang Tao
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
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12
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Vinsland E, Baskaran P, Mihaylov SR, Hobbs C, Wood H, Bouybayoune I, Shah K, Houart C, Tee AR, Murn J, Fernandes C, Bateman JM. The zinc finger/RING domain protein Unkempt regulates cognitive flexibility. Sci Rep 2021; 11:16299. [PMID: 34381067 PMCID: PMC8357790 DOI: 10.1038/s41598-021-95286-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Correct orchestration of nervous system development is a profound challenge that involves coordination of complex molecular and cellular processes. Mechanistic target of rapamycin (mTOR) signaling is a key regulator of nervous system development and synaptic function. The mTOR kinase is a hub for sensing inputs including growth factor signaling, nutrients and energy levels. Activation of mTOR signaling causes diseases with severe neurological manifestations, such as tuberous sclerosis complex and focal cortical dysplasia. However, the molecular mechanisms by which mTOR signaling regulates nervous system development and function are poorly understood. Unkempt is a conserved zinc finger/RING domain protein that regulates neurogenesis downstream of mTOR signaling in Drosophila. Unkempt also directly interacts with the mTOR complex I component Raptor. Here we describe the generation and characterisation of mice with a conditional knockout of Unkempt (UnkcKO) in the nervous system. Loss of Unkempt reduces Raptor protein levels in the embryonic nervous system but does not affect downstream mTORC1 targets. We also show that nervous system development occurs normally in UnkcKO mice. However, we find that Unkempt is expressed in the adult cerebellum and hippocampus and behavioural analyses show that UnkcKO mice have improved memory formation and cognitive flexibility to re-learn. Further understanding of the role of Unkempt in the nervous system will provide novel mechanistic insight into the role of mTOR signaling in learning and memory.
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Affiliation(s)
- Elin Vinsland
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Pranetha Baskaran
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Simeon R Mihaylov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Carl Hobbs
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Hannah Wood
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London, PO82SE5 8AF, UK
| | - Ihssane Bouybayoune
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Kriti Shah
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall 1415A - MURN, Riverside, CA, 92521, USA
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Andrew R Tee
- Cancer and Genetics Building, Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park Way, Cardiff, CF14 4XN, UK
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall 1415A - MURN, Riverside, CA, 92521, USA
| | - Cathy Fernandes
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London, PO82SE5 8AF, UK
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 4th Floor, New Hunt's House, London, SE1 1UL, UK
| | - Joseph M Bateman
- Maurice Wohl Clinical Neuroscience Institute, King's College London, 125 Coldharbour Lane, London, SE5 9NU, UK.
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