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Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB. Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. Nat Neurosci 2024; 27:822-835. [PMID: 38589584 PMCID: PMC11088998 DOI: 10.1038/s41593-024-01615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Learning and memory require activity-induced changes in dendritic translation, but which mRNAs are involved and how they are regulated are unclear. In this study, to monitor how depolarization impacts local dendritic biology, we employed a dendritically targeted proximity labeling approach followed by crosslinking immunoprecipitation, ribosome profiling and mass spectrometry. Depolarization of primary cortical neurons with KCl or the glutamate agonist DHPG caused rapid reprogramming of dendritic protein expression, where changes in dendritic mRNAs and proteins are weakly correlated. For a subset of pre-localized messages, depolarization increased the translation of upstream open reading frames (uORFs) and their downstream coding sequences, enabling localized production of proteins involved in long-term potentiation, cell signaling and energy metabolism. This activity-dependent translation was accompanied by the phosphorylation and recruitment of the non-canonical translation initiation factor eIF4G2, and the translated uORFs were sufficient to confer depolarization-induced, eIF4G2-dependent translational control. These studies uncovered an unanticipated mechanism by which activity-dependent uORF translational control by eIF4G2 couples activity to local dendritic remodeling.
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Affiliation(s)
- Ezgi Hacisuleyman
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
| | - Caryn R Hale
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natalie Noble
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - John J Fak
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Misa Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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2
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Kinyamu HK, Bennett BD, Ward JM, Archer TK. Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:1082-1099. [PMID: 38625038 PMCID: PMC11019832 DOI: 10.1158/2767-9764.crc-23-0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNA polymerase II (RNAPII) transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed differentially open chromatin regions (DOCR). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic superenhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology. SIGNIFICANCE Our study provides a strong basis for understanding the mechanisms by which proteasome inhibitors exert anticancer effects. We find open chromatin regions that change during proteasome inhibition, are typically accessible in non-basal breast cancers.
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Affiliation(s)
- H. Karimi Kinyamu
- Chromatin and Gene Expression Section, National Institute of Environmental Health Sciences, Durham, North Carolina
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
- National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Brian D. Bennett
- National Institute of Environmental Health Sciences, Durham, North Carolina
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, North Carolina
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - James M. Ward
- National Institute of Environmental Health Sciences, Durham, North Carolina
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, North Carolina
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Trevor K. Archer
- Chromatin and Gene Expression Section, National Institute of Environmental Health Sciences, Durham, North Carolina
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
- National Institute of Environmental Health Sciences, Durham, North Carolina
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3
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Li H, House J, Nichols C, Gruzdev A, Ward J, Li JL, Wyss A, Haque E, Edin M, Elmore S, Mahler B, Degraff L, Shi M, Zeldin D, London S. Adam19 Deficiency Impacts Pulmonary Function: Human GWAS Follow-up in Mouse. RESEARCH SQUARE 2024:rs.3.rs-4207678. [PMID: 38659817 PMCID: PMC11042436 DOI: 10.21203/rs.3.rs-4207678/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Purpose Over 550 loci have been associated with human pulmonary function in genome-wide association studies (GWAS); however, the causal role of most remains uncertain. Single nucleotide polymorphisms in a disintegrin and metalloprotease domain 19 (ADAM19) are consistently related to pulmonary function in GWAS. Thus, we used a mouse model to investigate the causal link between Adam19 and pulmonary function. Methods We created an Adam19 knockout (KO) mouse model and validated the gene targeting using RNA-Seq and RT-qPCR. Contrary to prior publications, the KO was not neonatal lethal. Thus, we phenotyped the Adam19 KO. Results KO mice had lower body weight and shorter tibial length than wild type (WT). Dual-energy X-ray Absorptiometry indicated lower soft weight, fat weight, and bone mineral content in KO mice. In lung function analyses using flexiVent, compared to WT, Adam19 KO had decreased baseline respiratory system elastance, minute work of breathing, tissue damping, tissue elastance, and forced expiratory flow at 50% forced vital capacity but higher FEV0.1 and FVC. Adam19 KO had attenuated tissue damping and tissue elastance in response to methacholine following LPS exposure. Adam19 KO also exhibited attenuated neutrophil extravasation into the airway after LPS administration compared to WT. RNA-Seq analysis of KO and WT lungs identified several differentially expressed genes (Cd300lg, Kpna2, and Pttg1) implicated in lung biology and pathogenesis. Gene set enrichment analysis identified negative enrichment for TNF pathways. Conclusion Our murine findings support a causal role of ADAM19, implicated in human GWAS, in regulating pulmonary function.
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Affiliation(s)
- Huiling Li
- National Institute of Environmental Health Sciences
| | - John House
- National Institute of Environmental Health Sciences
| | | | | | - James Ward
- National Institute of Environmental Health Sciences
| | | | | | - Ezazul Haque
- National Institute of Environmental Health Sciences
| | - Matthew Edin
- National Institute of Environmental Health Sciences
| | - Susan Elmore
- National Institute of Environmental Health Sciences
| | - Beth Mahler
- National Institute of Environmental Health Sciences
| | | | - Min Shi
- National Institute of Environmental Health Sciences
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4
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Pannoni KE, Fischer QS, Tarannum R, Cawley ML, Alsalman MM, Acosta N, Ezigbo C, Gil DV, Campbell LA, Farris S. MCU-enriched dendritic mitochondria regulate plasticity in distinct hippocampal circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566606. [PMID: 37986798 PMCID: PMC10659405 DOI: 10.1101/2023.11.10.566606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Mitochondria are dynamic organelles that are morphologically and functionally diverse across cell types and subcellular compartments in order to meet unique energy demands. Mitochondrial dysfunction has been implicated in a wide variety of neurological disorders, including psychiatric disorders like schizophrenia and bipolar disorder. Despite it being well known that mitochondria are essential for synaptic transmission and synaptic plasticity, the mechanisms regulating mitochondria in support of normal synapse function are incompletely understood. The mitochondrial calcium uniporter (MCU) regulates calcium entry into the mitochondria, which in turn regulates the bioenergetics and distribution of mitochondria to active synapses. Evidence suggests that calcium influx via MCU couples neuronal activity to mitochondrial metabolism and ATP production, which would allow neurons to rapidly adapt to changing energy demands. Intriguingly, MCU is uniquely enriched in hippocampal CA2 distal dendrites relative to neighboring hippocampal CA1 or CA3 distal dendrites, however, the functional significance of this enrichment is not clear. Synapses from the entorhinal cortex layer II (ECII) onto CA2 distal dendrites readily express long term potentiation (LTP), unlike the LTP-resistant synapses from CA3 onto CA2 proximal dendrites, but the mechanisms underlying these different plasticity profiles are unknown. We hypothesized that enrichment of MCU near ECII-CA2 synapses promotes LTP in an otherwise plasticity-restricted cell type. Using a CA2-specific MCU knockout (cKO) mouse, we found that MCU is required for LTP at distal dendrite synapses but does not affect the lack of LTP at proximal dendrite synapses. Loss of LTP at ECII-CA2 synapses correlated with a trend for decreased spine density in CA2 distal dendrites of cKO mice compared to control (CTL) mice, which was predominantly seen in immature spines. Moreover, mitochondria were significantly smaller and more numerous across all dendritic layers of CA2 in cKO mice compared to CTL mice, suggesting an overall increase in mitochondrial fragmentation. Fragmented mitochondria might have functional changes, such as altered ATP production, that might explain a deficit in synaptic plasticity. Collectively, our data reveal that MCU regulates layer-specific forms of plasticity in CA2 dendrites, potentially by maintaining proper mitochondria morphology and distribution within dendrites. Differences in MCU expression across different cell types and circuits might be a general mechanism to tune the sensitivity of mitochondria to cytoplasmic calcium levels to power synaptic plasticity.
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Affiliation(s)
- Katy E. Pannoni
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Quentin S. Fischer
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Renesa Tarannum
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mikel L. Cawley
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mayd M. Alsalman
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Nicole Acosta
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Chisom Ezigbo
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Daniela V. Gil
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Logan A. Campbell
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Shannon Farris
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
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5
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Garone C, De Giorgio F, Carli S. Mitochondrial metabolism in neural stem cells and implications for neurodevelopmental and neurodegenerative diseases. J Transl Med 2024; 22:238. [PMID: 38438847 PMCID: PMC10910780 DOI: 10.1186/s12967-024-05041-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/25/2024] [Indexed: 03/06/2024] Open
Abstract
Mitochondria are cytoplasmic organelles having a fundamental role in the regulation of neural stem cell (NSC) fate during neural development and maintenance.During embryonic and adult neurogenesis, NSCs undergo a metabolic switch from glycolytic to oxidative phosphorylation with a rise in mitochondrial DNA (mtDNA) content, changes in mitochondria shape and size, and a physiological augmentation of mitochondrial reactive oxygen species which together drive NSCs to proliferate and differentiate. Genetic and epigenetic modifications of proteins involved in cellular differentiation (Mechanistic Target of Rapamycin), proliferation (Wingless-type), and hypoxia (Mitogen-activated protein kinase)-and all connected by the common key regulatory factor Hypoxia Inducible Factor-1A-are deemed to be responsible for the metabolic shift and, consequently, NSC fate in physiological and pathological conditions.Both primary mitochondrial dysfunction due to mutations in nuclear DNA or mtDNA or secondary mitochondrial dysfunction in oxidative phosphorylation (OXPHOS) metabolism, mitochondrial dynamics, and organelle interplay pathways can contribute to the development of neurodevelopmental or progressive neurodegenerative disorders.This review analyses the physiology and pathology of neural development starting from the available in vitro and in vivo models and highlights the current knowledge concerning key mitochondrial pathways involved in this process.
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Affiliation(s)
- C Garone
- Department of Medical and Surgical Sciences, Alma Mater Studiorum-University of Bologna, Bologna, Italy.
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UO Neuropsichiatria Dell'età Pediatrica, Bologna, Italy.
| | - F De Giorgio
- Department of Medical and Surgical Sciences, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - S Carli
- Department of Medical and Surgical Sciences, Alma Mater Studiorum-University of Bologna, Bologna, Italy
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6
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Gladwell W, Yost O, Li H, Bell WJ, Chen SH, Ward JM, Kleeberger SR, Resnick MA, Menendez D. APOBEC3G Is a p53-Dependent Restriction Factor in Respiratory Syncytial Virus Infection of Human Cells Included in the p53/Immune Axis. Int J Mol Sci 2023; 24:16793. [PMID: 38069117 PMCID: PMC10706465 DOI: 10.3390/ijms242316793] [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: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Identifying and understanding genetic factors that influence the propagation of the human respiratory syncytial virus (RSV) can lead to health benefits and possibly augment recent vaccine approaches. We previously identified a p53/immune axis in which the tumor suppressor p53 directly regulates the expression of immune system genes, including the seven members of the APOBEC3 family of DNA cytidine deaminases (A3), which are innate immune sentinels against viral infections. Here, we examined the potential p53 and A3 influence in RSV infection, as well as the overall p53-dependent cellular and p53/immune axis responses to infection. Using a paired p53 model system of p53+ and p53- human lung tumor cells, we found that RSV infection activates p53, leading to the altered p53-dependent expression of A3D, A3F, and A3G, along with p53 site-specific binding. Focusing on A3G because of its 10-fold-greater p53 responsiveness to RSV, the overexpression of A3G can reduce RSV viral replication and syncytial formation. We also observed that RSV-infected cells undergo p53-dependent apoptosis. The study was expanded to globally address at the transcriptional level the p53/immune axis response to RSV. Nearly 100 genes can be directly targeted by the p53/immune axis during RSV infection based on our p53BAER analysis (Binding And Expression Resource). Overall, we identify A3G as a potential p53-responsive restriction factor in RSV infection. These findings have significant implications for RSV clinical and therapeutic studies and other p53-influenced viral infections, including using p53 adjuvants to boost the response of A3 genes.
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Affiliation(s)
- Wesley Gladwell
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
| | - Oriana Yost
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
| | - Heather Li
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
| | - Whitney J. Bell
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA
| | - Shih-Heng Chen
- Viral Vector Core Facility, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA;
| | - James M. Ward
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA
| | - Steven R. Kleeberger
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
| | - Michael A. Resnick
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA
| | - Daniel Menendez
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA; (W.G.); (O.Y.); (H.L.); (W.J.B.); (S.R.K.)
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, Durham, NC 27709, USA
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7
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Kucharski R, Ellis N, Jurkowski TP, Hurd PJ, Maleszka R. The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera. iScience 2023; 26:108193. [PMID: 37920666 PMCID: PMC10618690 DOI: 10.1016/j.isci.2023.108193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
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Affiliation(s)
- Robert Kucharski
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nancy Ellis
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Paul J. Hurd
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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8
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Bueno D, Narayan Dey P, Schacht T, Wolf C, Wüllner V, Morpurgo E, Rojas-Charry L, Sessinghaus L, Leukel P, Sommer C, Radyushkin K, Florin L, Baumgart J, Stamm P, Daiber A, Horta G, Nardi L, Vasic V, Schmeisser MJ, Hellwig A, Oskamp A, Bauer A, Anand R, Reichert AS, Ritz S, Nocera G, Jacob C, Peper J, Silies M, Frauenknecht KBM, Schäfer MKE, Methner A. NECAB2 is an endosomal protein important for striatal function. Free Radic Biol Med 2023; 208:643-656. [PMID: 37722569 DOI: 10.1016/j.freeradbiomed.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/29/2023] [Accepted: 09/02/2023] [Indexed: 09/20/2023]
Abstract
Synaptic signaling depends on ATP generated by mitochondria. Dysfunctional mitochondria shift the redox balance towards a more oxidative environment. Due to extensive connectivity, the striatum is especially vulnerable to mitochondrial dysfunction. We found that neuronal calcium-binding protein 2 (NECAB2) plays a role in striatal function and mitochondrial homeostasis. NECAB2 is a predominantly endosomal striatal protein which partially colocalizes with mitochondria. This colocalization is enhanced by mild oxidative stress. Global knockout of Necab2 in the mouse results in increased superoxide levels, increased DNA oxidation and reduced levels of the antioxidant glutathione which correlates with an altered mitochondrial shape and function. Striatal mitochondria from Necab2 knockout mice are more abundant and smaller and characterized by a reduced spare capacity suggestive of intrinsic uncoupling respectively mitochondrial dysfunction. In line with this, we also found an altered stress-induced interaction of endosomes with mitochondria in Necab2 knockout striatal cultures. The predominance of dysfunctional mitochondria and the pro-oxidative redox milieu correlates with a loss of striatal synapses and behavioral changes characteristic of striatal dysfunction like reduced motivation and altered sensory gating. Together this suggests an involvement of NECAB2 in an endosomal pathway of mitochondrial stress response important for striatal function.
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Affiliation(s)
- Diones Bueno
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Partha Narayan Dey
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Teresa Schacht
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Christina Wolf
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Verena Wüllner
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Elena Morpurgo
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
| | - Liliana Rojas-Charry
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany; University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Anatomy, Germany.
| | - Lena Sessinghaus
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute of Neuropathology, Germany.
| | - Petra Leukel
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute of Neuropathology, Germany.
| | - Clemens Sommer
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute of Neuropathology, Germany.
| | - Konstantin Radyushkin
- University Medical Center of the Johannes Gutenberg-University Mainz, Mouse Behavior Unit, Germany.
| | - Luise Florin
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Virology, Germany.
| | - Jan Baumgart
- University Medical Center of the Johannes Gutenberg-University Mainz, Translational Animal Research Center (TARC), Germany.
| | - Paul Stamm
- University Medical Center of the Johannes Gutenberg-University Mainz, Center for Cardiology, Germany.
| | - Andreas Daiber
- University Medical Center of the Johannes Gutenberg-University Mainz, Center for Cardiology, Germany.
| | - Guilherme Horta
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Anatomy, Germany.
| | - Leonardo Nardi
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Anatomy, Germany.
| | - Verica Vasic
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Anatomy, Germany.
| | - Michael J Schmeisser
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Anatomy, Germany.
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, Germany.
| | - Angela Oskamp
- Institute of Neuroscience and Medicine (INM-2), Forschungszentrum Jülich GmbH, Germany.
| | - Andreas Bauer
- Institute of Neuroscience and Medicine (INM-2), Forschungszentrum Jülich GmbH, Germany.
| | - Ruchika Anand
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Sandra Ritz
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany.
| | - Gianluigi Nocera
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Germany.
| | - Claire Jacob
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Germany.
| | - Jonas Peper
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Germany.
| | - Marion Silies
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Germany.
| | - Katrin B M Frauenknecht
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute of Neuropathology, Germany; Institute of Neuropathology, University and University Hospital Zurich, Switzerland.
| | - Michael K E Schäfer
- Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany.
| | - Axel Methner
- University Medical Center of the Johannes Gutenberg-University Mainz, Institute for Molecular Medicine, Germany.
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9
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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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10
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Ward JM, Ambatipudi M, O'Hanlon TP, Smith MA, de Los Reyes M, Schiffenbauer A, Rahman S, Zerrouki K, Miller FW, Sanjuan MA, Li JL, Casey KA, Rider LG. Shared and Distinctive Transcriptomic and Proteomic Pathways in Adult and Juvenile Dermatomyositis. Arthritis Rheumatol 2023; 75:2014-2026. [PMID: 37229703 PMCID: PMC10615891 DOI: 10.1002/art.42615] [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: 11/19/2022] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
OBJECTIVE Transcript and protein expression were interrogated to examine gene locus and pathway regulation in the peripheral blood of active adult dermatomyositis (DM) and juvenile DM patients receiving immunosuppressive therapies. METHODS Expression data from 14 DM and 12 juvenile DM patients were compared to matched healthy controls. Regulatory effects at the transcript and protein level were analyzed by multi-enrichment analysis for assessment of affected pathways within DM and juvenile DM. RESULTS Expression of 1,124 gene loci were significantly altered at the transcript or protein levels across DM or juvenile DM, with 70 genes shared. A subset of interferon-stimulated genes was elevated, including CXCL10, ISG15, OAS1, CLEC4A, and STAT1. Innate immune markers specific to neutrophil granules and neutrophil extracellular traps were up-regulated in both DM and juvenile DM, including BPI, CTSG, ELANE, LTF, MPO, and MMP8. Pathway analysis revealed up-regulation of PI3K/AKT, ERK, and p38 MAPK signaling, whose central components were broadly up-regulated in DM, while peripheral upstream and downstream components were differentially regulated in both DM and juvenile DM. Up-regulated components shared by DM and juvenile DM included cytokine:receptor pairs LGALS9:HAVCR2, LTF/NAMPT/S100A8/HSPA1A:TLR4, CSF2:CSF2RA, EPO:EPOR, FGF2/FGF8:FGFR, several Bcl-2 components, and numerous glycolytic enzymes. Pathways unique to DM included sirtuin signaling, aryl hydrocarbon receptor signaling, protein ubiquitination, and granzyme B signaling. CONCLUSION The combination of proteomics and transcript expression by multi-enrichment analysis broadened the identification of up- and down-regulated pathways among active DM and juvenile DM patients. These pathways, particularly those which feed into PI3K/AKT and MAPK signaling and neutrophil degranulation, may be potential therapeutic targets.
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Affiliation(s)
- James M Ward
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Mythri Ambatipudi
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | - Terrance P O'Hanlon
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | | | | | - Adam Schiffenbauer
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | - Saifur Rahman
- BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | | | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
| | | | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Kerry A Casey
- BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, Maryland and Research Triangle, Park, North Carolina
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11
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Metcalf CS. Brake Early: RGS14 in CA2 Limits Seizures and Oxidative Stress After SE. Epilepsy Curr 2023; 23:372-374. [PMID: 38269350 PMCID: PMC10805082 DOI: 10.1177/15357597231199343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
RGS14 Limits Seizure-Induced Mitochondrial Oxidative Stress and Pathology in Hippocampus Harbin NH, Lustberg DJ, Hurst C, Pare J, Crotty KM, Waters AL, Yeligar SM, Smith Y, Seyfried NT, Weinschenker D, Hepler JR. Neurobiol Dis. 2023;181:106128. doi:10.1016/j.nbd.2023.106128 . PMID: 37075948 RGS14 is a complex multifunctional scaffolding protein that is highly enriched within pyramidal cells (PCs) of hippocampal area CA2. In these neurons, RGS14 suppresses glutamate-induced calcium influx and related G protein and ERK signaling in dendritic spines to restrain postsynaptic signaling and plasticity. Previous findings show that, unlike PCs of hippocampal areas CA1 and CA3, CA2 PCs are resistant to a number of neurological insults, including degeneration caused by temporal lobe epilepsy (TLE). While RGS14 is protective against peripheral injury, similar roles for RGS14 during pathological injury in hippocampus remain unexplored. Recent studies showed that area CA2 modulates hippocampal excitability, generates epileptiform activity and promotes hippocampal pathology in animal models and patients with TLE. Because RGS14 suppresses CA2 excitability and signaling, we hypothesized that RGS14 would moderate seizure behavior and early hippocampal pathology following seizure activity, possibly affording protection to CA2 PCs. Using kainic acid (KA) to induce status epilepticus (KA-SE) in mice, we show that the loss of RGS14 (RGS14 KO) accelerated onset of limbic motor seizures and mortality compared to wild type (WT) mice, and that KA-SE upregulated RGS14 protein expression in CA2 and CA1 PCs of WT. Our proteomics data show that the loss of RGS14 impacted the expression of a number of proteins at baseline and after KA-SE, many of which associated unexpectedly with mitochondrial function and oxidative stress. RGS14 was shown to localize to the mitochondria in CA2 PCs of mice and reduce mitochondrial respiration in vitro. As a readout of oxidative stress, we found that RGS14 KO dramatically increased 3-nitrotyrosine levels in CA2 PCs, which was greatly exacerbated following KA-SE and correlated with a lack of superoxide dismutase 2 (SOD2) induction. Assessing for hallmarks of seizure pathology in RGS14 KO, we unexpectedly found no differences in neuronal injury in CA2 PCs. However, we observed a striking and surprising lack of microgliosis in CA1 and CA2 of RGS14 KO compared to WT. Together, our data demonstrate a newly appreciated role for RGS14 in limiting intense seizure activity and pathology in hippocampus. Our findings are consistent with a model where RGS14 limits seizure onset and mortality and, after seizure, is upregulated to support mitochondrial function, prevent oxidative stress in CA2 PCs, and promote microglial activation in hippocampus.
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12
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Kinyamu HK, Bennett BD, Ward JM, Archer T. Proteasome inhibition reprograms chromatin landscape in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562284. [PMID: 37904968 PMCID: PMC10614768 DOI: 10.1101/2023.10.13.562284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNAPII transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed Differentially Open Chromatin Regions (DOCRs). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic super enhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology. Highlights Proteasome inhibition uncovers de novo Differential Open Chromatin Regions (DOCRs) in breast cancer cells. Proteasome inhibitor sensitive promoters exhibit a distinctive chromatin architecture with discrete transcription initiation patterns.Proteasome inhibition reprograms accessibility of super enhancers.Proteasome inhibitor sensitive super enhancers distinguish basal from non-basal breast cancer subtypes.
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13
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Vanrobaeys Y, Mukherjee U, Langmack L, Beyer SE, Bahl E, Lin LC, Michaelson JJ, Abel T, Chatterjee S. Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation. Nat Commun 2023; 14:6100. [PMID: 37773230 PMCID: PMC10541893 DOI: 10.1038/s41467-023-41715-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Memory consolidation involves discrete patterns of transcriptional events in the hippocampus. Despite the emergence of single-cell transcriptomic profiling techniques, mapping the transcriptomic signature across subregions of the hippocampus has remained challenging. Here, we utilized unbiased spatial sequencing to delineate transcriptome-wide gene expression changes across subregions of the dorsal hippocampus of male mice following learning. We find that each subregion of the hippocampus exhibits distinct yet overlapping transcriptomic signatures. The CA1 region exhibited increased expression of genes related to transcriptional regulation, while the DG showed upregulation of genes associated with protein folding. Importantly, our approach enabled us to define the transcriptomic signature of learning within two less-defined hippocampal subregions, CA1 stratum radiatum, and oriens. We demonstrated that CA1 subregion-specific expression of a transcription factor subfamily has a critical functional role in the consolidation of long-term memory. This work demonstrates the power of spatial molecular approaches to reveal simultaneous transcriptional events across the hippocampus during memory consolidation.
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Affiliation(s)
- Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, 52242, USA
| | - Lucy Langmack
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Biochemistry and Molecular Biology Graduate Program, University of Iowa, Iowa City, IA, USA
| | - Stacy E Beyer
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Li-Chun Lin
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
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14
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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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15
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Ament SA, Poulopoulos A. The brain's dark transcriptome: Sequencing RNA in distal compartments of neurons and glia. Curr Opin Neurobiol 2023; 81:102725. [PMID: 37196598 PMCID: PMC10524153 DOI: 10.1016/j.conb.2023.102725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 05/19/2023]
Abstract
Transcriptomic approaches are powerful strategies to map the molecular diversity of cells in the brain. Single-cell genomic atlases have now been compiled for entire mammalian brains. However, complementary techniques are only just beginning to map the subcellular transcriptomes from distal cellular compartments. We review single-cell datasets alongside subtranscriptome data from the mammalian brain to explore the development of cellular and subcellular diversity. We discuss how single-cell RNA-seq misses transcripts localized away from cell bodies, which form the 'dark transcriptome' of the brain: a collection of subtranscriptomes in dendrites, axons, growth cones, synapses, and endfeet with important roles in brain development and function. Recent advances in subcellular transcriptome sequencing are beginning to reveal these elusive pools of RNA. We outline the success stories to date in uncovering the constituent subtranscriptomes of neurons and glia, as well as present the emerging toolkit that is accelerating the pace of subtranscriptome discovery.
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Affiliation(s)
- Seth A Ament
- Department of Psychiatry, UM-MIND, and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA.
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16
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Diethorn EJ, Gould E. Development of the hippocampal CA2 region and the emergence of social recognition. Dev Neurobiol 2023; 83:143-156. [PMID: 37326250 PMCID: PMC10529477 DOI: 10.1002/dneu.22919] [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: 02/20/2023] [Revised: 05/08/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
Social memories formed in early life, like those for family and unrelated peers, are known to contribute to healthy social interactions throughout life, although how the developing brain supports social memory remains relatively unexplored. The CA2 subregion of the hippocampus is involved in social memory function, but most literature on this subject is restricted to studies of adult rodents. Here, we review the current literature on the embryonic and postnatal development of hippocampal subregion CA2 in mammals, with a focus on the emergence of its unusual molecular and cellular characteristics, including its notably high expression of plasticity-suppressing molecules. We also consider the connectivity of the CA2 with other brain areas, including intrahippocampal regions, such as the dentate gyrus, CA3, and CA1 regions, and extrahippocampal regions, such as the hypothalamus, ventral tegmental area, basal forebrain, raphe nuclei, and the entorhinal cortex. We review developmental milestones of CA2 molecular, cellular, and circuit-level features that may contribute to emerging social recognition abilities for kin and unrelated conspecifics in early life. Lastly, we consider genetic mouse models related to neurodevelopmental disorders in humans in order to survey evidence about whether atypical formation of the CA2 may contribute to social memory dysfunction.
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Affiliation(s)
- Emma J Diethorn
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Elizabeth Gould
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
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17
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Samadi M, Hales CA, Lustberg DJ, Farris S, Ross MR, Zhao M, Hepler JR, Harbin NH, Robinson ESJ, Banks PJ, Bashir ZI, Dudek SM. Mechanisms of mGluR-dependent plasticity in hippocampal area CA2. Hippocampus 2023; 33:730-744. [PMID: 36971428 PMCID: PMC10213158 DOI: 10.1002/hipo.23529] [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: 02/18/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023]
Abstract
Pyramidal cells in hippocampal area CA2 have synaptic properties that are distinct from the other CA subregions. Notably, this includes a lack of typical long-term potentiation of stratum radiatum synapses. CA2 neurons express high levels of several known and potential regulators of metabotropic glutamate receptor (mGluR)-dependent signaling including Striatal-Enriched Tyrosine Phosphatase (STEP) and several Regulator of G-protein Signaling (RGS) proteins, yet the functions of these proteins in regulating mGluR-dependent synaptic plasticity in CA2 are completely unknown. Thus, the aim of this study was to examine mGluR-dependent synaptic depression and to determine whether STEP and the RGS proteins RGS4 and RGS14 are involved. Using whole cell voltage-clamp recordings from mouse pyramidal cells, we found that mGluR agonist-induced long-term depression (mGluR-LTD) is more pronounced in CA2 compared with that observed in CA1. This mGluR-LTD in CA2 was found to be protein synthesis and STEP dependent, suggesting that CA2 mGluR-LTD shares mechanistic processes with those seen in CA1, but in addition, RGS14, but not RGS4, was essential for mGluR-LTD in CA2. In addition, we found that exogenous application of STEP could rescue mGluR-LTD in RGS14 KO slices. Supporting a role for CA2 synaptic plasticity in social cognition, we found that RGS14 KO mice had impaired social recognition memory as assessed in a social discrimination task. These results highlight possible roles for mGluRs, RGS14, and STEP in CA2-dependent behaviors, perhaps by biasing the dominant form of synaptic plasticity away from LTP and toward LTD in CA2.
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Affiliation(s)
- Mahsa Samadi
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity Walk, University of BristolBristolUKBS8 1TD
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
- Present address:
Faculty Education Office, Faculty of Medicine, Imperial College London, Hammersmith Campus, Wolfson Education CentreLondonUKW12 0NN
| | - Claire A. Hales
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity Walk, University of BristolBristolUKBS8 1TD
- Present address:
Department of Psychology, Djavad Mowafaghian Centre for Brain HealthUniversity of British Columbia2215, Wesbrook MallVancouverBritish ColumbiaV6T 1Z3Canada
| | - Daniel J. Lustberg
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
- Present address:
Mouse Pharmacology GroupPsychogenics Inc215 College RoadParamusNew Jersey07652USA
| | - Shannon Farris
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
- Present address:
Fralin Biomedical Research Institute at Virginia TechRoanokeVirginia24014USA
| | - Madeleine R. Ross
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
| | - Meilan Zhao
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
| | - John R. Hepler
- Department of Pharmacology and Chemical BiologyEmory University School of Medicine100 Woodruff CircleAtlantaGeorgia30322USA
| | - Nicholas H. Harbin
- Department of Pharmacology and Chemical BiologyEmory University School of Medicine100 Woodruff CircleAtlantaGeorgia30322USA
| | - Emma S. J. Robinson
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity Walk, University of BristolBristolUKBS8 1TD
| | - Paul J. Banks
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity Walk, University of BristolBristolUKBS8 1TD
| | - Zafar I. Bashir
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity Walk, University of BristolBristolUKBS8 1TD
| | - Serena M. Dudek
- Neurobiology Laboratory, National Institute of Environmental Health Sciences (NIH)111 T.W. Alexander Drive, Research Triangle ParkDurhamNorth Carolina27709USA
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18
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Dietrich N, Trotter K, Ward JM, Archer TK. BRG1 HSA domain interactions with BCL7 proteins are critical for remodeling and gene expression. Life Sci Alliance 2023; 6:e202201770. [PMID: 36801810 PMCID: PMC9939006 DOI: 10.26508/lsa.202201770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
The SWI/SNF complex remodels chromatin in an ATP-dependent manner through the subunits BRG1 and BRM. Chromatin remodeling alters nucleosome structure to change gene expression; however, aberrant remodeling can result in cancer. We identified BCL7 proteins as critical SWI/SNF members that drive BRG1-dependent gene expression changes. BCL7s have been implicated in B-cell lymphoma, but characterization of their functional role within the SWI/SNF complex has been limited. This study implicates their function alongside BRG1 to drive large-scale changes in gene expression. Mechanistically, the BCL7 proteins bind to the HSA domain of BRG1 and require this domain for binding to chromatin. BRG1 proteins without the HSA domain fail to interact with the BCL7 proteins and have severely reduced chromatin remodeling activity. These results link the HSA domain and the formation of a functional SWI/SNF remodeling complex through the interaction with BCL7 proteins. These data highlight the importance of correct formation of the SWI/SNF complex to drive critical biological functions, as losses of individual accessory members or protein domains can cause loss of complex function.
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Affiliation(s)
- Nicholas Dietrich
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Kevin Trotter
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - James M Ward
- Integrative Bioinformatics, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
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19
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Dudek SM, Alexander GM, Farris S. Introduction to the special issue on: A new view of hippocampal area CA2. Hippocampus 2023; 33:127-132. [PMID: 36826426 DOI: 10.1002/hipo.23514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 02/25/2023]
Affiliation(s)
- Serena M Dudek
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, North Carolina, USA
| | - Georgia M Alexander
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, North Carolina, USA
| | - Shannon Farris
- Center for Neurobiology Research, Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, Virginia, USA
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20
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Oliva A, Fernandez-Ruiz A, Karaba LA. CA2 orchestrates hippocampal network dynamics. Hippocampus 2023; 33:241-251. [PMID: 36575880 PMCID: PMC9974898 DOI: 10.1002/hipo.23495] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/25/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022]
Abstract
The hippocampus is composed of various subregions: CA1, CA2, CA3, and the dentate gyrus (DG). Despite the abundant hippocampal research literature, until recently, CA2 received little attention. The development of new genetic and physiological tools allowed recent studies characterizing the unique properties and functional roles of this hippocampal subregion. Despite its small size, the cellular content of CA2 is heterogeneous at the molecular and physiological levels. CA2 has been heavily implicated in social behaviors, including social memory. More generally, the mechanisms by which the hippocampus is involved in memory include the reactivation of neuronal ensembles following experience. This process is coordinated by synchronous network events known as sharp-wave ripples (SWRs). Recent evidence suggests that CA2 plays an important role in the generation of SWRs. The unique connectivity and physiological properties of CA2 pyramidal cells make this region a computational hub at the core of hippocampal information processing. Here, we review recent findings that support the role of CA2 in coordinating hippocampal network dynamics from a systems neuroscience perspective.
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Affiliation(s)
- Azahara Oliva
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | | | - Lindsay A Karaba
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
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21
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Pannoni K, Gil D, Cawley M, Alsalman M, Campbell L, Farris S. Layer-specific mitochondrial diversity across hippocampal CA2 dendrites. Hippocampus 2023; 33:182-196. [PMID: 36762797 PMCID: PMC9974919 DOI: 10.1002/hipo.23512] [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: 08/24/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
CA2 is an understudied subregion of the hippocampus that is critical for social memory. Previous studies identified multiple components of the mitochondrial calcium uniporter (MCU) complex as selectively enriched in CA2. The MCU complex regulates calcium entry into mitochondria, which in turn regulates mitochondrial transport and localization to active synapses. We found that MCU is strikingly enriched in CA2 distal apical dendrites, precisely where CA2 neurons receive entorhinal cortical input carrying social information. Furthermore, MCU-enriched mitochondria in CA2 distal dendrites are larger compared to mitochondria in CA2 proximal apical dendrites and neighboring CA1 apical dendrites, which was confirmed in CA2 with genetically labeled mitochondria and electron microscopy. MCU overexpression in neighboring CA1 led to a preferential localization of MCU in the proximal dendrites of CA1 compared to the distal dendrites, an effect not seen in CA2. Our findings demonstrate that mitochondria are molecularly and structurally diverse across hippocampal cell types and circuits, and suggest that MCU can be differentially localized within dendrites, possibly to meet local energy demands.
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Affiliation(s)
- Katy Pannoni
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Daniela Gil
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Mikel Cawley
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mayd Alsalman
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Logan Campbell
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Shannon Farris
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
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22
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Radzicki D, Chong S, Dudek SM. Morphological and molecular markers of mouse area CA2 along the proximodistal and dorsoventral hippocampal axes. Hippocampus 2023; 33:133-149. [PMID: 36762588 PMCID: PMC10443601 DOI: 10.1002/hipo.23509] [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: 11/08/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/11/2023]
Abstract
Hippocampal area CA2 is a molecularly and functionally distinct region of the hippocampus that has classically been defined as the area with large pyramidal neurons lacking input from the dentate gyrus and the thorny excrescences (TEs) characteristic of CA3 neurons. A modern definition of CA2, however, makes use of the expression of several molecular markers that distinguish it from neighboring CA3 and CA1. Using immunohistochemistry, we sought to characterize the staining patterns of commonly used CA2 markers along the dorsal-ventral hippocampal axis and determine how these markers align along the proximodistal axis. We used a region of CA2 that stained for both Regulator of G-protein Signaling 14 (RGS14) and Purkinje Cell Protein 4 (PCP4; "double-labeled zone" [DLZ]) as a reference. Here, we report that certain commonly used CA2 molecular markers may be better suited for drawing distinct boundaries between CA2/3 and CA2/1. For example, RGS14+ and STEP+ neurons showed minimal to no extension into area CA1 while areas stained with VGluT2 and Wisteria Floribunda agglutinin were consistently smaller than the DLZ/CA2 borders by ~100 μ on the CA1 or CA3 sides respectively. In addition, these patterns are dependent on position along the dorsal-ventral hippocampal axis such that PCP4 labeling often extended beyond the distal border of the DLZ into CA1. Finally, we found that, consistent with previous findings, mossy fibers innervate a subset of RGS14 positive neurons (~65%-70%) and that mossy fiber bouton number and relative size in CA2 are less than that of boutons in CA3. Unexpectedly, we did find evidence of some complex spines on apical dendrites in CA2, though much fewer in number than in CA3. Our results indicate that certain molecular markers may be better suited than others when defining the proximal and distal borders of area CA2 and that the presence or absence of complex spines alone may not be suitable as a distinguishing feature differentiating CA3 from CA2 neurons.
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Affiliation(s)
- Daniel Radzicki
- Neurobiology Laboratory, National Institute of Environmental Health SciencesNational Institute of HealthResearch Triangle ParkNorth CarolinaUSA
| | - Sarah Chong
- Neurobiology Laboratory, National Institute of Environmental Health SciencesNational Institute of HealthResearch Triangle ParkNorth CarolinaUSA
| | - Serena M. Dudek
- Neurobiology Laboratory, National Institute of Environmental Health SciencesNational Institute of HealthResearch Triangle ParkNorth CarolinaUSA
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Kawalec M, Wojtyniak P, Bielska E, Lewczuk A, Boratyńska-Jasińska A, Beręsewicz-Haller M, Frontczak-Baniewicz M, Gewartowska M, Zabłocka B. Mitochondrial dynamics, elimination and biogenesis during post-ischemic recovery in ischemia-resistant and ischemia-vulnerable gerbil hippocampal regions. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166633. [PMID: 36566873 DOI: 10.1016/j.bbadis.2022.166633] [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: 07/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Transient ischemic attacks (TIA) result from a temporary blockage in blood circulation in the brain. As TIAs cause disabilities and often precede full-scale strokes, the effects of TIA are investigated to develop neuroprotective therapies. We analyzed changes in mitochondrial network dynamics, mitophagy and biogenesis in sections of gerbil hippocampus characterized by a different neuronal survival rate after 5-minute ischemia-reperfusion (I/R) insult. Our research revealed a significantly greater mtDNA/nDNA ratio in CA2-3, DG hippocampal regions (5.8 ± 1.4 vs 3.6 ± 0.8 in CA1) that corresponded to a neuronal resistance to I/R. During reperfusion, an increase of pro-fission (phospho-Ser616-Drp1/Drp1) and pro-fusion proteins (1.6 ± 0.5 and 1.4 ± 0.3 for Mfn2 and Opa1, respectively) was observed in CA2-3, DG. Selective autophagy markers, PINK1 and SQSTM1/p62, were elevated 24-96 h after I/R and accompanied by significant elevation of transcription factors proteins PGC-1α and Nrf1 (1.2 ± 0.4, 1.78 ± 0.6, respectively) and increased respiratory chain proteins (e.g., 1.5 ± 0.3 for complex IV at I/R 96 h). Contrastingly, decreased enzymatic activity of citrate synthase, reduced Hsp60 protein level and electron transport chain subunits (0.88 ± 0.03, 0.74 ± 0.1 and 0.71 ± 0.1 for complex IV at I/R 96 h, respectively) were observed in I/R-vulnerable CA1. The phospho-Ser616-Drp1/Drp1 was increased while Mfn2 and total Opa1 reduced to 0.88 ± 0.1 and 0.77 ± 0.17, respectively. General autophagy, measured as LC3-II/I ratio, was activated 3 h after reperfusion reaching 2.37 ± 0.9 of control. This study demonstrated that enhanced mitochondrial fusion, followed by late and selective mitophagy and mitochondrial biogenesis might together contribute to reduced susceptibility to TIA.
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Affiliation(s)
- Maria Kawalec
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland.
| | - Piotr Wojtyniak
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Ewelina Bielska
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Anita Lewczuk
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Boratyńska-Jasińska
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Magdalena Gewartowska
- Electron Microscopy Research Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Zabłocka
- Molecular Biology Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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24
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Bienkowski MS. Further refining the boundaries of the hippocampus CA2 with gene expression and connectivity: Potential subregions and heterogeneous cell types. Hippocampus 2023; 33:150-160. [PMID: 36786207 PMCID: PMC9987718 DOI: 10.1002/hipo.23508] [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: 10/11/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Over the last two decades, the definition of hippocampal area CA2 has evolved from Lorente de Nó's original Golgi-based morphological description with the discovery of specific CA2 gene expression markers. Exploiting the specificity of these molecules has allowed for the genetic dissection of CA2 structure and function in transgenic mice. With this change in criteria, the anatomical boundaries of the CA2 have expanded across the hippocampal axis but the CA2's full rostrocaudal extent is not consistently delineated across atlases. The Hippocampus Gene Expression Atlas (HGEA) provides a comprehensive map of 20 gene expression domains across the entire mouse hippocampus including the CA2. In this commentary, I will review the consensus gene expression patterns that demarcate the expanded CA2 boundaries in the HGEA. Using DropViz single-cell transcriptomics and Mouse Connectome Project connectomics data, I will then suggest potential differences in CA2 cell type heterogeneity and connectivity that may identify and characterize further CA2 subregions.
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Affiliation(s)
- Michael S Bienkowski
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
- USC Center for Integrative Connectomics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
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25
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Shinohara Y, Kohara K. Projections of hippocampal CA2 pyramidal neurons: Distinct innervation patterns of CA2 compared to CA3 in rodents. Hippocampus 2023; 33:691-699. [PMID: 36855258 DOI: 10.1002/hipo.23519] [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: 09/01/2022] [Revised: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
Abstract
The hippocampus is a center for spatial and episodic memory formation in rodents. Understanding the composition of subregions and circuitry maps of the hippocampus is essential for elucidating the mechanism of memory formation and recall. For decades, the trisynaptic circuit (entorhinal cortex layer II-dentate gyrus - CA3-CA1) has been considered the neural network substrate responsible for learning and memory. Recently, CA2 has emerged as an important area in the hippocampal circuitry, with distinct functions from those of CA3. In this article, we review the historical definition of the hippocampal area CA2 and the differential projection patterns between CA2 and CA3 pyramidal neurons. We provide a concise and comprehensive map of CA2 outputs by comparing (1) ipsi versus contra projections, (2) septal versus temporal projections, and (3) lamellar structures of CA2 and CA3 pyramidal neurons.
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Affiliation(s)
- Yoshiaki Shinohara
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Keigo Kohara
- KMU Biobank Center, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, Japan
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26
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Nicotine exposure decreases likelihood of SARS-CoV-2 RNA expression and neuropathology in the hACE2 mouse brain but not moribundity. Sci Rep 2023; 13:2042. [PMID: 36739463 PMCID: PMC9898857 DOI: 10.1038/s41598-023-29118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Individuals infected by SARS-CoV-2 are at risk of developing neurological-related post-acute disorders. Disputed epidemiological data indicated nicotine may reduce the severity of infection. Here we find exposure to nicotine in drinking water does not alter the moribundity of hACE2 mice. However, pre-exposure to nicotine decreased the likelihood of SARS-CoV-2 RNA expression and pathology in the brain. These results suggest mechanisms involving targets of nicotine could be leveraged to prevent the neurovirulence of SARS-CoV-2.
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27
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Harbin NH, Lustberg DJ, Hurst C, Pare JF, Crotty KM, Waters AL, Yeligar SM, Smith Y, Seyfried NT, Weinshenker D, Hepler JR. RGS14 is neuroprotective against seizure-induced mitochondrial oxidative stress and pathology in hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526349. [PMID: 36778349 PMCID: PMC9915580 DOI: 10.1101/2023.02.01.526349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RGS14 is a complex multifunctional scaffolding protein that is highly enriched within pyramidal cells (PCs) of hippocampal area CA2. There, RGS14 suppresses glutamate-induced calcium influx and related G protein and ERK signaling in dendritic spines to restrain postsynaptic signaling and plasticity. Previous findings show that, unlike PCs of hippocampal areas CA1 and CA3, CA2 PCs are resistant to a number of neurological insults, including degeneration caused by temporal lobe epilepsy (TLE). While RGS14 is protective against peripheral injury, similar roles for RGS14 during pathological injury in hippocampus remain unexplored. Recent studies show that area CA2 modulates hippocampal excitability, generates epileptiform activity and promotes hippocampal pathology in animal models and patients with TLE. Because RGS14 suppresses CA2 excitability and signaling, we hypothesized that RGS14 would moderate seizure behavior and early hippocampal pathology following seizure activity. Using kainic acid (KA) to induce status epilepticus (KA-SE) in mice, we show loss of RGS14 (RGS14 KO) accelerated onset of limbic motor seizures and mortality compared to wild type (WT) mice, and that KA-SE upregulated RGS14 protein expression in CA2 and CA1 PCs of WT. Utilizing proteomics, we saw loss of RGS14 impacted the expression of a number of proteins at baseline and after KA-SE, many of which associated unexpectedly with mitochondrial function and oxidative stress. RGS14 was shown to localize to the mitochondria in CA2 PCs of mice and reduce mitochondrial respiration in vitro . As a readout of oxidative stress, we found RGS14 KO dramatically increased 3-nitrotyrosine levels in CA2 PCs, which was greatly exacerbated following KA-SE and correlated with a lack of superoxide dismutase 2 (SOD2) induction. Assessing for hallmarks of seizure pathology in RGS14 KO, we observed worse neuronal injury in area CA3 (but none in CA2 or CA1), and a lack of microgliosis in CA1 and CA2 compared to WT. Together, our data demonstrates a newly appreciated neuroprotective role for RGS14 against intense seizure activity in hippocampus. Our findings are consistent with a model where, after seizure, RGS14 is upregulated to support mitochondrial function and prevent oxidative stress in CA2 PCs, limit seizure onset and hippocampal neuronal injury, and promote microglial activation in hippocampus.
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28
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Zhuang M, Geng X, Han P, Che P, Liang F, Liu C, Yang L, Yu J, Zhang Z, Dong W, Ji SJ. YTHDF2 in dentate gyrus is the m 6A reader mediating m 6A modification in hippocampus-dependent learning and memory. Mol Psychiatry 2023; 28:1679-1691. [PMID: 36670199 DOI: 10.1038/s41380-023-01953-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
N6-methyladenosine (m6A) has been demonstrated to regulate learning and memory in mice. To investigate the mechanism by which m6A modification exerts its function through its reader proteins in the hippocampus, as well as to unveil the specific subregions of the hippocampus that are crucial for memory formation, we generated dentate gyrus (DG)-, CA3-, and CA1-specific Ythdf1 and Ythdf2 conditional knockout (cKO) mice, respectively. Surprisingly, we found that only the DG-specific Ythdf2 cKO mice displayed impaired memory formation, which is inconsistent with the previous report showing that YTHDF1 was involved in this process. YTHDF2 controls the stability of its target transcripts which encode proteins that regulate the elongation of mossy fibers (MF), the axons of DG granule cells. DG-specific Ythdf2 ablation caused MF overgrowth and impairment of the MF-CA3 excitatory synapse development and transmission in the stratum lucidum. Thus, this study identifies the m6A reader YTHDF2 in dentate gyrus as the only regulator that mediates m6A modification in hippocampus-dependent learning and memory.
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Affiliation(s)
- Mengru Zhuang
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.,SUSTech-HKUST Joint PhD Program, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiaoqi Geng
- Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China.,Department of Neurosurgery, Neurosurgical Clinical Research Center of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Peng Han
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Pengfei Che
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Fanghao Liang
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Chao Liu
- Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Lixin Yang
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jun Yu
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Zhuxia Zhang
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Wei Dong
- Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China. .,Department of Neurosurgery, Neurosurgical Clinical Research Center of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China.
| | - Sheng-Jian Ji
- School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
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29
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Vanrobeys Y, Mukherjee U, Langmack L, Bahl E, Lin LC, Michaelson JJ, Abel T, Chatterjee S. Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524576. [PMID: 36711475 PMCID: PMC9882356 DOI: 10.1101/2023.01.18.524576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Memory consolidation involves discrete patterns of transcriptional events in the hippocampus. Despite the emergence of single-cell transcriptomic profiling techniques, defining learning-responsive gene expression across subregions of the hippocampus has remained challenging. Here, we utilized unbiased spatial sequencing to elucidate transcriptome-wide changes in gene expression in the hippocampus following learning, enabling us to define molecular signatures unique to each hippocampal subregion. We find that each subregion of the hippocampus exhibits distinct yet overlapping transcriptomic signatures. Although the CA1 region exhibited increased expression of genes related to transcriptional regulation, the DG showed upregulation of genes associated with protein folding. We demonstrate the functional relevance of subregion-specific gene expression by genetic manipulation of a transcription factor selectively in the CA1 hippocampal subregion, leading to long-term memory deficits. This work demonstrates the power of using spatial molecular approaches to reveal transcriptional events during memory consolidation.
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Affiliation(s)
- Yann Vanrobeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Utsav Mukherjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242, USA
| | - Lucy Langmack
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Biochemistry and Molecular Biology Graduate Program, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Li-Chun Lin
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
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30
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Andronie-Cioara FL, Ardelean AI, Nistor-Cseppento CD, Jurcau A, Jurcau MC, Pascalau N, Marcu F. Molecular Mechanisms of Neuroinflammation in Aging and Alzheimer's Disease Progression. Int J Mol Sci 2023; 24:ijms24031869. [PMID: 36768235 PMCID: PMC9915182 DOI: 10.3390/ijms24031869] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Aging is the most prominent risk factor for late-onset Alzheimer's disease. Aging associates with a chronic inflammatory state both in the periphery and in the central nervous system, the evidence thereof and the mechanisms leading to chronic neuroinflammation being discussed. Nonetheless, neuroinflammation is significantly enhanced by the accumulation of amyloid beta and accelerates the progression of Alzheimer's disease through various pathways discussed in the present review. Decades of clinical trials targeting the 2 abnormal proteins in Alzheimer's disease, amyloid beta and tau, led to many failures. As such, targeting neuroinflammation via different strategies could prove a valuable therapeutic strategy, although much research is still needed to identify the appropriate time window. Active research focusing on identifying early biomarkers could help translating these novel strategies from bench to bedside.
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Affiliation(s)
- Felicia Liana Andronie-Cioara
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Adriana Ioana Ardelean
- Department of Preclinical Sciences, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Carmen Delia Nistor-Cseppento
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
- Correspondence: (C.D.N.-C.); (N.P.)
| | - Anamaria Jurcau
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | | | - Nicoleta Pascalau
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
- Correspondence: (C.D.N.-C.); (N.P.)
| | - Florin Marcu
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
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31
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Beresewicz-Haller M. Hippocampal region-specific endogenous neuroprotection as an approach in the search for new neuroprotective strategies in ischemic stroke. Fiction or fact? Neurochem Int 2023; 162:105455. [PMID: 36410452 DOI: 10.1016/j.neuint.2022.105455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Ischemic stroke is the leading cause of death and long-term disability worldwide, and, while considerable progress has been made in understanding its pathophysiology, the lack of effective treatments remains a major concern. In that context, receiving more and more consideration as a promising therapeutic method is the activation of natural adaptive mechanisms (endogenous neuroprotection) - an approach that seeks to enhance and/or stimulate the endogenous processes of plasticity and protection of the neuronal system that trigger the brain's intrinsic capacity for self-defence. Ischemic preconditioning is a classic example of endogenous neuroprotection, being the process by which one or more brief, non-damaging episodes of ischemia-reperfusion (I/R) induce tissue resistance to subsequent prolonged, damaging ischemia. Another less-known example is resistance to an I/R episode mounted by the hippocampal region consisting of CA2, CA3, CA4 and the dentate gyrus (here abbreviated to CA2-4, DG). This can be contrasted with the ischemia-vulnerable CA1 region. There is not yet a good understanding of these different sensitivities of the hippocampal regions, and hence of the endogenous neuroprotection characteristic of CA2-4, DG. However, this region is widely reported to have properties distinct from CA1, and capable of generating resistance to an I/R episode. These include activation of neurotrophic and neuroprotective factors, greater activation of anti-excitotoxic and anti-oxidant mechanisms, increased plasticity potential, a greater energy reserve and improved mitochondrial function. This review seeks to summarize properties of CA2-4, DG in the context of endogenous neuroprotection, and then to assess the potential utility of these properties to therapeutic approaches. In so doing, it appears to represent the first such addressing of the issue of ischemia resistance attributable to CA2-4, DG.
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Letsinger AC, Ward JM, Fannin RD, Mahapatra D, Bridge MF, Sills RC, Gerrish KE, Yakel JL. Nicotine exposure decreases likelihood of SARS-CoV-2 RNA expression and neuropathology in the hACE2 mouse brain but not moribundity. RESEARCH SQUARE 2022:rs.3.rs-2183255. [PMID: 36380754 PMCID: PMC9645428 DOI: 10.21203/rs.3.rs-2183255/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Individuals infected by SARS-CoV-2 are at risk of developing neurological-related post-acute disorders. Disputed epidemiological data indicated nicotine may reduce the severity of infection. Here we find exposure to nicotine in drinking water does not alter the moribundity of hACE2 mice. However, pre-exposure to nicotine decreased the likelihood of SARS-CoV-2 RNA expression and pathology in the brain. These results suggest mechanisms involving targets of nicotine could be leveraged to prevent the neurovirulence of SARS-CoV-2.
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Machado JP, Athie MC, Matos AH, Lopes-Cendes I, Vieira A. The transcriptome of rat hippocampal subfields. IBRO Neurosci Rep 2022; 13:322-329. [PMID: 36247526 PMCID: PMC9561749 DOI: 10.1016/j.ibneur.2022.09.009] [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: 07/06/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022] Open
Abstract
The hippocampus comprises several neuronal populations such as CA1, CA2, CA3, and the dentate gyrus (DG), which present different neuronal origins, morphologies, and molecular mechanisms. Laser capture microdissection (LCM) allows selectively collecting samples from target regions and eliminating unwanted cells to obtain more specific results. LCM of hippocampus neuronal populations coupĺed with RNA-seq analysis has the potential to allow the exploration of the molecular machinery unique to each of these subfields. Previous RNA-seq investigation has already provided a molecular blueprint of the hippocampus, however, there is no RNA-seq data specific for each of the rat hippocampal regions. Serial tissue sections covering the hippocampus were produced from frozen brains of adult male Wistar rats, and the hippocampal subfields CA1, CA2, CA3, and DG were identified and isolated by LCM. We found evident segregation of the transcriptomic profile from different regions of the hippocampus and the expression of known, as well as novel, specific marker genes for each region. Gene ontology enrichment analysis of CA1 subfield indicates an enrichment of actin regulation and postsynaptic membrane AMPA receptors genes indispensable for long-term potentiation. CA2 and CA3 transcripts were found associated with the increased metabolic processes. DG expression was enriched for ribosome and spliceosome, both required for protein synthesis and maintenance of cell life. The present findings contribute to a deeper understanding of the differences in the molecular machinery expressed by the rat hippocampal neuronal populations, further exploring underlying mechanisms responsible for each subflied specific functions.
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Affiliation(s)
- João P.D. Machado
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Maria C.P. Athie
- Department of Translational Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Alexandre H.B. Matos
- Department of Translational Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - André.S. Vieira
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil,Correspondence to: Department of Structural and Functional Biology, Institute of Biology, Cidade Universitária “Zeferino Vaz”, University of Campinas, UNICAMP, Rua Monteiro Lobato, 255 - Bloco J - 1 piso - Sl 16, Campinas 13083-862, São Paulo, Brazil.
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34
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Groten CJ, MacVicar BA. Mitochondrial Ca 2+ uptake by the MCU facilitates pyramidal neuron excitability and metabolism during action potential firing. Commun Biol 2022; 5:900. [PMID: 36056095 PMCID: PMC9440007 DOI: 10.1038/s42003-022-03848-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/16/2022] [Indexed: 12/12/2022] Open
Abstract
Neuronal activation is fundamental to information processing by the brain and requires mitochondrial energy metabolism. Mitochondrial Ca2+ uptake by the mitochondrial Ca2+ uniporter (MCU) has long been implicated in the control of energy metabolism and intracellular Ca2+ signalling, but its importance to neuronal function in the brain remains unclear. Here, we used in situ electrophysiology and two-photon imaging of mitochondrial Ca2+, cytosolic Ca2+, and NAD(P)H to test the relevance of MCU activation to pyramidal neuron Ca2+ signalling and energy metabolism during action potential firing. We demonstrate that mitochondrial Ca2+ uptake by the MCU is tuned to enhanced firing rate and the strength of this relationship varied between neurons of discrete brain regions. MCU activation promoted electron transport chain activity and chemical reduction of NAD+ to NADH. Moreover, Ca2+ buffering by mitochondria attenuated cytosolic Ca2+ signals and thereby reduced the coupling between activity and the slow afterhyperpolarization, a ubiquitous regulator of excitability. Collectively, we demonstrate that the MCU is engaged by accelerated spike frequency to facilitate neuronal activity through simultaneous control of energy metabolism and excitability. As such, the MCU is situated to promote brain functions associated with high frequency signalling and may represent a target for controlling excessive neuronal activity.
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Affiliation(s)
- Christopher J Groten
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, V6T 1Z3, Canada.
| | - Brian A MacVicar
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, V6T 1Z3, Canada.
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35
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Mol P, Gopalakrishnan L, Chatterjee O, Mangalaparthi KK, Kumar M, Durgad SS, Nair B, Shankar SK, Mahadevan A, Prasad TSK. Proteomic Analysis of Adult Human Hippocampal Subfields Demonstrates Regional Heterogeneity in the Protein Expression. J Proteome Res 2022; 21:2293-2310. [PMID: 36039803 DOI: 10.1021/acs.jproteome.2c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background: Distinct hippocampal subfields are known to get affected during aging, psychiatric disorders, and various neurological and neurodegenerative conditions. To understand the biological processes associated with each subfield, it is important to understand its heterogeneity at the molecular level. To address this lacuna, we investigated the proteomic analysis of hippocampal subfields─the cornu ammonis sectors (CA1, CA2, CA3, CA4) and dentate gyrus (DG) from healthy adult human cohorts. Findings: Microdissection of hippocampal subfields from archived formalin-fixed paraffin-embedded tissue sections followed by TMT-based multiplexed proteomic analysis resulted in the identification of 5,593 proteins. Out of these, 890 proteins were found to be differentially abundant among the subfields. Further bioinformatics analysis suggested proteins related to gene splicing, transportation, myelination, structural activity, and learning processes to be differentially abundant in DG, CA4, CA3, CA2, and CA1, respectively. A subset of proteins was selected for immunohistochemistry-based validation in an independent set of hippocampal samples. Conclusions: We believe that our findings will effectively pave the way for further analysis of the hippocampal subdivisions and provide awareness of its subfield-specific association to various neurofunctional anomalies in the future. The current mass spectrometry data is deposited and publicly made available through ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029697.
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Affiliation(s)
- Praseeda Mol
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India.,Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore 560066,India.,Manipal Academy of Higher Education, Manipal 576104, India
| | - Shwetha S Durgad
- Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Susarla K Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India.,Human Brain Tissue Repository, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
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36
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Taliaferro JM. Transcriptome-scale methods for uncovering subcellular RNA localization mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119202. [PMID: 34998919 PMCID: PMC9035289 DOI: 10.1016/j.bbamcr.2021.119202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Across a variety of systems, thousands of RNAs are localized to specific subcellular locations. However, for the vast majority of these RNAs, the mechanisms that underlie their transport are unknown. Historically, these mechanisms were uncovered for a single transcript at a time by laboriously testing the ability of RNA fragments to direct transcript localization. Recently developed methods profile the content of subcellular transcriptomes using high-throughput sequencing, allowing the analysis of the localization of thousands of transcripts at once. By identifying commonalities shared among multiple localized transcripts, these methods have the potential to rapidly expand our understanding of RNA localization mechanisms.
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Affiliation(s)
- J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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37
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Kim M, Moon S, Jeon HS, Kim S, Koh SH, Chang MS, Kim YM, Choi YK. Dual Effects of Korean Red Ginseng on Astrocytes and Neural Stem Cells in Traumatic Brain Injury: The HO-1–Tom20 Axis as a Putative Target for Mitochondrial Function. Cells 2022; 11:cells11050892. [PMID: 35269514 PMCID: PMC8909112 DOI: 10.3390/cells11050892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
Astrocytes display regenerative potential in pathophysiologic conditions. In our previous study, heme oxygenase-1 (HO-1) promoted astrocytic mitochondrial functions in mice via the peroxisome-proliferator-activating receptor-γ coactivator-1α (PGC-1α) pathway on administering Korean red ginseng extract (KRGE) after traumatic brain injury (TBI). In this study, KRGE promoted astrocytic mitochondrial functions, assessed with oxygen consumption and adenosine triphosphate (ATP) production, which could be regulated by the translocase of the outer membrane of mitochondria 20 (Tom20) pathway with a PGC-1α-independent pathway. The HO-1–Tom20 axis induced an increase in mitochondrial functions, detected with cytochrome c oxidase subunit 2 and cytochrome c. HO-1 crosstalk with nicotinamide phosphoribosyltransferase was concomitant with the upregulated nicotinamide adenine dinucleotide (NAD)/NADH ratio, thereby upregulating NAD-dependent class I sirtuins. In adult neural stem cells (NSCs), KRGE-treated, astrocyte-conditioned media increased oxygen consumption and Tom20 levels through astrocyte-derived HO-1. HO inactivation by Sn(IV) protoporphyrin IX dichloride in TBI mice administered KRGE decreased neuronal markers, together with Tom20. Thus, astrocytic HO-1 induced astrocytic mitochondrial functions. HO-1-related, astrocyte-derived factors may also induce neuronal differentiation and mitochondrial functions of adult NSCs after TBI. KRGE-mediated astrocytic HO-1 induction may have a key role in repairing neurovascular function post-TBI in peri-injured regions by boosting astrocytic and NSC mitochondrial functions.
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Affiliation(s)
- Minsu Kim
- Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (S.M.); (H.S.J.); (S.K.)
| | - Sunhong Moon
- Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (S.M.); (H.S.J.); (S.K.)
| | - Hui Su Jeon
- Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (S.M.); (H.S.J.); (S.K.)
| | - Sueun Kim
- Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (S.M.); (H.S.J.); (S.K.)
| | - Seong-Ho Koh
- Department of Neurology, Hanyang University Guri Hospital, Guri 11923, Korea;
| | - Mi-Sook Chang
- Department of Oral Anatomy, Seoul National University School of Dentistry, Seoul 03080, Korea;
| | - Young-Myeong Kim
- Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Yoon Kyung Choi
- Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea; (M.K.); (S.M.); (H.S.J.); (S.K.)
- Correspondence: ; Tel.: +82-2-450-0558
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38
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Metaplastic Reinforcement of Long-Term Potentiation in Hippocampal Area CA2 by Cholinergic Receptor Activation. J Neurosci 2021; 41:9082-9098. [PMID: 34561235 DOI: 10.1523/jneurosci.2885-20.2021] [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: 11/13/2020] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 11/21/2022] Open
Abstract
Hippocampal CA2, an inconspicuously positioned area between the well-studied CA1 and CA3 subfields, has captured research interest in recent years because of its role in social memory formation. However, the role of cholinergic inputs to the CA2 area for the regulation of synaptic plasticity remains to be fully understood. We show that cholinergic receptor activation with the nonselective cholinergic agonist, carbachol (CCh), triggers a protein synthesis-dependent and NMDAR-independent long-term synaptic depression (CCh-LTD) at entorhinal cortical (EC)-CA2 and Schaffer collateral (SC)-CA2 synapses in the hippocampus of adult male Wistar rats. The activation of muscarinic acetylcholine receptors (mAChRs) is critical for the induction of CCh-LTD with the results suggesting an involvement of M3 and M1 mAChRs in the early facilitation of CCh-LTD, while nicotinic AChR activation plays a role in the late maintenance of CCh-LTD at CA2 synapses. Remarkably, we find that CCh priming lowers the threshold for the subsequent induction of persistent long-term potentiation (LTP) of synaptic transmission at EC-CA2 and the plasticity-resistant SC-CA2 pathways. The effects of such a cholinergic-dependent synaptic depression on subsequent LTP at EC-CA2 and SC-CA2 synapses have not been previously explored. Collectively, the results demonstrate that CA2 synaptic learning rules are regulated in a metaplastic manner, whereby modifications triggered by prior cholinergic stimulation can dictate the outcome of future plasticity events. Moreover, the reinforcement of LTP at EC inputs to CA2 following the priming stimulus coexists with concurrent sustained CCh-LTD at the SC-CA2 pathway and is dynamically scaled by modulation of SC-CA2 synaptic transmission.SIGNIFICANCE STATEMENT The release of the neuromodulator acetylcholine is critically involved in processes of hippocampus-dependent memory formation. Cholinergic afferents originating in the medial septum and diagonal bands of Broca terminating in the hippocampal area CA2 might play an important role in the modulation of area-specific synaptic plasticity. Our findings demonstrate that cholinergic receptor activation induces an LTD of synaptic transmission at entorhinal cortical- and Schaffer collateral-CA2 synapses. This cholinergic activation-mediated LTD displays a bidirectional metaplastic switch to LTP on a future timescale. This suggests that such bidirectional synaptic modifications triggered by the dynamic modulation of tonic cholinergic receptor activation may support the formation of CA2-dependent memories given the increased hippocampal cholinergic tone during active wakefulness observed in exploratory behavior.
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39
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Perez JD, Fusco CM, Schuman EM. A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons. Annu Rev Genet 2021; 55:183-207. [PMID: 34460296 DOI: 10.1146/annurev-genet-030321-054851] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Claudia M Fusco
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
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40
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Faitg J, Lacefield C, Davey T, White K, Laws R, Kosmidis S, Reeve AK, Kandel ER, Vincent AE, Picard M. 3D neuronal mitochondrial morphology in axons, dendrites, and somata of the aging mouse hippocampus. Cell Rep 2021; 36:109509. [PMID: 34380033 PMCID: PMC8423436 DOI: 10.1016/j.celrep.2021.109509] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 12/22/2022] Open
Abstract
The brain's ability to process complex information relies on the constant supply of energy through aerobic respiration by mitochondria. Neurons contain three anatomically distinct compartments-the soma, dendrites, and projecting axons-which have different energetic and biochemical requirements, as well as different mitochondrial morphologies in cultured systems. In this study, we apply quantitative three-dimensional electron microscopy to map mitochondrial network morphology and complexity in the mouse brain. We examine somatic, dendritic, and axonal mitochondria in the dentate gyrus and cornu ammonis 1 (CA1) of the mouse hippocampus, two subregions with distinct principal cell types and functions. We also establish compartment-specific differences in mitochondrial morphology across these cell types between young and old mice, highlighting differences in age-related morphological recalibrations. Overall, these data define the nature of the neuronal mitochondrial network in the mouse hippocampus, providing a foundation to examine the role of mitochondrial morpho-function in the aging brain.
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Affiliation(s)
- Julie Faitg
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Clay Lacefield
- New York State Psychiatric Institute, New York, NY 10032, USA
| | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Kathryn White
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Stylianos Kosmidis
- Zuckerman Mind Brain Behavior Institute, Kavli Institute for Brain Science, Department of Neuroscience, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Amy K Reeve
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eric R Kandel
- New York State Psychiatric Institute, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Kavli Institute for Brain Science, Department of Neuroscience, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Martin Picard
- New York State Psychiatric Institute, New York, NY 10032, USA; Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, The Merritt Center and Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA.
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41
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Swarnkar S, Avchalumov Y, Espadas I, Grinman E, Liu XA, Raveendra BL, Zucca A, Mediouni S, Sadhu A, Valente S, Page D, Miller K, Puthanveettil SV. Molecular motor protein KIF5C mediates structural plasticity and long-term memory by constraining local translation. Cell Rep 2021; 36:109369. [PMID: 34260917 PMCID: PMC8319835 DOI: 10.1016/j.celrep.2021.109369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/16/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
Synaptic structural plasticity, key to long-term memory storage, requires translation of localized RNAs delivered by long-distance transport from the neuronal cell body. Mechanisms and regulation of this system remain elusive. Here, we explore the roles of KIF5C and KIF3A, two members of kinesin superfamily of molecular motors (Kifs), and find that loss of function of either kinesin decreases dendritic arborization and spine density whereas gain of function of KIF5C enhances it. KIF5C function is a rate-determining component of local translation and is associated with ∼650 RNAs, including EIF3G, a regulator of translation initiation, and plasticity-associated RNAs. Loss of function of KIF5C in dorsal hippocampal CA1 neurons constrains both spatial and contextual fear memory, whereas gain of function specifically enhances spatial memory and extinction of contextual fear. KIF5C-mediated long-distance transport of local translation substrates proves a key mechanism underlying structural plasticity and memory.
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Affiliation(s)
- Supriya Swarnkar
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yosef Avchalumov
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Isabel Espadas
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eddie Grinman
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Xin-An Liu
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Bindu L Raveendra
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Aya Zucca
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sonia Mediouni
- Department of Immunology and Microbiology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Abhishek Sadhu
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Susana Valente
- Department of Immunology and Microbiology, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Damon Page
- Department of Neuroscience, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kyle Miller
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
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42
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Park J, Farris S. Spatiotemporal Regulation of Transcript Isoform Expression in the Hippocampus. Front Mol Neurosci 2021; 14:694234. [PMID: 34305526 PMCID: PMC8295539 DOI: 10.3389/fnmol.2021.694234] [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: 04/12/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development and plasticity of hippocampal neurons require specific RNA isoforms to be expressed in the right place at the right time. Precise spatiotemporal transcript regulation requires the incorporation of essential regulatory RNA sequences into expressed isoforms. In this review, we describe several RNA processing strategies utilized by hippocampal neurons to regulate the spatiotemporal expression of genes critical to development and plasticity. The works described here demonstrate how the hippocampus is an ideal investigative model for uncovering alternate isoform-specific mechanisms that restrict the expression of transcripts in space and time.
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Affiliation(s)
- Joun Park
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States
| | - Shannon Farris
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
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Ayhan F, Kulkarni A, Berto S, Sivaprakasam K, Douglas C, Lega BC, Konopka G. Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans. Neuron 2021; 109:2091-2105.e6. [PMID: 34051145 PMCID: PMC8273123 DOI: 10.1016/j.neuron.2021.05.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
The hippocampus supports many facets of cognition, including learning, memory, and emotional processing. Anatomically, the hippocampus runs along a longitudinal axis, posterior to anterior in primates. The structure, function, and connectivity of the hippocampus vary along this axis. In human hippocampus, longitudinal functional heterogeneity remains an active area of investigation, and structural heterogeneity has not been described. To understand the cellular and molecular diversity along the hippocampal long axis in human brain and define molecular signatures corresponding to functional domains, we performed single-nuclei RNA sequencing on surgically resected human anterior and posterior hippocampus from epilepsy patients, identifying differentially expressed genes at cellular resolution. We further identify axis- and cell-type-specific gene expression signatures that differentially intersect with human genetic signals, identifying cell-type-specific genes in the posterior hippocampus for cognitive function and the anterior hippocampus for mood and affect. These data are accessible as a public resource through an interactive website.
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Affiliation(s)
- Fatma Ayhan
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Stefano Berto
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Connor Douglas
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bradley C Lega
- Department of Neurosurgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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44
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Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. BMC Genomics 2021; 22:476. [PMID: 34174817 PMCID: PMC8234626 DOI: 10.1186/s12864-021-07781-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The sequence content of the 3' UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging. RESULTS To combat this problem, we developed LABRAT, an APA isoform quantification method. LABRAT takes advantage of newly developed transcriptome quantification techniques to accurately determine relative APA site usage and how it varies across conditions. Using LABRAT, we found consistent relationships between gene-distal APA and subcellular RNA localization in multiple cell types. We also observed connections between transcription speed and APA site choice as well as tumor-specific transcriptome-wide shifts in APA isoform abundance in hundreds of patient-derived tumor samples that were associated with patient prognosis. We investigated the effects of APA on transcript expression and found a weak overall relationship, although many individual genes showed strong correlations between relative APA isoform abundance and overall gene expression. We interrogated the roles of 191 RNA-binding proteins in the regulation of APA isoforms, finding that dozens promote broad, directional shifts in relative APA isoform abundance both in vitro and in patient-derived samples. Finally, we find that APA site shifts in the two classes of APA, tandem UTRs and alternative last exons, are strongly correlated across many contexts, suggesting that they are coregulated. CONCLUSIONS We conclude that LABRAT has the ability to accurately quantify APA isoform ratios from RNAseq data across a variety of sample types. Further, LABRAT is able to derive biologically meaningful insights that connect APA isoform regulation to cellular and molecular phenotypes.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Austin E Gillen
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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45
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RGS14 Regulation of Post-Synaptic Signaling and Spine Plasticity in Brain. Int J Mol Sci 2021; 22:ijms22136823. [PMID: 34201943 PMCID: PMC8268017 DOI: 10.3390/ijms22136823] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
The regulator of G-protein signaling 14 (RGS14) is a multifunctional signaling protein that regulates post synaptic plasticity in neurons. RGS14 is expressed in the brain regions essential for learning, memory, emotion, and stimulus-induced behaviors, including the basal ganglia, limbic system, and cortex. Behaviorally, RGS14 regulates spatial and object memory, female-specific responses to cued fear conditioning, and environmental- and psychostimulant-induced locomotion. At the cellular level, RGS14 acts as a scaffolding protein that integrates G protein, Ras/ERK, and calcium/calmodulin signaling pathways essential for spine plasticity and cell signaling, allowing RGS14 to naturally suppress long-term potentiation (LTP) and structural plasticity in hippocampal area CA2 pyramidal cells. Recent proteomics findings indicate that RGS14 also engages the actomyosin system in the brain, perhaps to impact spine morphogenesis. Of note, RGS14 is also a nucleocytoplasmic shuttling protein, where its role in the nucleus remains uncertain. Balanced nuclear import/export and dendritic spine localization are likely essential for RGS14 neuronal functions as a regulator of synaptic plasticity. Supporting this idea, human genetic variants disrupting RGS14 localization also disrupt RGS14’s effects on plasticity. This review will focus on the known and unexplored roles of RGS14 in cell signaling, physiology, disease and behavior.
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Epple R, Krüger D, Berulava T, Brehm G, Ninov M, Islam R, Köster S, Fischer A. The Coding and Small Non-coding Hippocampal Synaptic RNAome. Mol Neurobiol 2021; 58:2940-2953. [PMID: 33569760 PMCID: PMC8128755 DOI: 10.1007/s12035-021-02296-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: 09/24/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as microRNAs have also been described at synapses where they are believed to control mRNA availability for local translation. A combined dataset analyzing the synaptic coding and non-coding RNAome via next-generation sequencing approaches is, however, still lacking. Here, we isolate synaptosomes from the hippocampus of young wild-type mice and provide the coding and non-coding synaptic RNAome. These data are complemented by a novel approach for analyzing the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers. Our data show that synaptic microRNAs control almost the entire synaptic mRNAome, and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluidic chamber system, our findings also support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable for studying the dynamics of the synaptic RNAome in response to stimulation. In conclusion, our data provide a valuable resource and point to several important targets for further research.
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Affiliation(s)
- Robert Epple
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Dennis Krüger
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Tea Berulava
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Momchil Ninov
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rezaul Islam
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Andre Fischer
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany.
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany.
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Kay Y, Herring BE. An optogenetic method for investigating presynaptic molecular regulation. Sci Rep 2021; 11:11329. [PMID: 34059719 PMCID: PMC8166971 DOI: 10.1038/s41598-021-90244-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
While efficient methods are well established for studying postsynaptic protein regulation of glutamatergic synapses in the mammalian central nervous system, similarly efficient methods are lacking for studying proteins regulating presynaptic function. In the present study, we introduce an optical/electrophysiological method for investigating presynaptic molecular regulation. Here, using an optogenetic approach, we selectively stimulate genetically modified presynaptic CA3 pyramidal neurons in the hippocampus and measure optically-induced excitatory postsynaptic currents produced in unmodified postsynaptic CA1 pyramidal neurons. While such use of optogenetics is not novel, previous implementation methods do not allow basic quantification of the changes in synaptic strength produced by genetic manipulations. We find that incorporating simultaneous recordings of fiber volley amplitude provides a control for optical stimulation intensity and, as a result, creates a metric of synaptic efficacy that can be compared across experimental conditions. In the present study, we utilize our new method to demonstrate that inhibition of synaptotagmin 1 expression in CA3 pyramidal neurons leads to a significant reduction in Schaffer collateral synapse function, an effect that is masked with conventional electrical stimulation. Our hope is that this method will expedite our understanding of molecular regulatory pathways that govern presynaptic function.
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Affiliation(s)
- Yuni Kay
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Bruce E Herring
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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48
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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49
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McCann KE, Lustberg DJ, Shaughnessy EK, Carstens KE, Farris S, Alexander GM, Radzicki D, Zhao M, Dudek SM. Novel role for mineralocorticoid receptors in control of a neuronal phenotype. Mol Psychiatry 2021; 26:350-364. [PMID: 31745235 PMCID: PMC7234915 DOI: 10.1038/s41380-019-0598-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/11/2019] [Accepted: 11/06/2019] [Indexed: 12/25/2022]
Abstract
Mineralocorticoid receptors (MRs) in the brain play a role in learning and memory, neuronal differentiation, and regulation of the stress response. Within the hippocampus, the highest expression of MRs is in area CA2. CA2 pyramidal neurons have a distinct molecular makeup resulting in a plasticity-resistant phenotype, distinguishing them from neurons in CA1 and CA3. Thus, we asked whether MRs regulate CA2 neuron properties and CA2-related behaviors. Using three conditional knockout methods at different stages of development, we found a striking decrease in multiple molecular markers for CA2, an effect mimicked by chronic antagonism of MRs. Furthermore, embryonic deletion of MRs disrupted afferent inputs to CA2 and enabled synaptic potentiation of the normally LTP-resistant synaptic currents in CA2. We also found that CA2-targeted MR knockout was sufficient to disrupt social behavior and alter behavioral responses to novelty. Altogether, these results demonstrate an unappreciated role for MRs in controlling CA2 pyramidal cell identity and in facilitating CA2-dependent behaviors.
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Affiliation(s)
- Katharine E McCann
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Daniel J Lustberg
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- Molecular and Systems Pharmacology Graduate Program, Emory University, Atlanta, GA, USA
| | - Emma K Shaughnessy
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- Neuroscience Graduate Program, Georgia State University, Atlanta, GA, USA
| | - Kelly E Carstens
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Shannon Farris
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- Center for Neurobiology Research, Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, USA
| | - Georgia M Alexander
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Daniel Radzicki
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Meilan Zhao
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Serena M Dudek
- Synaptic and Developmental Plasticity Group, Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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50
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Goering R, Hudish LI, Guzman BB, Raj N, Bassell GJ, Russ HA, Dominguez D, Taliaferro JM. FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences. eLife 2020; 9:e52621. [PMID: 32510328 PMCID: PMC7279889 DOI: 10.7554/elife.52621] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/15/2020] [Indexed: 12/15/2022] Open
Abstract
The sorting of RNA molecules to subcellular locations facilitates the activity of spatially restricted processes. We have analyzed subcellular transcriptomes of FMRP-null mouse neuronal cells to identify transcripts that depend on FMRP for efficient transport to neurites. We found that these transcripts contain an enrichment of G-quadruplex sequences in their 3' UTRs, suggesting that FMRP recognizes them to promote RNA localization. We observed similar results in neurons derived from Fragile X Syndrome patients. We identified the RGG domain of FMRP as important for binding G-quadruplexes and the transport of G-quadruplex-containing transcripts. Finally, we found that the translation and localization targets of FMRP were distinct and that an FMRP mutant that is unable to bind ribosomes still promoted localization of G-quadruplex-containing messages. This suggests that these two regulatory modes of FMRP may be functionally separated. These results provide a framework for the elucidation of similar mechanisms governed by other RNA-binding proteins.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusBoulderUnited States
| | - Laura I Hudish
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical CampusBoulderUnited States
| | - Bryan B Guzman
- Department of Pharmacology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Nisha Raj
- Departments of Cell Biology and Neurology, Emory University School of MedicineAtlantaGeorgia
| | - Gary J Bassell
- Departments of Cell Biology and Neurology, Emory University School of MedicineAtlantaGeorgia
| | - Holger A Russ
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical CampusBoulderUnited States
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel HillChapel HillUnited States
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusBoulderUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusBoulderUnited States
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