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Junaid M, Lee EJ, Lim SB. Single-cell and spatial omics: exploring hypothalamic heterogeneity. Neural Regen Res 2025; 20:1525-1540. [PMID: 38993130 DOI: 10.4103/nrr.nrr-d-24-00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.
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Affiliation(s)
- Muhammad Junaid
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
| | - Eun Jeong Lee
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, South Korea
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
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2
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Al Harrach M, Yochum M, Ruffini G, Bartolomei F, Wendling F, Benquet P. NeoCoMM: A neocortical neuroinspired computational model for the reconstruction and simulation of epileptiform events. Comput Biol Med 2024; 180:108934. [PMID: 39079417 DOI: 10.1016/j.compbiomed.2024.108934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/13/2024] [Accepted: 07/20/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND Understanding the pathophysiological dynamics that underline Interictal Epileptiform Events (IEEs) such as epileptic spikes, spike-and-waves or High-Frequency Oscillations (HFOs) is of major importance in the context of neocortical refractory epilepsy, as it paves the way for the development of novel therapies. Typically, these events are detected in Local Field Potential (LFP) recordings obtained through depth electrodes during pre-surgical investigations. Although essential, the underlying pathophysiological mechanisms for the generation of these epileptic neuromarkers remain unclear. The aim of this paper is to propose a novel neurophysiologically relevant reconstruction of the neocortical microcircuitry in the context of epilepsy. This reconstruction intends to facilitate the analysis of a comprehensive set of parameters encompassing physiological, morphological, and biophysical aspects that directly impact the generation and recording of different IEEs. METHOD a novel microscale computational model of an epileptic neocortical column was introduced. This model incorporates the intricate multilayered structure of the cortex and allows for the simulation of realistic interictal epileptic signals. The proposed model was validated through comparisons with real IEEs recorded using intracranial stereo-electroencephalography (SEEG) signals from both humans and animals. Using the model, the user can recreate epileptiform patterns observed in different species (human, rodent, and mouse) and study the intracellular activity associated with these patterns. RESULTS Our model allowed us to unravel the relationship between glutamatergic and GABAergic synaptic transmission of the epileptic neural network and the type of generated IEE. Moreover, sensitivity analyses allowed for the exploration of the pathophysiological parameters responsible for the transitions between these events. Finally, the presented modeling framework also provides an Electrode Tissue Model (ETI) that adds realism to the simulated signals and offers the possibility of studying their sensitivity to the electrode characteristics. CONCLUSION The model (NeoCoMM) presented in this work can be of great use in different applications since it offers an in silico framework for sensitivity analysis and hypothesis testing. It can also be used as a starting point for more complex studies.
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Affiliation(s)
- M Al Harrach
- University of Rennes, INSERM, LTSI-U1099, 35000 Rennes, France.
| | - M Yochum
- Neuroelectrics, Av. Tibidabo 47b, 08035 Barcelona, Spain
| | - G Ruffini
- Neuroelectrics, Av. Tibidabo 47b, 08035 Barcelona, Spain
| | - F Bartolomei
- Hopitaux de Marseille, Service d'Epileptologie et de Rythmologie Cerebrale, Hopital La Timone, Marseille, France
| | - F Wendling
- University of Rennes, INSERM, LTSI-U1099, 35000 Rennes, France
| | - P Benquet
- University of Rennes, INSERM, LTSI-U1099, 35000 Rennes, France
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3
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Iannone AF, Akgül G, Zhang R, Wacks S, Hussein N, Macias CG, Donatelle A, Bauriedel JMJ, Wright C, Abramov D, Johnson MA, Govek EE, Burré J, Milner TA, De Marco García NV. The chemokine Cxcl14 regulates interneuron differentiation in layer I of the somatosensory cortex. Cell Rep 2024; 43:114531. [PMID: 39058591 PMCID: PMC11373301 DOI: 10.1016/j.celrep.2024.114531] [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: 02/01/2024] [Revised: 06/10/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Spontaneous and sensory-evoked activity sculpts developing circuits. Yet, how these activity patterns intersect with cellular programs regulating the differentiation of neuronal subtypes is not well understood. Through electrophysiological and in vivo longitudinal analyses, we show that C-X-C motif chemokine ligand 14 (Cxcl14), a gene previously characterized for its association with tumor invasion, is expressed by single-bouquet cells (SBCs) in layer I (LI) of the somatosensory cortex during development. Sensory deprivation at neonatal stages markedly decreases Cxcl14 expression. Additionally, we report that loss of function of this gene leads to increased intrinsic excitability of SBCs-but not LI neurogliaform cells-and augments neuronal complexity. Furthermore, Cxcl14 loss impairs sensory map formation and compromises the in vivo recruitment of superficial interneurons by sensory inputs. These results indicate that Cxcl14 is required for LI differentiation and demonstrate the emergent role of chemokines as key players in cortical network development.
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Affiliation(s)
- Andrew F Iannone
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Gülcan Akgül
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Robin Zhang
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sam Wacks
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nisma Hussein
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Carmen Ginelly Macias
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander Donatelle
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julia M J Bauriedel
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Cora Wright
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Debra Abramov
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA; Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Megan A Johnson
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY 10065, USA
| | - Jacqueline Burré
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Natalia V De Marco García
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA.
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4
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Abbaspoor S, Hoffman KL. Circuit dynamics of superficial and deep CA1 pyramidal cells and inhibitory cells in freely moving macaques. Cell Rep 2024; 43:114519. [PMID: 39018243 DOI: 10.1016/j.celrep.2024.114519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/23/2024] [Accepted: 07/02/2024] [Indexed: 07/19/2024] Open
Abstract
Diverse neuron classes in hippocampal CA1 have been identified through the heterogeneity of their cellular/molecular composition. How these classes relate to hippocampal function and the network dynamics that support cognition in primates remains unclear. Here, we report inhibitory functional cell groups in CA1 of freely moving macaques whose diverse response profiles to network states and each other suggest distinct and specific roles in the functional microcircuit of CA1. In addition, pyramidal cells that were grouped by their superficial or deep layer position differed in firing rate, burstiness, and sharp-wave ripple-associated firing. They also showed strata-specific spike-timing interactions with inhibitory cell groups, suggestive of segregated neural populations. Furthermore, ensemble recordings revealed that cell assemblies were preferentially organized according to these strata. These results suggest that hippocampal CA1 in freely moving macaques bears a sublayer-specific circuit organization that may shape its role in cognition.
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Affiliation(s)
- Saman Abbaspoor
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
| | - Kari L Hoffman
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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5
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Curry RN, Ma Q, McDonald MF, Ko Y, Srivastava S, Chin PS, He P, Lozzi B, Athukuri P, Jing J, Wang S, Harmanci AO, Arenkiel B, Jiang X, Deneen B, Rao G, Serin Harmanci A. Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma. Cancer Cell 2024:S1535-6108(24)00308-8. [PMID: 39241781 DOI: 10.1016/j.ccell.2024.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/15/2024] [Accepted: 08/08/2024] [Indexed: 09/09/2024]
Abstract
Prior studies have described the complex interplay that exists between glioma cells and neurons; however, the electrophysiological properties endogenous to glioma cells remain obscure. To address this, we employed Patch-sequencing (Patch-seq) on human glioma specimens and found that one-third of patched cells in IDH mutant (IDHmut) tumors demonstrate properties of both neurons and glia. To define these hybrid cells (HCs), which fire single, short action potentials, and discern if they are of tumoral origin, we developed the single cell rule association mining (SCRAM) computational tool to annotate each cell individually. SCRAM revealed that HCs possess select features of GABAergic neurons and oligodendrocyte precursor cells, and include both tumor and non-tumor cells. These studies characterize the combined electrophysiological and molecular properties of human glioma cells and describe a cell type in human glioma with unique electrophysiological and transcriptomic properties that may also exist in the non-tumor brain.
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Affiliation(s)
- Rachel N Curry
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Qianqian Ma
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Malcolm F McDonald
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA; Program in Development, Disease Models, and Therapeutics, Baylor College of Medicine, Houston, TX, USA
| | - Yeunjung Ko
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Snigdha Srivastava
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA; Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pey-Shyuan Chin
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Peihao He
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA; Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Brittney Lozzi
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Prazwal Athukuri
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Junzhan Jing
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Su Wang
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Arif O Harmanci
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, USA
| | - Benjamin Arenkiel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaolong Jiang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA.
| | - Benjamin Deneen
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Program in Development, Disease Models, and Therapeutics, Baylor College of Medicine, Houston, TX, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA; Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Ganesh Rao
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.
| | - Akdes Serin Harmanci
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.
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6
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Li M, Jiang YQ, Lee DK, Wang H, Lu MC, Sun Q. Dorsoventral Heterogeneity of Synaptic Connectivity in Hippocampal CA3 Pyramidal Neurons. J Neurosci 2024; 44:e0370242024. [PMID: 39025678 PMCID: PMC11326861 DOI: 10.1523/jneurosci.0370-24.2024] [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: 02/25/2024] [Revised: 06/11/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
The hippocampal CA3 region plays an important role in learning and memory. CA3 pyramidal neurons (PNs) receive two prominent excitatory inputs-mossy fibers (MFs) from dentate gyrus (DG) and recurrent collaterals (RCs) from CA3 PNs-that play opposing roles in pattern separation and pattern completion, respectively. Although the dorsoventral heterogeneity of the hippocampal anatomy, physiology, and behavior has been well established, nothing is known about the dorsoventral heterogeneity of synaptic connectivity in CA3 PNs. In this study, we performed Timm's sulfide silver staining, dendritic and spine morphological analyses, and ex vivo electrophysiology in mice of both sexes to investigate the heterogeneity of MF and RC pathways along the CA3 dorsoventral axis. Our morphological analyses demonstrate that ventral CA3 (vCA3) PNs possess greater dendritic lengths and more complex dendritic arborization, compared with dorsal CA3 (dCA3) PNs. Moreover, using ChannelRhodopsin2 (ChR2)-assisted patch-clamp recording, we found that the ratio of the RC-to-MF excitatory drive onto CA3 PNs increases substantially from dCA3 to vCA3, with vCA3 PNs receiving significantly weaker MFs, but stronger RCs, excitation than dCA3 PNs. Given the distinct roles of MF versus RC inputs in pattern separation versus completion, our findings of the significant dorsoventral variations of MF and RC excitation in CA3 PNs may have important functional implications for the contribution of CA3 circuit to the dorsoventral difference in hippocampal function.
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Affiliation(s)
- Minghua Li
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Yu-Qiu Jiang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Daniel K Lee
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Haoran Wang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Melissa C Lu
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Qian Sun
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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7
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Sui X, Lo JA, Luo S, He Y, Tang Z, Lin Z, Zhou Y, Wang WX, Liu J, Wang X. Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606553. [PMID: 39149316 PMCID: PMC11326170 DOI: 10.1101/2024.08.05.606553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 μm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D in situ quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 200-μm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring, and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.
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Affiliation(s)
- Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Jennifer A. Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA USA
- These authors contributed equally
| | - Shuchen Luo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yichun He
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Zefang Tang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zuwan Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Yiming Zhou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy Xueyi Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Jia Liu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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8
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Gliko O, Mallory M, Dalley R, Gala R, Gornet J, Zeng H, Sorensen SA, Sümbül U. High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy. Nat Commun 2024; 15:6337. [PMID: 39068160 PMCID: PMC11283452 DOI: 10.1038/s41467-024-50728-9] [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: 12/01/2023] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Neuronal anatomy is central to the organization and function of brain cell types. However, anatomical variability within apparently homogeneous populations of cells can obscure such insights. Here, we report large-scale automation of neuronal morphology reconstruction and analysis on a dataset of 813 inhibitory neurons characterized using the Patch-seq method, which enables measurement of multiple properties from individual neurons, including local morphology and transcriptional signature. We demonstrate that these automated reconstructions can be used in the same manner as manual reconstructions to understand the relationship between some, but not all, cellular properties used to define cell types. We uncover gene expression correlates of laminar innervation on multiple transcriptomically defined neuronal subclasses and types. In particular, our results reveal correlates of the variability in Layer 1 (L1) axonal innervation in a transcriptomically defined subpopulation of Martinotti cells in the adult mouse neocortex.
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Affiliation(s)
| | | | | | | | - James Gornet
- California Institute of Technology, Pasadena, CA, USA
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9
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Agmon A, Barth AL. A brief history of somatostatin interneuron taxonomy or: how many somatostatin subtypes are there, really? Front Neural Circuits 2024; 18:1436915. [PMID: 39091993 PMCID: PMC11292610 DOI: 10.3389/fncir.2024.1436915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
We provide a brief (and unabashedly biased) overview of the pre-transcriptomic history of somatostatin interneuron taxonomy, followed by a chronological summary of the large-scale, NIH-supported effort over the last ten years to generate a comprehensive, single-cell RNA-seq-based taxonomy of cortical neurons. Focusing on somatostatin interneurons, we present the perspective of experimental neuroscientists trying to incorporate the new classification schemes into their own research while struggling to keep up with the ever-increasing number of proposed cell types, which seems to double every two years. We suggest that for experimental analysis, the most useful taxonomic level is the subdivision of somatostatin interneurons into ten or so "supertypes," which closely agrees with their more traditional classification by morphological, electrophysiological and neurochemical features. We argue that finer subdivisions ("t-types" or "clusters"), based on slight variations in gene expression profiles but lacking clear phenotypic differences, are less useful to researchers and may actually defeat the purpose of classifying neurons to begin with. We end by stressing the need for generating novel tools (mouse lines, viral vectors) for genetically targeting distinct supertypes for expression of fluorescent reporters, calcium sensors and excitatory or inhibitory opsins, allowing neuroscientists to chart the input and output synaptic connections of each proposed subtype, reveal the position they occupy in the cortical network and examine experimentally their roles in sensorimotor behaviors and cognitive brain functions.
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Affiliation(s)
- Ariel Agmon
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
| | - Alison L. Barth
- Department of Biological Sciences, Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, United States
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10
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Zhang SR, Wu DY, Luo R, Wu JL, Chen H, Li ZM, Zhuang JP, Hu NY, Li XW, Yang JM, Gao TM, Chen YH. A Prelimbic Cortex-Thalamus Circuit Bidirectionally Regulates Innate and Stress-Induced Anxiety-Like Behavior. J Neurosci 2024; 44:e2103232024. [PMID: 38886059 PMCID: PMC11255430 DOI: 10.1523/jneurosci.2103-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Anxiety-related disorders respond to cognitive behavioral therapies, which involved the medial prefrontal cortex (mPFC). Previous studies have suggested that subregions of the mPFC have different and even opposite roles in regulating innate anxiety. However, the specific causal targets of their descending projections in modulating innate anxiety and stress-induced anxiety have yet to be fully elucidated. Here, we found that among the various downstream pathways of the prelimbic cortex (PL), a subregion of the mPFC, PL-mediodorsal thalamic nucleus (MD) projection, and PL-ventral tegmental area (VTA) projection exhibited antagonistic effects on anxiety-like behavior, while the PL-MD projection but not PL-VTA projection was necessary for the animal to guide anxiety-related behavior. In addition, MD-projecting PL neurons bidirectionally regulated remote but not recent fear memory retrieval. Notably, restraint stress induced high-anxiety state accompanied by strengthening the excitatory inputs onto MD-projecting PL neurons, and inhibiting PL-MD pathway rescued the stress-induced anxiety. Our findings reveal that the activity of PL-MD pathway may be an essential factor to maintain certain level of anxiety, and stress increased the excitability of this pathway, leading to inappropriate emotional expression, and suggests that targeting specific PL circuits may aid the development of therapies for the treatment of stress-related disorders.
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Affiliation(s)
- Sheng-Rong Zhang
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ding-Yu Wu
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Rong Luo
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jian-Lin Wu
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Chen
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zi-Ming Li
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jia-Pai Zhuang
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Neng-Yuan Hu
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiao-Wen Li
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jian-Ming Yang
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tian-Ming Gao
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yi-Hua Chen
- State Key Laboratory of Organ Failure Research, Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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11
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Wang F, Sun H, Chen M, Feng B, Lu Y, Lyu M, Cui D, Zhai Y, Zhang Y, Zhu Y, Wang C, Wu H, Ma X, Zhu F, Wang Q, Li Y. The thalamic reticular nucleus orchestrates social memory. Neuron 2024; 112:2368-2385.e11. [PMID: 38701789 DOI: 10.1016/j.neuron.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
Social memory has been developed in humans and other animals to recognize familiar conspecifics and is essential for their survival and reproduction. Here, we demonstrated that parvalbumin-positive neurons in the sensory thalamic reticular nucleus (sTRNPvalb) are necessary and sufficient for mice to memorize conspecifics. sTRNPvalb neurons receiving glutamatergic projections from the posterior parietal cortex (PPC) transmit individual information by inhibiting the parafascicular thalamic nucleus (PF). Mice in which the PPCCaMKII→sTRNPvalb→PF circuit was inhibited exhibited a disrupted ability to discriminate familiar conspecifics from novel ones. More strikingly, a subset of sTRNPvalb neurons with high electrophysiological excitability and complex dendritic arborizations is involved in the above corticothalamic pathway and stores social memory. Single-cell RNA sequencing revealed the biochemical basis of these subset cells as a robust activation of protein synthesis. These findings elucidate that sTRNPvalb neurons modulate social memory by coordinating a hitherto unknown corticothalamic circuit and inhibitory memory engram.
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Affiliation(s)
- Feidi Wang
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Shaanxi Belt and Road Joint Laboratory of Precision Medicine in Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Huan Sun
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Mingyue Chen
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ban Feng
- Department of Pharmacology, School of Pharmacy, Air Force Medical University (Fourth Military Medical University), Xi'an 710032, China
| | - Yu Lu
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Mi Lyu
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Dongqi Cui
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yifang Zhai
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Ying Zhang
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yaomin Zhu
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Changhe Wang
- Neuroscience Research Center, Institute of Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Core Facilities Sharing Platform, Xi'an Jiaotong University, Xi'an 710049, China
| | - Haitao Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiancang Ma
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Shaanxi Belt and Road Joint Laboratory of Precision Medicine in Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Feng Zhu
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Shaanxi Belt and Road Joint Laboratory of Precision Medicine in Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qiang Wang
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Li
- Center for Brain Science, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China; Shaanxi Belt and Road Joint Laboratory of Precision Medicine in Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
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12
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Bakina O, Conrad T, Mitic N, Vidal RO, Obrusnik T, Sai S, Nolte C, Semtner M, Kettenmann H. In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia. PLoS One 2024; 19:e0302376. [PMID: 38990806 PMCID: PMC11239014 DOI: 10.1371/journal.pone.0302376] [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: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 07/13/2024] Open
Abstract
We applied the patch-seq technique to harvest transcripts from individual microglial cells from cortex, hippocampus and corpus callosum of acute brain slices from adult mice. After recording membrane currents with the patch-clamp technique, the cytoplasm was collected via the pipette and underwent adapted SMART-seq2 preparation with subsequent sequencing. On average, 4138 genes were detected in 113 cells from hippocampus, corpus callosum and cortex, including microglia markers such as Tmem119, P2ry12 and Siglec-H. Comparing our dataset to previously published single cell mRNA sequencing data from FACS-isolated microglia indicated that two clusters of cells were absent in our patch-seq dataset. Pathway analysis of marker genes in FACS-specific clusters revealed association with microglial activation and stress response. This indicates that under normal conditions microglia in situ lack transcripts associated with a stress-response, and that the microglia-isolation procedure by mechanical dissociation and FACS triggers the expression of genes related to activation and stress.
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Affiliation(s)
- Olga Bakina
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Humboldt Universität, Berlin, Germany
| | - Thomas Conrad
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ramon Oliveira Vidal
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Tessa Obrusnik
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Somesh Sai
- Genomics Platform, BIMSB, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christiane Nolte
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marcus Semtner
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Helmut Kettenmann
- Cellular Neurosciences, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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13
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Marghi Y, Gala R, Baftizadeh F, Sümbül U. Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560574. [PMID: 37873271 PMCID: PMC10592946 DOI: 10.1101/2023.10.02.560574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Reproducible definition and identification of cell types is essential to enable investigations into their biological function, and understanding their relevance in the context of development, disease and evolution. Current approaches model variability in data as continuous latent factors, followed by clustering as a separate step, or immediately apply clustering on the data. We show that such approaches can suffer from qualitative mistakes in identifying cell types robustly, particularly when the number of such cell types is in the hundreds or even thousands. Here, we propose an unsupervised method, MMIDAS, which combines a generalized mixture model with a multi-armed deep neural network, to jointly infer the discrete type and continuous type-specific variability. Using four recent datasets of brain cells spanning different technologies, species, and conditions, we demonstrate that MMIDAS can identify reproducible cell types and infer cell type-dependent continuous variability in both uni-modal and multi-modal datasets.
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Affiliation(s)
| | - Rohan Gala
- Allen Institute, 615 Westlake Ave N, Seattle, WA, USA
| | | | - Uygar Sümbül
- Allen Institute, 615 Westlake Ave N, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
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14
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Aceto G, Nardella L, Nanni S, Pecci V, Bertozzi A, Nutarelli S, Viscomi MT, Colussi C, D'Ascenzo M, Grassi C. Glycine-induced activation of GPR158 increases the intrinsic excitability of medium spiny neurons in the nucleus accumbens. Cell Mol Life Sci 2024; 81:268. [PMID: 38884814 PMCID: PMC11335193 DOI: 10.1007/s00018-024-05260-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: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/18/2024]
Abstract
It has been recently established that GPR158, a class C orphan G protein-coupled receptor, serves as a metabotropic glycine receptor. GPR158 is highly expressed in the nucleus accumbens (NAc), a major input structure of the basal ganglia that integrates information from cortical and subcortical structures to mediate goal-directed behaviors. However, whether glycine modulates neuronal activity in the NAc through GPR158 activation has not been investigated yet. Using whole-cell patch-clamp recordings, we found that glycine-dependent activation of GPR158 increased the firing rate of NAc medium spiny neurons (MSNs) while it failed to significantly affect the excitability of cholinergic interneurons (CIN). In MSNs GPR158 activation reduced the latency to fire, increased the action potential half-width, and reduced action potential afterhyperpolarization, effects that are all consistent with negative modulation of potassium M-currents, that in the central nervous system are mainly carried out by Kv7/KCNQ-channels. Indeed, we found that the GPR158-induced increase in MSN excitability was associated with decreased M-current amplitude, and selective pharmacological inhibition of the M-current mimicked and occluded the effects of GPR158 activation. In addition, when the protein kinase A (PKA) or extracellular signal-regulated kinase (ERK) signaling was pharmacologically blocked, modulation of MSN excitability by GPR158 activation was suppressed. Moreover, GPR158 activation increased the phosphorylation of ERK and Kv7.2 serine residues. Collectively, our findings suggest that GPR158/PKA/ERK signaling controls MSN excitability via Kv7.2 modulation. Glycine-dependent activation of GPR158 may significantly affect MSN firing in vivo, thus potentially mediating specific aspects of goal-induced behaviors.
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Affiliation(s)
- Giuseppe Aceto
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, 00168, Italy
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Luca Nardella
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Simona Nanni
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, 00168, Italy
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Valeria Pecci
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Alessia Bertozzi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, Rome, Italy
| | - Sofia Nutarelli
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Maria Teresa Viscomi
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
| | - Claudia Colussi
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, 00168, Italy
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, Rome, Italy
| | - Marcello D'Ascenzo
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, 00168, Italy.
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy.
| | - Claudio Grassi
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Rome, 00168, Italy
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
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15
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Ma X, Miraucourt LS, Qiu H, Xu M, Cook EP, Krishnaswamy A, Sharif-Naeini R, Khadra A. ElecFeX is a user-friendly toolbox for efficient feature extraction from single-cell electrophysiological recordings. CELL REPORTS METHODS 2024; 4:100791. [PMID: 38848714 PMCID: PMC11228277 DOI: 10.1016/j.crmeth.2024.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/17/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Characterizing neurons by their electrophysiological phenotypes is essential for understanding the neural basis of behavioral and cognitive functions. Technological developments have enabled the collection of hundreds of neural recordings; this calls for new tools capable of performing feature extraction efficiently. To address the urgent need for a powerful and accessible tool, we developed ElecFeX, an open-source MATLAB-based toolbox that (1) has an intuitive graphical user interface, (2) provides customizable measurements for a wide range of electrophysiological features, (3) processes large-size datasets effortlessly via batch analysis, and (4) yields formatted output for further analysis. We implemented ElecFeX on a diverse set of neural recordings; demonstrated its functionality, versatility, and efficiency in capturing electrical features; and established its significance in distinguishing neuronal subgroups across brain regions and species. ElecFeX is thus presented as a user-friendly toolbox to benefit the neuroscience community by minimizing the time required for extracting features from their electrophysiological datasets.
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Affiliation(s)
- Xinyue Ma
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Loïs S Miraucourt
- Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Haoyi Qiu
- Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Mengyi Xu
- Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Erik P Cook
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Quantitative Life Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Arjun Krishnaswamy
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Quantitative Life Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Reza Sharif-Naeini
- Alan Edwards Center for Research on Pain, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada.
| | - Anmar Khadra
- Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Quantitative Life Sciences, McGill University, Montreal, QC H3G 1Y6, Canada.
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16
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Sandoval SO, Cappuccio G, Kruth K, Osenberg S, Khalil SM, Méndez-Albelo NM, Padmanabhan K, Wang D, Niciu MJ, Bhattacharyya A, Stein JL, Sousa AMM, Waxman EA, Buttermore ED, Whye D, Sirois CL, Williams A, Maletic-Savatic M, Zhao X. Rigor and reproducibility in human brain organoid research: Where we are and where we need to go. Stem Cell Reports 2024; 19:796-816. [PMID: 38759644 PMCID: PMC11297560 DOI: 10.1016/j.stemcr.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.
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Affiliation(s)
- Soraya O Sandoval
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gerarda Cappuccio
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Karina Kruth
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Sivan Osenberg
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Saleh M Khalil
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Natasha M Méndez-Albelo
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Krishnan Padmanabhan
- Department of Neuroscience, Center for Visual Science, Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mark J Niciu
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Dosh Whye
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Carissa L Sirois
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Aislinn Williams
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA.
| | - Mirjana Maletic-Savatic
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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17
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Csillag V, Noble JC, Calvigioni D, Reinius B, Fuzik J. All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq. Nat Protoc 2024:10.1038/s41596-024-01005-y. [PMID: 38834919 DOI: 10.1038/s41596-024-01005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/18/2024] [Indexed: 06/06/2024]
Abstract
Neuronal pathways recruit large postsynaptic populations and maintain connections via distinct postsynaptic response types (PRTs). Until recently, PRTs were accessible as a selection criterion for single-cell RNA sequencing only through probing by low-throughput whole-cell electrophysiology. To overcome these limitations and target neurons on the basis of specific PRTs for soma collection and subsequent single-cell RNA sequencing, we developed Voltage-Seq using the genetically encoded voltage indicator Voltron in acute brain slices from mice. We also created an onsite analysis tool, VoltView, to guide soma collection of specific PRTs using a classifier based on a previously acquired database of connectomes from multiple animals. Here we present our procedure for preparing the optical path, the imaging setup and detailing the imaging and analysis steps, as well as a complete procedure for sequencing library preparation. This enables researchers to conduct our high-throughput all-optical synaptic assay and to obtain single-cell transcriptomic data from selected postsynaptic neurons. This also allows researchers to resolve the connectivity ratio of a specific pathway and explore the diversity of PRTs within that connectome. Furthermore, combining high throughput with quick analysis gives unique access to find specific connections within a large postsynaptic connectome. Voltage-Seq also allows the investigation of correlations between connectivity and gene expression changes in a postsynaptic cell-type-specific manner for both excitatory and inhibitory connections. The Voltage-Seq workflow can be completed in ~6 weeks, including 4-5 weeks for viral expression of the Voltron sensor. The technique requires knowledge of basic laboratory techniques, micromanipulator handling skills and experience in molecular biology and bioinformatics.
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Affiliation(s)
- Veronika Csillag
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - J C Noble
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Björn Reinius
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - János Fuzik
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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18
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Yagishita H, Sasaki T. Integrating physiological and transcriptomic analyses at the single-neuron level. Neurosci Res 2024:S0168-0102(24)00065-8. [PMID: 38821412 DOI: 10.1016/j.neures.2024.05.003] [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: 05/12/2024] [Revised: 04/30/2024] [Accepted: 05/12/2024] [Indexed: 06/02/2024]
Abstract
Neurons generate various spike patterns to execute different functions. Understanding how these physiological neuronal spike patterns are related to their molecular characteristics is a long-standing issue in neuroscience. Herein, we review the results of recent studies that have addressed this issue by integrating physiological and transcriptomic techniques. A sequence of experiments, including in vivo recording and/or labeling, brain tissue slicing, cell collection, and transcriptomic analysis, have identified the gene expression profiles of brain neurons at the single-cell level, with activity patterns recorded in living animals. Although these techniques are still in the early stages, this methodological idea is principally applicable to various brain regions and neuronal activity patterns. Accumulating evidence will contribute to a deeper understanding of neuronal characteristics by integrating insights from molecules to cells, circuits, and behaviors.
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Affiliation(s)
- Haruya Yagishita
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-Ku, Sendai 980-8578, Japan
| | - Takuya Sasaki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-Ku, Sendai 980-8578, Japan; Department of Neuropharmacology, Tohoku University School of Medicine, 4-1 Seiryo-machi, Aoba-Ku, Sendai 980-8575, Japan.
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19
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Gao Y, Dong Q, Arachchilage KH, Risgaard R, Sheng J, Syed M, Schmidt DK, Jin T, Liu S, Knaack SA, Doherty D, Glass I, Levine JE, Wang D, Chang Q, Zhao X, Sousa AM. Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543460. [PMID: 37398253 PMCID: PMC10312516 DOI: 10.1101/2023.06.02.543460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown of CHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, including RAPGEF4. Restoring the expression of RAPGEF4 rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.
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20
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Sokolov AV, Lafta MS, Nordberg DOT, Jonsson J, Schiöth HB. Depression proteomic profiling in adolescents with transcriptome analyses in independent cohorts. Front Psychiatry 2024; 15:1372106. [PMID: 38812487 PMCID: PMC11133714 DOI: 10.3389/fpsyt.2024.1372106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Depression is a major global burden with unclear pathophysiology and poor treatment outcomes. Diagnosis of depression continues to rely primarily on behavioral rather than biological methods. Investigating tools that might aid in diagnosing and treating early-onset depression is essential for improving the prognosis of the disease course. While there is increasing evidence of possible biomarkers in adult depression, studies investigating this subject in adolescents are lacking. Methods In the current study, we analyzed protein levels in 461 adolescents assessed for depression using the Development and Well-Being Assessment (DAWBA) questionnaire as part of the domestic Psychiatric Health in Adolescent Study conducted in Uppsala, Sweden. We used the Proseek Multiplex Neuro Exploratory panel with Proximity Extension Assay technology provided by Olink Bioscience, followed by transcriptome analyses for the genes corresponding to the significant proteins, using four publicly available cohorts. Results We identified a total of seven proteins showing different levels between DAWBA risk groups at nominal significance, including RBKS, CRADD, ASGR1, HMOX2, PPP3R1, CD63, and PMVK. Transcriptomic analyses for these genes showed nominally significant replication of PPP3R1 in two of four cohorts including whole blood and prefrontal cortex, while ASGR1 and CD63 were replicated in only one cohort. Discussion Our study on adolescent depression revealed protein-level and transcriptomic differences, particularly in PPP3R1, pointing to the involvement of the calcineurin pathway in depression. Our findings regarding PPP3R1 also support the role of the prefrontal cortex in depression and reinforce the significance of investigating prefrontal cortex-related mechanisms in depression.
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Affiliation(s)
| | | | | | | | - Helgi B. Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
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21
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Curry RN, Ma Q, McDonald MF, Ko Y, Srivastava S, Chin PS, He P, Lozzi B, Athukuri P, Jing J, Wang S, Harmanci AO, Arenkiel B, Jiang X, Deneen B, Rao G, Harmanci AS. Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583026. [PMID: 38496434 PMCID: PMC10942290 DOI: 10.1101/2024.03.02.583026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Prior studies have described the complex interplay that exists between glioma cells and neurons, however, the electrophysiological properties endogenous to tumor cells remain obscure. To address this, we employed Patch-sequencing on human glioma specimens and found that one third of patched cells in IDH mutant (IDH mut ) tumors demonstrate properties of both neurons and glia by firing single, short action potentials. To define these hybrid cells (HCs) and discern if they are tumor in origin, we developed a computational tool, Single Cell Rule Association Mining (SCRAM), to annotate each cell individually. SCRAM revealed that HCs represent tumor and non-tumor cells that feature GABAergic neuron and oligodendrocyte precursor cell signatures. These studies are the first to characterize the combined electrophysiological and molecular properties of human glioma cells and describe a new cell type in human glioma with unique electrophysiological and transcriptomic properties that are likely also present in the non-tumor mammalian brain.
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22
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Beau M, Herzfeld DJ, Naveros F, Hemelt ME, D’Agostino F, Oostland M, Sánchez-López A, Chung YY, Michael Maibach, Kyranakis S, Stabb HN, Martínez Lopera MG, Lajko A, Zedler M, Ohmae S, Hall NJ, Clark BA, Cohen D, Lisberger SG, Kostadinov D, Hull C, Häusser M, Medina JF. A deep-learning strategy to identify cell types across species from high-density extracellular recordings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577845. [PMID: 38352514 PMCID: PMC10862837 DOI: 10.1101/2024.01.30.577845] [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: 02/23/2024]
Abstract
High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but don't reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals, revealing the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetic activation and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep-learning classifier that predicts cell types with greater than 95% accuracy based on waveform, discharge statistics, and layer of the recorded neuron. The classifier's predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across animal species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously-recorded cell types during behavior.
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Affiliation(s)
- Maxime Beau
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - David J. Herzfeld
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Francisco Naveros
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Engineering, Automation and Robotics, Research Centre for Information and Communication Technologies, University of Granada, Granada, Spain
| | - Marie E. Hemelt
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Federico D’Agostino
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Marlies Oostland
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Young Yoon Chung
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Michael Maibach
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Stephen Kyranakis
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Hannah N. Stabb
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | - Agoston Lajko
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Marie Zedler
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Shogo Ohmae
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Nathan J. Hall
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Beverley A. Clark
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Dana Cohen
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Dimitar Kostadinov
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Centre for Developmental Neurobiology, King’s College London, London, UK
| | - Court Hull
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Javier F. Medina
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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23
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Yang L, Liu F, Hahm H, Okuda T, Li X, Zhang Y, Kalyanaraman V, Heitmeier MR, Samineni VK. Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590975. [PMID: 38712231 PMCID: PMC11071495 DOI: 10.1101/2024.04.24.590975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.
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Affiliation(s)
- Lite Yang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
- Neuroscience Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Fang Liu
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Hannah Hahm
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Takao Okuda
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiaoyue Li
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Yufen Zhang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vani Kalyanaraman
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Monique R. Heitmeier
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vijay K. Samineni
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
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24
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Chamberland S, Grant G, Machold R, Nebet ER, Tian G, Stich J, Hanani M, Kullander K, Tsien RW. Functional specialization of hippocampal somatostatin-expressing interneurons. Proc Natl Acad Sci U S A 2024; 121:e2306382121. [PMID: 38640347 PMCID: PMC11047068 DOI: 10.1073/pnas.2306382121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 02/27/2024] [Indexed: 04/21/2024] Open
Abstract
Hippocampal somatostatin-expressing (Sst) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single-cell transcriptome analyses have provided a comprehensive Sst-IN subpopulations census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst-INs that largely tiled the morpho-functional parameter space of the Sst-INs superfamily. Notably, the Sst;;Tac1 intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were sufficient to interrupt their firing. In contrast, the Ndnf;;Nkx2-1 intersection identified a population of oriens lacunosum-moleculare INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal Sst-INs.
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Affiliation(s)
- Simon Chamberland
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Gariel Grant
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Robert Machold
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Erica R. Nebet
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Guoling Tian
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Joshua Stich
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Monica Hanani
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Klas Kullander
- Developmental Genetics, Department of Neuroscience, Uppsala University, Uppsala, Uppsala län752 37, Sweden
| | - Richard W. Tsien
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Center for Neural Science, New York University, New York, NY10003
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25
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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26
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Shi J, Nutkovich B, Kushinsky D, Rao BY, Herrlinger SA, Mihaila TS, Malina KCK, O’Toole CK, Conde Paredes ME, Yong HC, Varol E, Losonczy A, Spiegel I. 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586118. [PMID: 38585980 PMCID: PMC10996538 DOI: 10.1101/2024.03.21.586118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neural circuits are characterized by genetically and functionally diverse cell types. A mechanistic understanding of circuit function is predicated on linking the genetic and physiological properties of individual neurons. However, it remains highly challenging to map the functional properties of transcriptionally heterogeneous neuronal subtypes in mammalian cortical circuits in vivo. Here, we introduce a high-throughput two-photon nuclear phototagging (2P-NucTag) approach optimized for on-demand and indelible labeling of single neurons via a photoactivatable red fluorescent protein following in vivo functional characterization in behaving mice. We demonstrate the utility of this function-forward pipeline by selectively labeling and transcriptionally profiling previously inaccessible 'place' and 'silent' cells in the mouse hippocampus. Our results reveal unexpected differences in gene expression between these hippocampal pyramidal neurons with distinct spatial coding properties. Thus, 2P-NucTag opens a new way to uncover the molecular principles that govern the functional organization of neural circuits.
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Affiliation(s)
- Jingcheng Shi
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
| | - Boaz Nutkovich
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Dahlia Kushinsky
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Bovey Y. Rao
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
| | - Stephanie A. Herrlinger
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Tiberiu S. Mihaila
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Cliodhna K. O’Toole
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Margaret E. Conde Paredes
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Hyun Choong Yong
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Erdem Varol
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
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27
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Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [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: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
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Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
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28
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Shi Y, Wang G. Protocol to study microcircuits in the medial entorhinal cortex in mice using multiple patch-clamp recordings and morphological reconstruction. STAR Protoc 2024; 5:102917. [PMID: 38421863 PMCID: PMC10910315 DOI: 10.1016/j.xpro.2024.102917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Multiple patch-clamp recordings and morphological reconstruction are powerful approaches for neuronal microcircuitry dissection and cell type classification but are challenging due to the sophisticated expertise needed. Here, we present a protocol for applying these techniques to neurons in the medial entorhinal cortex (MEC) of mice. We detail steps to prepare brain slices containing MEC and perform simultaneous multiple whole-cell recordings, followed by procedures of histological staining and neuronal reconstruction. We then describe how we analyze morphological and electrophysiological features. For complete details on the use and execution of this protocol, please refer to Shi et al.1.
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Affiliation(s)
- Yuying Shi
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Guangfu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
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29
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Khodosevich K, Dragicevic K, Howes O. Drug targeting in psychiatric disorders - how to overcome the loss in translation? Nat Rev Drug Discov 2024; 23:218-231. [PMID: 38114612 DOI: 10.1038/s41573-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
In spite of major efforts and investment in development of psychiatric drugs, many clinical trials have failed in recent decades, and clinicians still prescribe drugs that were discovered many years ago. Although multiple reasons have been discussed for the drug development deadlock, we focus here on one of the major possible biological reasons: differences between the characteristics of drug targets in preclinical models and the corresponding targets in patients. Importantly, based on technological advances in single-cell analysis, we propose here a framework for the use of available and newly emerging knowledge from single-cell and spatial omics studies to evaluate and potentially improve the translational predictivity of preclinical models before commencing preclinical and, in particular, clinical studies. We believe that these recommendations will improve preclinical models and the ability to assess drugs in clinical trials, reducing failure rates in expensive late-stage trials and ultimately benefitting psychiatric drug discovery and development.
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Affiliation(s)
- Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health, University of Copenhagen, Copenhagen, Denmark.
| | - Katarina Dragicevic
- Biotech Research and Innovation Centre, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Oliver Howes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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30
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Price MS, Moore TI, Venkatachalam K. Intracellular Lactate Dynamics Reveal the Metabolic Diversity of Drosophila Glutamatergic Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582095. [PMID: 38464270 PMCID: PMC10925175 DOI: 10.1101/2024.02.26.582095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Lactate, an intermediary between glycolysis and mitochondrial oxidative phosphorylation, reflects the metabolic state of neurons. Here, we utilized a genetically-encoded lactate FRET biosensor to uncover subpopulations of distinct metabolic states among Drosophila glutamatergic neurons. Neurons within specific subpopulations exhibited correlated lactate flux patterns that stemmed from inherent cellular properties rather than neuronal interconnectivity. Further, individual neurons exhibited consistent patterns of lactate flux over time such that stimulus-evoked changes in lactate were correlated with pre-treatment fluctuations. Leveraging these temporal autocorrelations, deep-learning models accurately predicted post-stimulus responses from pre-stimulus fluctuations. These findings point to the existence of distinct neuronal subpopulations, each characterized by unique lactate dynamics, and raise the possibility that neurons with correlated metabolic activities might synchronize across different neural circuits. Such synchronization, rooted in neuronal metabolic states, could influence information processing in the brain.
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Affiliation(s)
- Matthew S. Price
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Molecular and Translational Biology Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
| | - Travis I. Moore
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Molecular and Translational Biology Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
- Molecular and Translational Biology Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences
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31
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Camunas-Soler J. Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca 2+ imaging and electrophysiology. Biophys Rev 2024; 16:89-107. [PMID: 38495444 PMCID: PMC10937895 DOI: 10.1007/s12551-023-01174-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/29/2023] [Indexed: 03/19/2024] Open
Abstract
I review recent technological advancements in coupling single-cell transcriptomics with cellular phenotypes including morphology, calcium signaling, and electrophysiology. Single-cell RNA sequencing (scRNAseq) has revolutionized cell type classifications by capturing the transcriptional diversity of cells. A new wave of methods to integrate scRNAseq and biophysical measurements is facilitating the linkage of transcriptomic data to cellular function, which provides physiological insight into cellular states. I briefly discuss critical factors of these phenotypical characterizations such as timescales, information content, and analytical tools. Dedicated sections focus on the integration with cell morphology, calcium imaging, and electrophysiology (patch-seq), emphasizing their complementary roles. I discuss their application in elucidating cellular states, refining cell type classifications, and uncovering functional differences in cell subtypes. To illustrate the practical applications and benefits of these methods, I highlight their use in tissues with excitable cell-types such as the brain, pancreatic islets, and the retina. The potential of combining functional phenotyping with spatial transcriptomics for a detailed mapping of cell phenotypes in situ is explored. Finally, I discuss open questions and future perspectives, emphasizing the need for a shift towards broader accessibility through increased throughput.
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Affiliation(s)
- Joan Camunas-Soler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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32
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Zhou K, Wei W, Yang D, Zhang H, Yang W, Zhang Y, Nie Y, Hao M, Wang P, Ruan H, Zhang T, Wang S, Liu Y. Dual electrical stimulation at spinal-muscular interface reconstructs spinal sensorimotor circuits after spinal cord injury. Nat Commun 2024; 15:619. [PMID: 38242904 PMCID: PMC10799086 DOI: 10.1038/s41467-024-44898-9] [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: 01/12/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
The neural signals produced by varying electrical stimulation parameters lead to characteristic neural circuit responses. However, the characteristics of neural circuits reconstructed by electrical signals remain poorly understood, which greatly limits the application of such electrical neuromodulation techniques for the treatment of spinal cord injury. Here, we develop a dual electrical stimulation system that combines epidural electrical and muscle stimulation to mimic feedforward and feedback electrical signals in spinal sensorimotor circuits. We demonstrate that a stimulus frequency of 10-20 Hz under dual stimulation conditions is required for structural and functional reconstruction of spinal sensorimotor circuits, which not only activates genes associated with axonal regeneration of motoneurons, but also improves the excitability of spinal neurons. Overall, the results provide insights into neural signal decoding during spinal sensorimotor circuit reconstruction, suggesting that the combination of epidural electrical and muscle stimulation is a promising method for the treatment of spinal cord injury.
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Affiliation(s)
- Kai Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Wei Wei
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
| | - Dan Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
- Department of Anatomy, School of Basic Medical Science, Guizhou Medical University, Guiyang, 550025, China
| | - Hui Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
| | - Wei Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China
| | - Yunpeng Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Yingnan Nie
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Mingming Hao
- i-Lab, Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, Jiangsu, 215123, China
- Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang, 315048, China
| | - Pengcheng Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Hang Ruan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ting Zhang
- i-Lab, Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou, Jiangsu, 215123, China
| | - Shouyan Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Yaobo Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
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33
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Jehasse K, Jouhanneau JS, Wetz S, Schwedt A, Poulet JFA, Neumann-Raizel P, Kampa BM. Immediate reuse of patch-clamp pipettes after ultrasonic cleaning. Sci Rep 2024; 14:1660. [PMID: 38238544 PMCID: PMC10796327 DOI: 10.1038/s41598-024-51837-7] [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: 05/26/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
The patch-clamp technique has revolutionized neurophysiology by allowing to study single neuronal excitability, synaptic connectivity, morphology, and the transcriptomic profile. However, the throughput in recordings is limited because of the manual replacement of patch-pipettes after each attempt which are often also unsuccessful. This has been overcome by automated cleaning the tips in detergent solutions, allowing to reuse the pipette for further recordings. Here, we developed a novel method of automated cleaning by sonicating the tips within the bath solution wherein the cells are placed, reducing the risk of contaminating the bath solution or internal solution of the recording pipette by any detergent and avoiding the necessity of a separate chamber for cleaning. We showed that the patch-pipettes can be used consecutively at least ten times and that the cleaning process does not negatively impact neither the brain slices nor other patched neurons. This method, combined with automated patch-clamp, highly improves the throughput for single and especially multiple recordings.
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Affiliation(s)
- Kevin Jehasse
- Systems Neurophysiology, Institute of Biology II, RWTH-Aachen University, Aachen, Germany.
| | - Jean-Sébastien Jouhanneau
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Neuroscience Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sophie Wetz
- Systems Neurophysiology, Institute of Biology II, RWTH-Aachen University, Aachen, Germany
- Research Training Group 2610 InnoRetVision, RWTH-Aachen University, Aachen, Germany
| | - Alexander Schwedt
- Central Facility for Electron Microscopy, RWTH-Aachen University, Aachen, Germany
| | - James F A Poulet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Neuroscience Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Björn M Kampa
- Systems Neurophysiology, Institute of Biology II, RWTH-Aachen University, Aachen, Germany.
- JARA BRAIN, Institute of Neuroscience and Medicine (INM-10), Forschungszentrum Jülich, Jülich, Germany.
- Research Training Group 2610 InnoRetVision, RWTH-Aachen University, Aachen, Germany.
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34
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Jeong M, Choi JH, Jang H, Sohn DH, Wang Q, Lee J, Yao L, Lee EJ, Fan J, Pratelli M, Wang EH, Snyder CN, Wang XY, Shin S, Gittis AH, Sung TC, Spitzer NC, Lim BK. Viral vector-mediated transgene delivery with novel recombinase systems for targeting neuronal populations defined by multiple features. Neuron 2024; 112:56-72.e4. [PMID: 37909037 PMCID: PMC10916502 DOI: 10.1016/j.neuron.2023.09.038] [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: 07/18/2022] [Revised: 05/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023]
Abstract
A comprehensive understanding of neuronal diversity and connectivity is essential for understanding the anatomical and cellular mechanisms that underlie functional contributions. With the advent of single-cell analysis, growing information regarding molecular profiles leads to the identification of more heterogeneous cell types. Therefore, the need for additional orthogonal recombinase systems is increasingly apparent, as heterogeneous tissues can be further partitioned into increasing numbers of specific cell types defined by multiple features. Critically, new recombinase systems should work together with pre-existing systems without cross-reactivity in vivo. Here, we introduce novel site-specific recombinase systems based on ΦC31 bacteriophage recombinase for labeling multiple cell types simultaneously and a novel viral strategy for versatile and robust intersectional expression of any transgene. Together, our system will help researchers specifically target different cell types with multiple features in the same animal.
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Affiliation(s)
- Minju Jeong
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyeonseok Jang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Qingdi Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joann Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Yao
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Ji Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiachen Fan
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Pratelli
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric H Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christen N Snyder
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiao-Yun Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sora Shin
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA, USA; Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - Aryn H Gittis
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tsung-Chang Sung
- Transgenic Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas C Spitzer
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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35
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Li AH, Kuo YY, Yang SB, Chen PC. Central Channelopathies in Obesity. CHINESE J PHYSIOL 2024; 67:15-26. [PMID: 38780269 DOI: 10.4103/ejpi.ejpi-d-23-00029] [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: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 05/25/2024] Open
Abstract
As obesity has raised heightening awareness, researchers have attempted to identify potential targets that can be treated for therapeutic intervention. Focusing on the central nervous system (CNS), the key organ in maintaining energy balance, a plethora of ion channels that are expressed in the CNS have been inspected and determined through manipulation in different hypothalamic neural subpopulations for their roles in fine-tuning neuronal activity on energy state alterations, possibly acting as metabolic sensors. However, a remaining gap persists between human clinical investigations and mouse studies. Despite having delineated the pathways and mechanisms of how the mouse study-identified ion channels modulate energy homeostasis, only a few targets overlap with the obesity-related risk genes extracted from human genome-wide association studies. Here, we present the most recently discovered CNS-specific metabolism-correlated ion channels using reverse and forward genetics approaches in mice and humans, respectively, in the hope of illuminating the prospects for future therapeutic development.
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Affiliation(s)
- Athena Hsu Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ying Kuo
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Chun Chen
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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36
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Cadwell CR, Tolias AS. Patch-seq: Multimodal Profiling of Single-Cell Morphology, Electrophysiology, and Gene Expression. Methods Mol Biol 2024; 2752:227-243. [PMID: 38194038 DOI: 10.1007/978-1-0716-3621-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Cells exhibit diverse morphologic phenotypes, biophysical and functional properties, and gene expression patterns. Understanding how these features are interrelated at the level of single cells has been challenging due to the lack of techniques for multimodal profiling of individual cells. We recently developed Patch-seq, a technique that combines whole-cell patch clamp recording, immunohistochemistry, and single-cell RNA-sequencing (scRNA-seq) to comprehensively profile single cells. Here we present a detailed step-by-step protocol for obtaining high-quality morphological, electrophysiological, and transcriptomic data from single cells. Patch-seq enables researchers to explore the rich, multidimensional phenotypic variability among cells and to directly correlate gene expression with phenotype at the level of single cells.
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Affiliation(s)
- Cathryn R Cadwell
- Departments of Neurological Surgery and Pathology, School of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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37
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Martini L, Amprimo G, Di Carlo S, Olmo G, Ferraris C, Savino A, Bardini R. Neuronal Spike Shapes (NSS): A straightforward approach to investigate heterogeneity in neuronal excitability states. Comput Biol Med 2024; 168:107783. [PMID: 38056213 DOI: 10.1016/j.compbiomed.2023.107783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The mammalian brain exhibits a remarkable diversity of neurons, contributing to its intricate architecture and functional complexity. The analysis of multimodal single-cell datasets enables the investigation of cell types and states heterogeneity. In this study, we introduce the Neuronal Spike Shapes (NSS), a straightforward approach for the exploration of excitability states of neurons based on their Action Potential (AP) waveforms. The NSS method describes the AP waveform based on a triangular representation complemented by a set of derived electrophysiological (EP) features. To support this hypothesis, we validate the proposed approach on two datasets of murine cortical neurons, focusing it on GABAergic neurons. The validation process involves a combination of NSS-based clustering analysis, features exploration, Differential Expression (DE), and Gene Ontology (GO) enrichment analysis. Results show that the NSS-based analysis captures neuronal excitability states that possess biological relevance independently of cell subtype. In particular, Neuronal Spike Shapes (NSS) captures, among others, a well-characterized fast-spiking excitability state, supported by both electrophysiological and transcriptomic validation. Gene Ontology Enrichment Analysis reveals voltage-gated potassium (K+) channels as specific markers of the identified NSS partitions. This finding strongly corroborates the biological relevance of NSS partitions as excitability states, as the expression of voltage-gated K+ channels regulates the hyperpolarization phase of the AP, being directly implicated in the regulation of neuronal excitability.
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Affiliation(s)
- Lorenzo Martini
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy.
| | - Gianluca Amprimo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy; Institute of Electronics, Information Engineering and Telecommunications, National Research Council, Corso Duca degli Abruzzi, 24, Turin, 10029, Italy.
| | - Stefano Di Carlo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.smilies.polito.it
| | - Gabriella Olmo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.sysbio.polito.it/analytics-technologies-health/
| | - Claudia Ferraris
- Institute of Electronics, Information Engineering and Telecommunications, National Research Council, Corso Duca degli Abruzzi, 24, Turin, 10029, Italy. https://www.ieiit.cnr.it/people/Ferraris-Claudia
| | - Alessandro Savino
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.smilies.polito.it
| | - Roberta Bardini
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy.
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38
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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39
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Kim HJ, Saikia JM, Monte KMA, Ha E, Romaus-Sanjurjo D, Sanchez JJ, Moore AX, Hernaiz-Llorens M, Chavez-Martinez CL, Agba CK, Li H, Zhang J, Lusk DT, Cervantes KM, Zheng B. Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration. Neuron 2023; 111:3953-3969.e5. [PMID: 37848024 PMCID: PMC10843387 DOI: 10.1016/j.neuron.2023.09.019] [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: 03/17/2023] [Revised: 07/26/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023]
Abstract
Despite substantial progress in understanding the biology of axon regeneration in the CNS, our ability to promote regeneration of the clinically important corticospinal tract (CST) after spinal cord injury remains limited. To understand regenerative heterogeneity, we conducted patch-based single-cell RNA sequencing on rare regenerating CST neurons at high depth following PTEN and SOCS3 deletion. Supervised classification with Garnett gave rise to a Regeneration Classifier, which can be broadly applied to predict the regenerative potential of diverse neuronal types across developmental stages or after injury. Network analyses highlighted the importance of antioxidant response and mitochondrial biogenesis. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Our data demonstrate a universal transcriptomic signature underlying the regenerative potential of vastly different neuronal populations and illustrate that deep sequencing of only hundreds of phenotypically identified neurons has the power to advance regenerative biology.
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Affiliation(s)
- Hugo J Kim
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Junmi M Saikia
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA
| | - Katlyn Marie A Monte
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eunmi Ha
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel Romaus-Sanjurjo
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joshua J Sanchez
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrea X Moore
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marc Hernaiz-Llorens
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Carmine L Chavez-Martinez
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Graduate program in Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Chimuanya K Agba
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA
| | - Haoyue Li
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joseph Zhang
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel T Lusk
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kayla M Cervantes
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Binhai Zheng
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Research Service, San Diego, CA, USA.
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40
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Shao M, Zhang W, Li Y, Tang L, Hao ZZ, Liu S. Patch-seq: Advances and Biological Applications. Cell Mol Neurobiol 2023; 44:8. [PMID: 38123823 DOI: 10.1007/s10571-023-01436-3] [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: 05/11/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Multimodal analysis of gene-expression patterns, electrophysiological properties, and morphological phenotypes at the single-cell/single-nucleus level has been arduous because of the diversity and complexity of neurons. The emergence of Patch-sequencing (Patch-seq) directly links transcriptomics, morphology, and electrophysiology, taking neuroscience research to a multimodal era. In this review, we summarized the development of Patch-seq and recent applications in the cortex, hippocampus, and other nervous systems. Through generating multimodal cell type atlases, targeting specific cell populations, and correlating transcriptomic data with phenotypic information, Patch-seq has provided new insight into outstanding questions in neuroscience. We highlight the challenges and opportunities of Patch-seq in neuroscience and hope to shed new light on future neuroscience research.
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Affiliation(s)
- Mingting Shao
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Wei Zhang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Ye Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Lei Tang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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41
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Qiao M. Factorized discriminant analysis for genetic signatures of neuronal phenotypes. Front Neuroinform 2023; 17:1265079. [PMID: 38156117 PMCID: PMC10752939 DOI: 10.3389/fninf.2023.1265079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/06/2023] [Indexed: 12/30/2023] Open
Abstract
Navigating the complex landscape of single-cell transcriptomic data presents significant challenges. Central to this challenge is the identification of a meaningful representation of high-dimensional gene expression patterns that sheds light on the structural and functional properties of cell types. Pursuing model interpretability and computational simplicity, we often look for a linear transformation of the original data that aligns with key phenotypic features of cells. In response to this need, we introduce factorized linear discriminant analysis (FLDA), a novel method for linear dimensionality reduction. The crux of FLDA lies in identifying a linear function of gene expression levels that is highly correlated with one phenotypic feature while minimizing the influence of others. To augment this method, we integrate it with a sparsity-based regularization algorithm. This integration is crucial as it selects a subset of genes pivotal to a specific phenotypic feature or a combination thereof. To illustrate the effectiveness of FLDA, we apply it to transcriptomic datasets from neurons in the Drosophila optic lobe. We demonstrate that FLDA not only captures the inherent structural patterns aligned with phenotypic features but also uncovers key genes associated with each phenotype.
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42
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Liu E, Pang K, Liu M, Tan X, Hang Z, Mu S, Han W, Yue Q, Comai S, Sun J. Activation of Kv7 channels normalizes hyperactivity of the VTA-NAcLat circuit and attenuates methamphetamine-induced conditioned place preference and sensitization in mice. Mol Psychiatry 2023; 28:5183-5194. [PMID: 37604975 DOI: 10.1038/s41380-023-02218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Abstract
The brain circuit projecting from the ventral tegmental area (VTA) to the nucleus accumbens lateral shell (NAcLat) has a key role in methamphetamine (MA) addiction. As different dopamine (DA) neuron subpopulations in the VTA participate in different neuronal circuits, it is a challenge to isolate these DA neuron subtypes. Using retrograde tracing and Patch-seq, we isolated DA neurons in the VTA-NAcLat circuit in MA-treated mice and performed gene expression profiling. Among the differentially expressed genes, KCNQ genes were dramatically downregulated. KCNQ genes encode Kv7 channel proteins, which modulate neuronal excitability. Injection of both the Kv7.2/3 agonist ICA069673 and the Kv7.4 agonist fasudil into the VTA attenuated MA-induced conditioned place preference and locomotor sensitization and decreased neuronal excitability. Increasing Kv7.2/3 activity decreased neural oscillations, synaptic plasticity and DA release in the VTA-NacLat circuit in MA-treated mice. Furthermore, overexpression of only Kv7.3 channels in the VTA-NacLat circuit was sufficient to attenuate MA-induced reward behavior and decrease VTA neuron excitability. Activation of Kv7 channels in the VTA may become a novel treatment strategy for MA abuse.
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Affiliation(s)
- E Liu
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Kunkun Pang
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
- Department of Ultrasound, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Min Liu
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Xu Tan
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Zhaofang Hang
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Shouhong Mu
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Weikai Han
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Qingwei Yue
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China
| | - Stefano Comai
- Department of Psychiatry, McGill University, Montréal, QC, Canada
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Jinhao Sun
- Department of Anatomy and Neurobiology, Shandong University School of Basic Medicine, Jinan, Shandong, China.
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43
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Elliott MAT, Schweiger HE, Robbins A, Vera-Choqqueccota S, Ehrlich D, Hernandez S, Voitiuk K, Geng J, Sevetson JL, Core C, Rosen YM, Teodorescu M, Wagner NO, Haussler D, Mostajo-Radji MA. Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education. eNeuro 2023; 10:ENEURO.0308-23.2023. [PMID: 38016807 PMCID: PMC10755643 DOI: 10.1523/eneuro.0308-23.2023] [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: 08/20/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
The introduction of Internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell (PSC)-derived cortical organoids in two different settings: using microscopy to monitor organoid growth in an introductory tissue culture course and using high-density (HD) multielectrode arrays (MEAs) to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training.
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Affiliation(s)
- Matthew A T Elliott
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Hunter E Schweiger
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Ash Robbins
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Samira Vera-Choqqueccota
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Drew Ehrlich
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Computational Media, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Sebastian Hernandez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Kateryna Voitiuk
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Jinghui Geng
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Jess L Sevetson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Cordero Core
- Scientific Software Engineering Center, eScience Institute, University of Washington, Seattle, WA 98195
| | - Yohei M Rosen
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Mircea Teodorescu
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Nico O Wagner
- College of Arts and Sciences, University of San Francisco, San Francisco, CA 94117
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
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44
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Sorensen SA, Gouwens NW, Wang Y, Mallory M, Budzillo A, Dalley R, Lee B, Gliko O, Kuo HC, Kuang X, Mann R, Ahmadinia L, Alfiler L, Baftizadeh F, Baker K, Bannick S, Bertagnolli D, Bickley K, Bohn P, Brown D, Bomben J, Brouner K, Chen C, Chen K, Chvilicek M, Collman F, Daigle T, Dawes T, de Frates R, Dee N, DePartee M, Egdorf T, El-Hifnawi L, Enstrom R, Esposito L, Farrell C, Gala R, Glomb A, Gamlin C, Gary A, Goldy J, Gu H, Hadley K, Hawrylycz M, Henry A, Hill D, Hirokawa KE, Huang Z, Johnson K, Juneau Z, Kebede S, Kim L, Lee C, Lesnar P, Li A, Glomb A, Li Y, Liang E, Link K, Maxwell M, McGraw M, McMillen DA, Mukora A, Ng L, Ochoa T, Oldre A, Park D, Pom CA, Popovich Z, Potekhina L, Rajanbabu R, Ransford S, Reding M, Ruiz A, Sandman D, Siverts L, Smith KA, Stoecklin M, Sulc J, Tieu M, Ting J, Trinh J, Vargas S, Vumbaco D, Walker M, Wang M, Wanner A, Waters J, Williams G, Wilson J, Xiong W, Lein E, Berg J, Kalmbach B, Yao S, Gong H, Luo Q, Ng L, Sümbül U, Jarsky T, Yao Z, Tasic B, Zeng H. Connecting single-cell transcriptomes to projectomes in mouse visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.25.568393. [PMID: 38168270 PMCID: PMC10760188 DOI: 10.1101/2023.11.25.568393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.
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Affiliation(s)
| | | | - Yun Wang
- Allen Institute for Brain Science
| | | | | | | | | | | | | | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | - Chao Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Kai Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science
| | | | | | | | | | | | | | | | | | | | | | | | - Hong Gu
- Allen Institute for Brain Science
| | | | | | | | | | | | - Zili Huang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | - Lisa Kim
- Allen Institute for Brain Science
| | | | | | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | | | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | - Zoran Popovich
- University of Washington, Dept. of Computer Science and Engineering
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wei Xiong
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Ed Lein
- Allen Institute for Brain Science
| | - Jim Berg
- Allen Institute for Brain Science
| | | | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Qingming Luo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lydia Ng
- Allen Institute for Brain Science
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45
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Blankenship HE, Carter KA, Cassidy NT, Markiewicz AN, Thellmann MI, Sharpe AL, Freeman WM, Beckstead MJ. VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567486. [PMID: 38014232 PMCID: PMC10680865 DOI: 10.1101/2023.11.16.567486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Alzheimer's disease (AD) patients exhibit neuropsychiatric symptoms that extend beyond classical cognitive deficits, suggesting involvement of subcortical areas. Here, we investigated the role of midbrain dopamine (DA) neurons in AD using the amyloid + tau-driven 3xTg-AD mouse model. We found deficits in reward-based operant learning in AD mice, suggesting possible VTA DA neuron dysregulation. Physiological assessment revealed hyperexcitability and disrupted firing in DA neurons caused by reduced activity of small-conductance calcium-activated potassium (SK) channels. RNA sequencing from contents of single patch-clamped DA neurons (Patch-seq) identified up-regulation of the SK channel modulator casein kinase 2 (CK2). Pharmacological inhibition of CK2 restored SK channel activity and normal firing patterns in 3xTg-AD mice. These findings shed light on a complex interplay between neuropsychiatric symptoms and subcortical circuits in AD, paving the way for novel treatment strategies.
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46
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Konopka G, Bhaduri A. Functional genomics and systems biology in human neuroscience. Nature 2023; 623:274-282. [PMID: 37938705 DOI: 10.1038/s41586-023-06686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Neuroscience research has entered a phase of key discoveries in the realm of neurogenomics owing to strong financial and intellectual support for resource building and tool development. The previous challenge of tissue heterogeneity has been met with the application of techniques that can profile individual cells at scale. Moreover, the ability to perturb genes, gene regulatory elements and neuronal activity in a cell-type-specific manner has been integrated with gene expression studies to uncover the functional underpinnings of the genome at a systems level. Although these insights have necessarily been grounded in model systems, we now have the opportunity to apply these approaches in humans and in human tissue, thanks to advances in human genetics, brain imaging and tissue collection. We acknowledge that there will probably always be limits to the extent to which we can apply the genomic tools developed in model systems to human neuroscience; however, as we describe in this Perspective, the neuroscience field is now primed with an optimal foundation for tackling this ambitious challenge. The application of systems-level network analyses to these datasets will facilitate a deeper appreciation of human neurogenomics that cannot otherwise be achieved from directly observable phenomena.
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Affiliation(s)
- Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA.
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47
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Jing J, Hu M, Ngodup T, Ma Q, Lau SNN, Ljungberg C, McGinley MJ, Trussell LO, Jiang X. Comprehensive analysis of cellular specializations that initiate parallel auditory processing pathways in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.539065. [PMID: 37293040 PMCID: PMC10245571 DOI: 10.1101/2023.05.15.539065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cochlear nuclear complex (CN) is the starting point for all central auditory processing and comprises a suite of neuronal cell types that are highly specialized for neural coding of acoustic signals. To examine how their striking functional specializations are determined at the molecular level, we performed single-nucleus RNA sequencing of the mouse CN to molecularly define all constituent cell types and related them to morphologically- and electrophysiologically-defined neurons using Patch-seq. We reveal an expanded set of molecular cell types encompassing all previously described major types and discover new subtypes both in terms of topographic and cell-physiologic properties. Our results define a complete cell-type taxonomy in CN that reconciles anatomical position, morphological, physiological, and molecular criteria. This high-resolution account of cellular heterogeneity and specializations from the molecular to the circuit level illustrates molecular underpinnings of functional specializations and enables genetic dissection of auditory processing and hearing disorders with unprecedented specificity.
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Affiliation(s)
- Junzhan Jing
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Ming Hu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Tenzin Ngodup
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Qianqian Ma
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shu-Ning Natalie Lau
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew J. McGinley
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Laurence O. Trussell
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Xiaolong Jiang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
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48
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Chartrand T, Dalley R, Close J, Goriounova NA, Lee BR, Mann R, Miller JA, Molnar G, Mukora A, Alfiler L, Baker K, Bakken TE, Berg J, Bertagnolli D, Braun T, Brouner K, Casper T, Csajbok EA, Dee N, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, Leon G, Long B, Mallory M, McGraw M, McMillen D, Melief EJ, Mihut N, Ng L, Nyhus J, Oláh G, Ozsvár A, Omstead V, Peterfi Z, Pom A, Potekhina L, Rajanbabu R, Rozsa M, Ruiz A, Sandle J, Sunkin SM, Szots I, Tieu M, Toth M, Trinh J, Vargas S, Vumbaco D, Williams G, Wilson J, Yao Z, Barzo P, Cobbs C, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Jarsky T, Keene CD, Ko AL, Koch C, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sorensen SA, Tasic B, Ting JT, Waters J, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Kalmbach B, Lein ES. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. Science 2023; 382:eadf0805. [PMID: 37824667 DOI: 10.1126/science.adf0805] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neurons with extensive L1 branching, but whether L1 interneurons are similarly diverse is underexplored. Using Patch-seq recordings from human neurosurgical tissue, we identified four transcriptomic subclasses with mouse L1 homologs, along with distinct subtypes and types unmatched in mouse L1. Subclass and subtype comparisons showed stronger transcriptomic differences in human L1 and were correlated with strong morphoelectric variability along dimensions distinct from mouse L1 variability. Accompanied by greater layer thickness and other cytoarchitecture changes, these findings suggest that L1 has diverged in evolution, reflecting the demands of regulating the expanded human neocortical circuit.
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Affiliation(s)
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalia A Goriounova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Gabor Molnar
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Eva Adrienn Csajbok
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Anna A Galakhova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim S Heistek
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Agnes Katalin Kocsis
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Norbert Mihut
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gáspár Oláh
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Attila Ozsvár
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Zoltan Peterfi
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Marton Rozsa
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Joanna Sandle
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Ildiko Szots
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Martin Toth
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | | | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Christiaan P J de Kock
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Huib D Mansvelder
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Gabor Tamas
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
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49
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Lee BR, Dalley R, Miller JA, Chartrand T, Close J, Mann R, Mukora A, Ng L, Alfiler L, Baker K, Bertagnolli D, Brouner K, Casper T, Csajbok E, Donadio N, Driessens SLW, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Hou WH, Johansen N, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, León G, Long B, Mallory M, Maxwell M, McGraw M, McMillen D, Melief EJ, Molnar G, Mortrud MT, Newman D, Nyhus J, Opitz-Araya X, Ozsvár A, Pham T, Pom A, Potekhina L, Rajanbabu R, Ruiz A, Sunkin SM, Szöts I, Taskin N, Thyagarajan B, Tieu M, Trinh J, Vargas S, Vumbaco D, Waleboer F, Walling-Bell S, Weed N, Williams G, Wilson J, Yao S, Zhou T, Barzó P, Bakken T, Cobbs C, Dee N, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Hodge R, Jarsky T, Keene CD, Ko AL, Korshoej AR, Levi BP, Meier K, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sørensen JC, Waters J, Zeng H, Berg J, Capogna M, Goriounova NA, Kalmbach B, de Kock CPJ, Mansvelder HD, Sorensen SA, Tamas G, Lein ES, Ting JT. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. Science 2023; 382:eadf6484. [PMID: 37824669 DOI: 10.1126/science.adf6484] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Human cortex transcriptomic studies have revealed a hierarchical organization of γ-aminobutyric acid-producing (GABAergic) neurons from subclasses to a high diversity of more granular types. Rapid GABAergic neuron viral genetic labeling plus Patch-seq (patch-clamp electrophysiology plus single-cell RNA sequencing) sampling in human brain slices was used to reliably target and analyze GABAergic neuron subclasses and individual transcriptomic types. This characterization elucidated transitions between PVALB and SST subclasses, revealed morphological heterogeneity within an abundant transcriptomic type, identified multiple spatially distinct types of the primate-specialized double bouquet cells (DBCs), and shed light on cellular differences between homologous mouse and human neocortical GABAergic neuron types. These results highlight the importance of multimodal phenotypic characterization for refinement of emerging transcriptomic cell type taxonomies and for understanding conserved and specialized cellular properties of human brain cell types.
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Affiliation(s)
- Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Thomas Chartrand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lauren Alfiler
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eva Csajbok
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Stan L W Driessens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Enstrom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Dijon Hill
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wen-Hsien Hou
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Agnes Katalin Kocsis
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Kunst
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Gabriela León
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Attila Ozsvár
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ram Rajanbabu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ildikó Szöts
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jessica Trinh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Vumbaco
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Pál Barzó
- Department of Neurosurgery, University of Szeged, 6725 Szeged, Hungary
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Ryder P Gwinn
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kaare Meier
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Anesthesiology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jens Christian Sørensen
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Center for Experimental Neuroscience, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Marco Capogna
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Huib D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
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50
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Han X, Guo S, Ji N, Li T, Liu J, Ye X, Wang Y, Yun Z, Xiong F, Rong J, Liu D, Ma H, Wang Y, Huang Y, Zhang P, Wu W, Ding L, Hawrylycz M, Lein E, Ascoli GA, Xie W, Liu L, Zhang L, Peng H. Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy. SCIENCE ADVANCES 2023; 9:eadf3771. [PMID: 37824619 PMCID: PMC10569712 DOI: 10.1126/sciadv.adf3771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/18/2023] [Indexed: 10/14/2023]
Abstract
Quantifying neuron morphology and distribution at the whole-brain scale is essential to understand the structure and diversity of cell types. It is exceedingly challenging to reuse recent technologies of single-cell labeling and whole-brain imaging to study human brains. We propose adaptive cell tomography (ACTomography), a low-cost, high-throughput, and high-efficacy tomography approach, based on adaptive targeting of individual cells. We established a platform to inject dyes into cortical neurons in surgical tissues of 18 patients with brain tumors or other conditions and one donated fresh postmortem brain. We collected three-dimensional images of 1746 cortical neurons, of which 852 neurons were reconstructed to quantify local dendritic morphology, and mapped to standard atlases. In our data, human neurons are more diverse across brain regions than by subject age or gender. The strong stereotypy within cohorts of brain regions allows generating a statistical tensor field of neuron morphology to characterize anatomical modularity of a human brain.
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Affiliation(s)
- Xiaofeng Han
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Shuxia Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Tian Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Xiangqiao Ye
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhixi Yun
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Feng Xiong
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Jing Rong
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Di Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Hui Ma
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yujin Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yue Huang
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Peng Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenhao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liya Ding
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Krasnow Institute for Advanced Studies and Bioengineering Department, College of Engineering and Computing, George Mason University, Fairfax, VA, USA
| | - Wei Xie
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Lijuan Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
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