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Xiang LY, Chen XY, Lu LM, Kong MH, Ji Q, Xiong Y, Xie MM, Jian XL, Zhu ZR. Mechanisms of Neuronal Reactivation in Memory Consolidation: A Perspective from Pathological Conditions. Neuroscience 2024; 551:196-204. [PMID: 38810690 DOI: 10.1016/j.neuroscience.2024.05.030] [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: 01/29/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Memory consolidation refers to a process by which labile newly formed memory traces are progressively strengthened into long term memories and become more resistant to interference. Recent work has revealed that spontaneous hippocampal activity during rest, commonly referred to as "offline" activity, plays a critical role in the process of memory consolidation. Hippocampal reactivation occurs during sharp-wave ripples (SWRs), which are events associated with highly synchronous neural firing in the hippocampus and modulation of neural activity in distributed brain regions. Memory consolidation occurs primarily through a coordinated communication between hippocampus and neocortex. Cortical slow oscillations drive the repeated reactivation of hippocampal memory representations together with SWRs and thalamo-cortical spindles, inducing long-lasting cellular and network modifications responsible for memory stabilization.In this review, we aim to comprehensively cover the field of "reactivation and memory consolidation" research by detailing the physiological mechanisms of neuronal reactivation and firing patterns during SWRs and providing a discussion of more recent key findings. Several mechanistic explanations of neuropsychiatric diseases propose that impaired neural replay may underlie some of the symptoms of the disorders. Abnormalities in neuronal reactivation are a common phenomenon and cause pathological impairment in several diseases, such as Alzheimer's disease (AD), epilepsy and schizophrenia. However, the specific pathological changes and mechanisms of reactivation in each disease are different. Recent work has also enlightened some of the underlying pathological mechanisms of neuronal reactivation in these diseases. In this review, we further describe how SWRs, ripples and slow oscillations are affected in Alzheimer's disease, epilepsy, and schizophrenia. We then compare the differences of neuronal reactivation and discuss how different reactivation abnormalities cause pathological changes in these diseases. Aberrant neural reactivation provides insights into disease pathogenesis and may even serve as biomarkers for early disease progression and treatment response.
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Affiliation(s)
- Lei-Ying Xiang
- School of Educational Sciences, Chongqing Normal University, Chongqing, PR China
| | - Xiao-Yi Chen
- School of Educational Sciences, Chongqing Normal University, Chongqing, PR China
| | - Li-Ming Lu
- School of Educational Sciences, Chongqing Normal University, Chongqing, PR China
| | - Ming-Hui Kong
- School of Educational Sciences, Chongqing Normal University, Chongqing, PR China
| | - Qi Ji
- Department of Medical Psychology, Army Medical University, Chongqing, PR China
| | - Yu Xiong
- Department of Stomatology, Southwest Hospital, Chongqing, PR China
| | - Mei-Ming Xie
- Chinese People's Liberation Army Western Theater General Hospital, Chengdu, PR China
| | - Xin-Ling Jian
- No. 950 Hospital of the Chinese People's Liberation Army, Yecheng, PR China
| | - Zhi-Ru Zhu
- Department of Medical Psychology, Army Medical University, Chongqing, PR China.
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2
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Carbonero D, Noueihed J, Kramer MA, White JA. Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.11.561797. [PMID: 37905071 PMCID: PMC10614735 DOI: 10.1101/2023.10.11.561797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Calcium imaging allows recording from hundreds of neurons in vivo with the ability to resolve single cell activity. Evaluating and analyzing neuronal responses, while also considering all dimensions of the data set to make specific conclusions, is extremely difficult. Often, descriptive statistics are used to analyze these forms of data. These analyses, however, remove variance by averaging the responses of single neurons across recording sessions, or across combinations of neurons, to create single quantitative metrics, losing the temporal dynamics of neuronal activity, and their responses relative to each other. Dimensionally Reduction (DR) methods serve as a good foundation for these analyses because they reduce the dimensions of the data into components, while still maintaining the variance. Non-negative Matrix Factorization (NMF) is an especially promising DR analysis method for analyzing activity recorded in calcium imaging because of its mathematical constraints, which include positivity and linearity. We adapt NMF for our analyses and compare its performance to alternative dimensionality reduction methods on both artificial and in vivo data. We find that NMF is well-suited for analyzing calcium imaging recordings, accurately capturing the underlying dynamics of the data, and outperforming alternative methods in common use.
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Affiliation(s)
- Daniel Carbonero
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America
- Neurophotonics Center, Boston University, Boston, Massachusetts, United States of America
| | - Jad Noueihed
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America
- Neurophotonics Center, Boston University, Boston, Massachusetts, United States of America
| | - Mark A. Kramer
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America
- Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America
| | - John A. White
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America
- Neurophotonics Center, Boston University, Boston, Massachusetts, United States of America
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3
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Hu G, Zheng Y, Zhang B, Zhao C, Xu L, Wei J, Jing J, Liu Y, Zeng T, Zhou Y. Histone methyltransferase SETD2 is required for proper hippocampal lamination and neuronal maturation. Mol Biol Cell 2024; 35:ar54. [PMID: 38446615 PMCID: PMC11064668 DOI: 10.1091/mbc.e23-12-0492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Proper formation of the hippocampus is crucial for the brain to execute memory and learning functions. However, many questions remain regarding how pyramidal neurons (PNs) of the hippocampus mature and precisely position. Here we revealed that Setd2, the methyltransferase for histone 3 lysine 36 trimethylation (H3K36me3), is essential for the precise localization and maturation of PNs in the hippocampal CA1. The ablation of Setd2 in neural progenitors leads to irregular lamination of the CA1 and increased numbers of PNs in the stratum oriens. Setd2 deletion in postmitotic neurons causes mislocalization and immaturity of CA1 PNs. Transcriptome analyses revealed that SETD2 maintains the expressions of clustered protocadherin (cPcdh) genes. Together, Setd2 is required for proper hippocampal lamination and maturation of CA1 PNs.
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Affiliation(s)
- Guangda Hu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yue Zheng
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bo Zhang
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chen Zhao
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Lichao Xu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jiayi Wei
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Jing Jing
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ying Liu
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Tao Zeng
- Department of Neurosurgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine; Shanghai 200072, China
| | - Yan Zhou
- Department of Neurosurgery, Medical Research Institute, Frontier Science Center of Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
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4
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Li X, Quan P, Si Y, Liu F, Fan Y, Ding F, Sun L, Liu H, Huang S, Sun L, Yang F, Yao L. The microRNA-211-5p/P2RX7/ERK/GPX4 axis regulates epilepsy-associated neuronal ferroptosis and oxidative stress. J Neuroinflammation 2024; 21:13. [PMID: 38191407 PMCID: PMC10773122 DOI: 10.1186/s12974-023-03009-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024] Open
Abstract
Ferroptosis is an iron-dependent cell death mechanism involving the accumulation of lipid peroxides. As a critical regulator, glutathione peroxidase 4 (GPX4) has been demonstrated to be downregulated in epilepsy. However, the mechanism of ferroptosis in epilepsy remains unclear. In this study, bioinformatics analysis, analysis of epilepsy patient blood samples and cell and mouse experiments revealed strong associations among epilepsy, ferroptosis, microRNA-211-5p and purinergic receptor P2X 7 (P2RX7). P2RX7 is a nonselective ligand-gated homotrimeric cation channel, and its activation mainly increases neuronal activity during epileptic seizures. In our study, the upregulation of P2RX7 in epilepsy was attributed to the downregulation of microRNA (miR)-211-5p. Furthermore, P2RX7 has been found to regulate GPX4/HO-1 by alleviating lipid peroxidation induced by suppression of the MAPK/ERK signaling pathway in murine models. The dynamic decrease in miR-211-5p expression induces hypersynchronization and both nonconvulsive and convulsive seizures, and forebrain miR-211-5p suppression exacerbates long-lasting pentylenetetrazole-induced seizures. Additionally, in this study, induction of miR-211-5p expression or genetic-silencing of P2RX7 significantly reduced the seizure score and duration in murine models through the abovementioned pathways. These results suggest that the miR-211-5p/P2RX7 axis is a novel target for suppressing both ferroptosis and epilepsy.
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Affiliation(s)
- Xueying Li
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Pusheng Quan
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
- Department of Neurology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yao Si
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Fei Liu
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Yuwei Fan
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Feifan Ding
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Lina Sun
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Han Liu
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Shuo Huang
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Linlin Sun
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China.
| | - Fan Yang
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China.
| | - Lifen Yao
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China.
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Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Iorgulescu JB, Yoon CH, Wu CJ, Macosko EZ, Chen F. Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature 2024; 625:101-109. [PMID: 38093010 PMCID: PMC10764288 DOI: 10.1038/s41586-023-06837-4] [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: 03/26/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed1-6. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 μm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor-ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire.
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Affiliation(s)
- Andrew J C Russell
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jackson A Weir
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
| | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Vipin Kumar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sandeep Kambhampati
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard University, Boston, MA, USA
| | - Ruth Raichur
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Sophia Liu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Biophysics Program, Harvard University, Boston, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Vignesh Shanmugam
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luyi Tian
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Guangzhou Laboratory, Guangdong, China
| | - J Bryan Iorgulescu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA, USA
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles H Yoon
- Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Stem Cell Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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6
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Galvis-Montes DS, van Loo KMJ, van Waardenberg AJ, Surges R, Schoch S, Becker AJ, Pitsch J. Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus. Sci Rep 2023; 13:22187. [PMID: 38092829 PMCID: PMC10719343 DOI: 10.1038/s41598-023-49310-y] [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: 08/07/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Transient brain insults including status epilepticus (SE) can initiate a process termed 'epileptogenesis' that results in chronic temporal lobe epilepsy. As a consequence, the entire tri-synaptic circuit of the hippocampus is fundamentally impaired. A key role in epileptogenesis has been attributed to the CA1 region as the last relay station in the hippocampal circuit and as site of aberrant plasticity, e.g. mediated by acquired channelopathies. The transcriptional profiles of the distinct hippocampal neurons are highly dynamic during epileptogenesis. Here, we aimed to elucidate the early SE-elicited mRNA signature changes and the respective upstream regulatory cascades in CA1. RNA sequencing of CA1 was performed in the mouse pilocarpine-induced SE model at multiple time points ranging from 6 to 72 h after the initial insult. Bioinformatics was used to decipher altered gene expression, signalling cascades and their corresponding cell type profiles. Robust transcriptomic changes were detected at 6 h after SE and at subsequent time points during early epileptogenesis. Major differentially expressed mRNAs encoded primarily immediate early and excitability-related gene products, as well as genes encoding immune signalling factors. Binding sites for the transcription factors Nfkb1, Spi1, Irf8, and two Runx family members, were enriched within promoters of differentially expressed genes related to major inflammatory processes, whereas the transcriptional repressors Suz12, Nfe2l2 and Rest were associated with hyperexcitability and GABA / glutamate receptor activity. CA1 quickly responds to SE by inducing transcription of genes linked to inflammation and excitation stress. Transcription factors mediating this transcriptomic switch represent targets for new highly selected, cell type and time window-specific anti-epileptogenic strategies.
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Grants
- SCHO 820/4-1, SCHO 820/6-1, SCHO 820/7-1, SCHO 820/5-2, SPP1757, SFB1089, FOR 2715 Deutsche Forschungsgemeinschaft
- SCHO 820/4-1, SCHO 820/6-1, SCHO 820/7-1, SCHO 820/5-2, SPP1757, SFB1089, FOR 2715 Deutsche Forschungsgemeinschaft
- Promotionskolleg 'NeuroImmunology' Else Kröner-Fresenius-Stiftung
- Promotionskolleg 'NeuroImmunology' Else Kröner-Fresenius-Stiftung
- BONFOR program of the Medical Faculty, University of Bonn
- Rheinische Friedrich-Wilhelms-Universität Bonn (1040)
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Affiliation(s)
- Daniel S Galvis-Montes
- Department of Epileptology, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Karen M J van Loo
- Department of Epileptology, Neurology, RWTH Aachen University, Aachen, Germany
| | | | - Rainer Surges
- Department of Epileptology, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Susanne Schoch
- Department of Epileptology, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Section for Translational Epilepsy Research, Department of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Albert J Becker
- Section for Translational Epilepsy Research, Department of Neuropathology, University Hospital Bonn, Bonn, Germany
| | - Julika Pitsch
- Department of Epileptology, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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Hoffman OR, Patterson A, Gohar E, Coleman E, Espina JEC, Schoenike B, Espinosa-Garcia C, Paredes F, Dingledine R, Maguire J, Roopra A. Profound seizure suppression and disease modification by targeting JAK1, a key driver of a pro-epileptogenic gene network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552299. [PMID: 37662337 PMCID: PMC10473616 DOI: 10.1101/2023.08.07.552299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Epilepsy is the 4th most prevalent neurological disorder with over 50 million cases worldwide. While a number of drugs exist to suppress seizures, approximately 1/3 of patients remain drug resistant, and no current treatments are disease modifying. Using network and systems-based approaches, we find that the histone methylase EZH2 suppresses epileptogenesis and slows disease progression, via repression of JAK1 and STAT3 signaling in hippocampal neurons. Pharmacological inhibition of JAK1 with the orally available, FDA-approved drug CP690550 (Tofacitinib) profoundly suppresses behavioral and electrographic seizures after the onset of epilepsy across preclinical rodent models of acquired epilepsy. This seizure suppression persists for weeks after drug withdrawal. Identification of an endogenous protective response to status epilepticus in the form of EZH2 induction has highlighted a critical role for the JAK1 kinase and STAT3 in both the initiation and propagation of epilepsy across preclinical rodent models and human disease. Overall, we find that STAT3 is transiently activated after insult, reactivates with spontaneous seizures, and remains targetable for disease modification in chronic epilepsy.
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8
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Varghese N, Moscoso B, Chavez A, Springer K, Ortiz E, Soh H, Santaniello S, Maheshwari A, Tzingounis AV. KCNQ2/3 Gain-of-Function Variants and Cell Excitability: Differential Effects in CA1 versus L2/3 Pyramidal Neurons. J Neurosci 2023; 43:6479-6494. [PMID: 37607817 PMCID: PMC10513074 DOI: 10.1523/jneurosci.0980-23.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023] Open
Abstract
Gain-of-function (GOF) pathogenic variants in the potassium channels KCNQ2 and KCNQ3 lead to hyperexcitability disorders such as epilepsy and autism spectrum disorders. However, the underlying cellular mechanisms of how these variants impair forebrain function are unclear. Here, we show that the R201C variant in KCNQ2 has opposite effects on the excitability of two types of mouse pyramidal neurons of either sex, causing hyperexcitability in layer 2/3 (L2/3) pyramidal neurons and hypoexcitability in CA1 pyramidal neurons. Similarly, the homologous R231C variant in KCNQ3 leads to hyperexcitability in L2/3 pyramidal neurons and hypoexcitability in CA1 pyramidal neurons. However, the effects of KCNQ3 gain-of-function on excitability are specific to superficial CA1 pyramidal neurons. These findings reveal a new level of complexity in the function of KCNQ2 and KCNQ3 channels in the forebrain and provide a framework for understanding the effects of gain-of-function variants and potassium channels in the brain.SIGNIFICANCE STATEMENT KCNQ2/3 gain-of-function (GOF) variants lead to severe forms of neurodevelopmental disorders, but the mechanisms by which these channels affect neuronal activity are poorly understood. In this study, using a series of transgenic mice we demonstrate that the same KCNQ2/3 GOF variants can lead to either hyperexcitability or hypoexcitability in different types of pyramidal neurons [CA1 vs layer (L)2/3]. Additionally, we show that expression of the recurrent KCNQ2 GOF variant R201C in forebrain pyramidal neurons could lead to seizures and SUDEP. Our data suggest that the effects of KCNQ2/3 GOF variants depend on specific cell types and brain regions, possibly accounting for the diverse range of phenotypes observed in individuals with KCNQ2/3 GOF variants.
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Affiliation(s)
- Nissi Varghese
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut 06269
| | - Bruno Moscoso
- Department of Neurology, Baylor College of Medicine, Houston, Texas 77030
| | - Ana Chavez
- Department of Neurology, Baylor College of Medicine, Houston, Texas 77030
| | - Kristen Springer
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut 06269
| | - Erika Ortiz
- Department of Neurology, Baylor College of Medicine, Houston, Texas 77030
| | - Heun Soh
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut 06269
| | - Sabato Santaniello
- Department of Biomedical Engineering and Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Atul Maheshwari
- Department of Neurology, Baylor College of Medicine, Houston, Texas 77030
| | - Anastasios V Tzingounis
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut 06269
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9
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Zhang L, Yang Q, Yuan R, Li M, Lv M, Zhang L, Xie X, Liang W, Chen X. Single-nucleus transcriptomic mapping of blast-induced traumatic brain injury in mice hippocampus. Sci Data 2023; 10:638. [PMID: 37730716 PMCID: PMC10511629 DOI: 10.1038/s41597-023-02552-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
As a significant type of traumatic brain injury (TBI), blast-induced traumatic brain injury (bTBI) frequently results in severe neurological and psychological impairments. Due to its unique mechanistic and clinical features, bTBI presents diagnostic and therapeutic challenges compared to other TBI forms. The hippocampus, an important site for secondary injury of bTBI, serves as a key niche for neural regeneration and repair post-injury, and is closely associated with the neurological outcomes of bTBI patients. Nonetheless, the pathophysiological alterations of hippocampus underpinning bTBI remain enigmatic, and a corresponding transcriptomic dataset for research reference is yet to be established. In this investigation, the single-nucleus RNA sequencing (snRNA-seq) technique was employed to sequence individual hippocampal nuclei of mice from bTBI and sham group. Upon stringent quality control, gene expression data from 17,278 nuclei were obtained, with the dataset's reliability substantiated through various analytical methods. This dataset holds considerable potential for exploring secondary hippocampal injury and neurogenesis mechanisms following bTBI, with important reference value for the identification of specific diagnostic and therapeutic targets for bTBI.
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Affiliation(s)
- Lingxuan Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Qiuyun Yang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
- West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruixuan Yuan
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Manrui Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lin Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiaoqi Xie
- Department of Critical Care Medicine, Sichuan University, Chengdu, 610041, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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10
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Sanchez-Aguilera A, Masmudi-Martín M, Navas-Olive A, Baena P, Hernández-Oliver C, Priego N, Cordón-Barris L, Alvaro-Espinosa L, García S, Martínez S, Lafarga M, Lin MZ, Al-Shahrour F, Menendez de la Prida L, Valiente M. Machine learning identifies experimental brain metastasis subtypes based on their influence on neural circuits. Cancer Cell 2023; 41:1637-1649.e11. [PMID: 37652007 PMCID: PMC10507426 DOI: 10.1016/j.ccell.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/26/2023] [Accepted: 07/26/2023] [Indexed: 09/02/2023]
Abstract
A high percentage of patients with brain metastases frequently develop neurocognitive symptoms; however, understanding how brain metastasis co-opts the function of neuronal circuits beyond a tumor mass effect remains unknown. We report a comprehensive multidimensional modeling of brain functional analyses in the context of brain metastasis. By testing different preclinical models of brain metastasis from various primary sources and oncogenic profiles, we dissociated the heterogeneous impact on local field potential oscillatory activity from cortical and hippocampal areas that we detected from the homogeneous inter-model tumor size or glial response. In contrast, we report a potential underlying molecular program responsible for impairing neuronal crosstalk by scoring the transcriptomic and mutational profiles in a model-specific manner. Additionally, measurement of various brain activity readouts matched with machine learning strategies confirmed model-specific alterations that could help predict the presence and subtype of metastasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sonia Martínez
- Experimental Therapeutics Programme, CNIO, 28029 Madrid, Spain
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology and CIBERNED, University of Cantabria- IDIVAL, 39011 Santander, Spain
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University, Stanford, CA 94305-5090, USA
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11
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Lillo A, Serrano-Marín J, Lillo J, Raïch I, Navarro G, Franco R. Differential Gene Expression in Activated Microglia Treated with Adenosine A 2A Receptor Antagonists Highlights Olfactory Receptor 56 and T-Cell Activation GTPase-Activating Protein 1 as Potential Biomarkers of the Polarization of Activated Microglia. Cells 2023; 12:2213. [PMID: 37759436 PMCID: PMC10526142 DOI: 10.3390/cells12182213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Microglial activation often accompanies the plastic changes occurring in the brain of patients with neurodegenerative diseases. A2A and A3 adenosine receptors have been proposed as therapeutic targets to combat neurodegeneration. RNAseq was performed using samples isolated from lipopolysaccharide/interferon-γ activated microglia treated with SCH 58261, a selective A2A receptor antagonist, and with both SCH 58261 and 2-Cl-IB-MECA, a selective A3 receptor agonist. None of the treatments led to any clear microglial phenotype when gene expression for classical biomarkers of microglial polarization was assessed. However, many of the downregulated genes were directly or indirectly related to immune system-related events. Searching for genes whose expression was both significantly and synergistically affected when treated with the two adenosine receptor ligands, the AC122413.1 and Olfr56 were selected among those that were, respectively, upregulated and downregulated. We therefore propose that the products of these genes, olfactory receptor 56 and T-cell activation GTPase-activating protein 1, deserve attention as potential biomarkers of phenotypes that occur upon microglial activation.
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Affiliation(s)
- Alejandro Lillo
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
| | - Joan Serrano-Marín
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Jaume Lillo
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Iu Raïch
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Gemma Navarro
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, Universitat de Barcelona, 08007 Barcelona, Spain; (A.L.); (J.L.); (I.R.); (G.N.)
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Institute of Neurosciences, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Rafael Franco
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28029 Madrid, Spain
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
- School of Chemistry, Universitat de Barcelona, 08028 Barcelona, Spain
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12
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Shen W, Pristov JB, Nobili P, Nikolić L. Can glial cells save neurons in epilepsy? Neural Regen Res 2023; 18:1417-1422. [PMID: 36571336 PMCID: PMC10075109 DOI: 10.4103/1673-5374.360281] [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: 11/19/2022] Open
Abstract
Epilepsy is a neurological disorder caused by the pathological hyper-synchronization of neuronal discharges. The fundamental research of epilepsy mechanisms and the targets of drug design options for its treatment have focused on neurons. However, approximately 30% of patients suffering from epilepsy show resistance to standard anti-epileptic chemotherapeutic agents while the symptoms of the remaining 70% of patients can be alleviated but not completely removed by the current medications. Thus, new strategies for the treatment of epilepsy are in urgent demand. Over the past decades, with the increase in knowledge on the role of glia in the genesis and development of epilepsy, glial cells are receiving renewed attention. In a normal brain, glial cells maintain neuronal health and in partnership with neurons regulate virtually every aspect of brain function. In epilepsy, however, the supportive roles of glial cells are compromised, and their interaction with neurons is altered, which disrupts brain function. In this review, we will focus on the role of glia-related processes in epileptogenesis and their contribution to abnormal neuronal activity, with the major focus on the dysfunction of astroglial potassium channels, water channels, gap junctions, glutamate transporters, purinergic signaling, synaptogenesis, on the roles of microglial inflammatory cytokines, microglia-astrocyte interactions in epilepsy, and on the oligodendroglial potassium channels and myelin abnormalities in the epileptic brain. These recent findings suggest that glia should be considered as the promising next-generation targets for designing anti-epileptic drugs that may improve epilepsy and drug-resistant epilepsy.
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Affiliation(s)
- Weida Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang Province, China
| | - Jelena Bogdanović Pristov
- Department of Life Sciences, University of Belgrade, Institute for Multidisciplinary Research, Belgrade, Serbia
| | - Paola Nobili
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Ljiljana Nikolić
- Department of Neurophysiology, Institute for Biological Research Siniša Stanković, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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13
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Ghirardini E, Sagona G, Marquez-Galera A, Calugi F, Navarron CM, Cacciante F, Chen S, Di Vetta F, Dadà L, Mazziotti R, Lupori L, Putignano E, Baldi P, Lopez-Atalaya JP, Pizzorusso T, Baroncelli L. Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency. Acta Neuropathol Commun 2023; 11:34. [PMID: 36882863 PMCID: PMC9990224 DOI: 10.1186/s40478-023-01533-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Mutations in the solute carrier family 6-member 8 (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with intellectual disability, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood, hindering the development of therapies. In this study, we generated an extensive transcriptomic profile of CTD showing that Cr deficiency causes perturbations of gene expression in excitatory neurons, inhibitory cells, and oligodendrocytes which result in remodeling of circuit excitability and synaptic wiring. We also identified specific alterations of parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional electrophysiological phenotype. Mice lacking Slc6a8 only in PV+ interneurons recapitulated numerous CTD features, including cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ interneurons is sufficient to determine the neurological phenotype of CTD. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses significantly improved cortical activity in Slc6a8 knock-out animals. Altogether, these data demonstrate that Slc6a8 is critical for the normal function of PV+ interneurons and that impairment of these cells is central in the disease pathogenesis, suggesting a novel therapeutic venue for CTD.
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Affiliation(s)
- Elsa Ghirardini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone (PI), Italy. .,Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Giulia Sagona
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy
| | - Angel Marquez-Galera
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramon Y Cajal, S/N, 03550, Sant Joan d'Alacant, Alicante, Spain
| | - Francesco Calugi
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, Via Di San Salvi 12, 50135, Florence, Italy.,BIO@SNS Lab, Scuola Normale Superiore Di Pisa, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Carmen M Navarron
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramon Y Cajal, S/N, 03550, Sant Joan d'Alacant, Alicante, Spain
| | - Francesco Cacciante
- BIO@SNS Lab, Scuola Normale Superiore Di Pisa, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Siwei Chen
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697-3435, USA
| | - Federica Di Vetta
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy
| | - Lorenzo Dadà
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy
| | - Raffaele Mazziotti
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.,Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA, University of Florence, Via Di San Salvi 12, 50135, Florence, Italy
| | - Leonardo Lupori
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone (PI), Italy
| | - Elena Putignano
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy
| | - Pierre Baldi
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92697-3435, USA
| | - Jose P Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramon Y Cajal, S/N, 03550, Sant Joan d'Alacant, Alicante, Spain
| | - Tommaso Pizzorusso
- Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.,BIO@SNS Lab, Scuola Normale Superiore Di Pisa, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Laura Baroncelli
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Viale del Tirreno 331, 56128, Calambrone (PI), Italy.,Institute of Neuroscience, National Research Council (CNR), Via Giuseppe Moruzzi 1, 56124, Pisa, Italy
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14
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González-Martínez R, Márquez-Galera A, Del Blanco B, López-Atalaya JP, Barco A, Herrera E. CBP and p300 Jointly Maintain Neural Progenitor Viability but Play Unique Roles in the Differentiation of Neural Lineages. Cells 2022; 11:cells11244118. [PMID: 36552882 PMCID: PMC9777331 DOI: 10.3390/cells11244118] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
The paralogous lysine acetyltransferases 3 (KAT3), CBP and P300, play critical roles during neurodevelopment, but their specific roles in neural precursors maintenance and differentiation remain obscure. In fact, it is still unclear whether these proteins are individually or jointly essential in processes such as proliferation of neural precursors, differentiation to specific neural cell types, or both. Here, we use subventricular zone-derived neurospheres as a potential ex vivo developmental model to analyze the proliferation and differentiation of neural stem cells (NSCs) lacking CBP, p300, or both proteins. The results showed that CBP and p300 are not individually essential for maintenance and proliferation of NSCs, although their combined ablation seriously compromised cell division. In turn, the absence of either of the two proteins compromised the differentiation of NSC into the neuronal and astrocytic lineages. Single-nucleus RNA sequencing analysis of neural cell cultures derived from CBP or p300 mutant neurospheres revealed divergent trajectories of neural differentiation upon CBP or p300 ablation, confirming unique functions and nonredundant roles in neural development. These findings contribute to a better understanding of the shared and individual roles of KAT3 proteins in neural differentiation and the etiology of neurodevelopmental disorders caused by their deficiency.
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15
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Vijayaragavan K, Cannon BJ, Tebaykin D, Bossé M, Baranski A, Oliveria JP, Bukhari SA, Mrdjen D, Corces MR, McCaffrey EF, Greenwald NF, Sigal Y, Marquez D, Khair Z, Bruce T, Goldston M, Bharadwaj A, Montine KS, Angelo RM, Montine TJ, Bendall SC. Single-cell spatial proteomic imaging for human neuropathology. Acta Neuropathol Commun 2022; 10:158. [PMID: 36333818 PMCID: PMC9636771 DOI: 10.1186/s40478-022-01465-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimer's disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves broadly as a methodology for spatial proteomic analysis of archival human neuropathology. TEASER: Multiplex Ion beam Imaging enables deep spatial phenotyping of human neuropathology-associated cellular and disease features.
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Affiliation(s)
| | - Bryan J Cannon
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bossé
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - J P Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Syed A Bukhari
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Erin F McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Diana Marquez
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Trevor Bruce
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mako Goldston
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kathleen S Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - R Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
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16
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van Vliet EA, Hildebrand MS, Mills JD, Brennan GP, Eid T, Masino SA, Whittemore V, Bindila L, Wang KK, Patel M, Perucca P, Reid CA. A companion to the preclinical common data elements for genomics, transcriptomics, and epigenomics data in rodent epilepsy models. A report of the TASK3-WG4 omics working group of the ILAE/AES joint translational TASK force. Epilepsia Open 2022. [PMID: 35950645 DOI: 10.1002/epi4.12640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/22/2022] [Indexed: 11/06/2022] Open
Abstract
The International League Against Epilepsy/American Epilepsy Society (ILAE/AES) Joint Translational Task Force established the TASK3 working groups to create common data elements (CDEs) for various preclinical epilepsy research disciplines. The aim of the CDEs is to improve the standardization of experimental designs across a range of epilepsy research-related methods. Here, we have generated CDE tables with key parameters and case report forms (CRFs) containing the essential contents of the study protocols for genomics, transcriptomics, and epigenomics in rodent models of epilepsy, with a specific focus on adult rats and mice. We discuss the important elements that need to be considered for genomics, transcriptomics, and epigenomics methodologies, providing a rationale for the parameters that should be collected. This is the first in a two-part series of omics papers with the second installment to cover proteomics, lipidomics, and metabolomics in adult rodents.
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Affiliation(s)
- Erwin A van Vliet
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Gary P Brennan
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tore Eid
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Susan A Masino
- Neuroscience Program and Psychology Department, Life Sciences Center, Trinity College, Hartford, Connecticut, USA
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Kevin K Wang
- Department of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, Florida, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
| | - Manisha Patel
- Department of Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Austin Health, Heidelberg, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Christopher A Reid
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
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17
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Almeida C, Pongilio RP, Móvio MI, Higa GSV, Resende RR, Jiang J, Kinjo ER, Kihara AH. Distinct Cell-specific Roles of NOX2 and MyD88 in Epileptogenesis. Front Cell Dev Biol 2022; 10:926776. [PMID: 35859905 PMCID: PMC9289522 DOI: 10.3389/fcell.2022.926776] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
It is well established that temporal lobe epilepsy (TLE) is often related to oxidative stress and neuroinflammation. Both processes subserve alterations observed in epileptogenesis and ultimately involve distinct classes of cells, including astrocytes, microglia, and specific neural subtypes. For this reason, molecules associated with oxidative stress response and neuroinflammation have been proposed as potential targets for therapeutic strategies. However, these molecules can participate in distinct intracellular pathways depending on the cell type. To illustrate this, we reviewed the potential role of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 2 (NOX2) and myeloid differentiation primary response 88 (MyD88) in astrocytes, microglia, and neurons in epileptogenesis. Furthermore, we presented approaches to study genes in different cells, employing single-cell RNA-sequencing (scRNAseq) transcriptomic analyses, transgenic technologies and viral serotypes carrying vectors with specific promoters. We discussed the importance of identifying particular roles of molecules depending on the cell type, endowing more effective therapeutic strategies to treat TLE.
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Affiliation(s)
- Cayo Almeida
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | | | - Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, Brazil
| | | | - Rodrigo Ribeiro Resende
- Laboratório de Sinalização Celular e Nanobiotecnologia, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jianxiong Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Erika Reime Kinjo
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, Brazil
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18
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Nelson RS, Dammer EB, Santiago JV, Seyfried NT, Rangaraju S. Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms. Front Neurosci 2022; 16:902146. [PMID: 35784845 PMCID: PMC9243337 DOI: 10.3389/fnins.2022.902146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023] Open
Abstract
Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.
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Affiliation(s)
- Ruth S. Nelson
- Department of Neurology, Emory University, Atlanta, GA, United States
| | - Eric B. Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, United States
| | | | | | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, United States,*Correspondence: Srikant Rangaraju
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19
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Marquez-Galera A, de la Prida LM, Lopez-Atalaya JP. A protocol to extract cell-type-specific signatures from differentially expressed genes in bulk-tissue RNA-seq. STAR Protoc 2022; 3:101121. [PMID: 35118429 PMCID: PMC8792262 DOI: 10.1016/j.xpro.2022.101121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Bulk-tissue RNA-seq is widely used to dissect variation in gene expression levels across tissues and under different experimental conditions. Here, we introduce a protocol that leverages existing single-cell expression data to deconvolve patterns of cell-type-specific gene expression in differentially expressed gene lists from highly heterogeneous tissue. We apply this protocol to interrogate cell-type-specific gene expression and variation in cell type composition between the distinct sublayers of the hippocampal CA1 region of the brain in a rodent model of epilepsy. For complete details on the use and execution of this protocol, please refer to Cid et al. (2021). A protocol to explore gene signatures from bulk RNA-seq at the cell-type-specific level Deconvolution of complex gene signatures from highly heterogeneous tissues Publicly available single-cell gene expression dataset is retrieved and curated Gene signatures across brain regions and disease states are surveyed in scRNA-seq data
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Lévesque M, Biagini G, de Curtis M, Gnatkovsky V, Pitsch J, Wang S, Avoli M. The pilocarpine model of mesial temporal lobe epilepsy: Over one decade later, with more rodent species and new investigative approaches. Neurosci Biobehav Rev 2021; 130:274-291. [PMID: 34437936 DOI: 10.1016/j.neubiorev.2021.08.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 01/19/2023]
Abstract
Fundamental work on the mechanisms leading to focal epileptic discharges in mesial temporal lobe epilepsy (MTLE) often rests on the use of rodent models in which an initial status epilepticus (SE) is induced by kainic acid or pilocarpine. In 2008 we reviewed how, following systemic injection of pilocarpine, the main subsequent events are the initial SE, the latent period, and the chronic epileptic state. Up to a decade ago, rats were most often employed and they were frequently analysed only behaviorally. However, the use of transgenic mice has revealed novel information regarding this animal model. Here, we review recent findings showing the existence of specific neuronal events during both latent and chronic states, and how optogenetic activation of specific cell populations modulate spontaneous seizures. We also address neuronal damage induced by pilocarpine treatment, the role of neuroinflammation, and the influence of circadian and estrous cycles. Updating these findings leads us to propose that the rodent pilocarpine model continues to represent a valuable tool for identifying the basic pathophysiology of MTLE.
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Affiliation(s)
- Maxime Lévesque
- Montreal Neurological Institute-Hospital and Departments of Neurology & Neurosurgery, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Giuseppe Biagini
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena & Reggio Emilia, 41100 Modena, Italy
| | - Marco de Curtis
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milano, Italy
| | - Vadym Gnatkovsky
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milano, Italy; Department of Epileptology, University Hospital Bonn, 53127 Bonn, Germany
| | - Julika Pitsch
- Department of Epileptology, University Hospital Bonn, 53127 Bonn, Germany
| | - Siyan Wang
- Montreal Neurological Institute-Hospital and Departments of Neurology & Neurosurgery, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Massimo Avoli
- Montreal Neurological Institute-Hospital and Departments of Neurology & Neurosurgery, McGill University, Montreal, QC, H3A 2B4, Canada; Departments of Physiology, McGill University, Montreal, QC, H3A 2B4, Canada; Department of Experimental Medicine, Sapienza University of Rome, 00185 Roma, Italy.
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