1
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Liu Y, Zhang J, Jiang Z, Qin M, Xu M, Zhang S, Ma G. Organization of corticocortical and thalamocortical top-down inputs in the primary visual cortex. Nat Commun 2024; 15:4495. [PMID: 38802410 DOI: 10.1038/s41467-024-48924-8] [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: 10/16/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Unified visual perception requires integration of bottom-up and top-down inputs in the primary visual cortex (V1), yet the organization of top-down inputs in V1 remains unclear. Here, we used optogenetics-assisted circuit mapping to identify how multiple top-down inputs from higher-order cortical and thalamic areas engage V1 excitatory and inhibitory neurons. Top-down inputs overlap in superficial layers yet segregate in deep layers. Inputs from the medial secondary visual cortex (V2M) and anterior cingulate cortex (ACA) converge on L6 Pyrs, whereas ventrolateral orbitofrontal cortex (ORBvl) and lateral posterior thalamic nucleus (LP) inputs are processed in parallel in Pyr-type-specific subnetworks (Pyr←ORBvl and Pyr←LP) and drive mutual inhibition between them via local interneurons. Our study deepens understanding of the top-down modulation mechanisms of visual processing and establishes that V2M and ACA inputs in L6 employ integrated processing distinct from the parallel processing of LP and ORBvl inputs in L5.
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Affiliation(s)
- Yanmei Liu
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiahe Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhishan Jiang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Meiling Qin
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Siyu Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guofen Ma
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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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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3
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Pang JJ, Jiang X, Wu SM. Linear and Nonlinear Behaviors of the Photoreceptor Coupled Network. J Neurosci 2024; 44:e1433232024. [PMID: 38423760 PMCID: PMC11026348 DOI: 10.1523/jneurosci.1433-23.2024] [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: 07/28/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
Photoreceptors are electrically coupled to one another, and the spatiotemporal properties of electrical synapses in a two-dimensional retinal network are still not well studied, because of the limitation of the single electrode or pair recording techniques which do not allow simultaneously measuring responses of multiple photoreceptors at various locations in the retina. A multiple electrode recording system is needed. In this study, we investigate the network properties of the two-dimensional rod coupled array of the salamander retina (both sexes were used) by using the newly available multiple patch electrode system that allows simultaneous recordings from up to eight cells and to determine the electrical connectivity among multiple rods. We found direct evidence that voltage signal spread in the rod-rod coupling network in the absence of I h (mediated by HCN channels) is passive and follows the linear cable equation. Under physiological conditions, I h shapes the network signal by progressively shortening the response time-to-peak of distant rods, compensating the time loss of signal traveling from distant rods to bipolar cell somas and facilitating synchronization of rod output signals. Under voltage-clamp conditions, current flow within the coupled rods follows Ohm's law, supporting the idea that nonlinear behaviors of the rod network are dependent on membrane voltage. Rod-rod coupling is largely symmetrical in the 2D array, and voltage-clamp blocking the next neighboring rod largely suppresses rod signal spread into the second neighboring rod, suggesting that indirect coupling pathways play a minor role in rod-rod coupling.
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Affiliation(s)
- Ji-Jie Pang
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030
| | - Xiaolong Jiang
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel M Wu
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030
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4
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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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5
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Ding J, Liu R, Wen H, Tang W, Li Z, Venegas J, Su R, Molho D, Jin W, Wang Y, Lu Q, Li L, Zuo W, Chang Y, Xie Y, Tang J. DANCE: a deep learning library and benchmark platform for single-cell analysis. Genome Biol 2024; 25:72. [PMID: 38504331 PMCID: PMC10949782 DOI: 10.1186/s13059-024-03211-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 popular tasks with 32 state-of-art methods on 21 benchmark datasets. People can easily reproduce the results of supported algorithms across major benchmark datasets via minimal efforts, such as using only one command line. In addition, DANCE provides an ecosystem of deep learning architectures and tools for researchers to facilitate their own model development. DANCE is an open-source Python package that welcomes all kinds of contributions.
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Affiliation(s)
- Jiayuan Ding
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA.
| | - Renming Liu
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Hongzhi Wen
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA
| | - Wenzhuo Tang
- Department of Statistics and Probability, Michigan State University, East Lansing, USA
| | - Zhaoheng Li
- Department of Biostatistics, University of Washington, Seattle, USA
| | - Julian Venegas
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Runze Su
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
- Department of Statistics and Probability, Michigan State University, East Lansing, USA
| | - Dylan Molho
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA
| | - Wei Jin
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA
| | - Yixin Wang
- Department of Bioengineering, Stanford University, Palo Alto, USA
| | - Qiaolin Lu
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Lingxiao Li
- Department of Computer Science, Boston University, Boston, USA
| | - Wangyang Zuo
- Department of Computer Science, Zhejiang University of Technology, Zhejiang, China
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Yuying Xie
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA.
- Department of Statistics and Probability, Michigan State University, East Lansing, USA.
| | - Jiliang Tang
- Department of Computer Science and Engineering, Michigan State University, East Lansing, USA.
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6
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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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7
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Goshisht MK. Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges. ACS OMEGA 2024; 9:9921-9945. [PMID: 38463314 PMCID: PMC10918679 DOI: 10.1021/acsomega.3c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Machine learning (ML), particularly deep learning (DL), has made rapid and substantial progress in synthetic biology in recent years. Biotechnological applications of biosystems, including pathways, enzymes, and whole cells, are being probed frequently with time. The intricacy and interconnectedness of biosystems make it challenging to design them with the desired properties. ML and DL have a synergy with synthetic biology. Synthetic biology can be employed to produce large data sets for training models (for instance, by utilizing DNA synthesis), and ML/DL models can be employed to inform design (for example, by generating new parts or advising unrivaled experiments to perform). This potential has recently been brought to light by research at the intersection of engineering biology and ML/DL through achievements like the design of novel biological components, best experimental design, automated analysis of microscopy data, protein structure prediction, and biomolecular implementations of ANNs (Artificial Neural Networks). I have divided this review into three sections. In the first section, I describe predictive potential and basics of ML along with myriad applications in synthetic biology, especially in engineering cells, activity of proteins, and metabolic pathways. In the second section, I describe fundamental DL architectures and their applications in synthetic biology. Finally, I describe different challenges causing hurdles in the progress of ML/DL and synthetic biology along with their solutions.
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Affiliation(s)
- Manoj Kumar Goshisht
- Department of Chemistry, Natural and
Applied Sciences, University of Wisconsin—Green
Bay, Green
Bay, Wisconsin 54311-7001, United States
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8
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Choi TY, Jeon H, Jeong S, Kim EJ, Kim J, Jeong YH, Kang B, Choi M, Koo JW. Distinct prefrontal projection activity and transcriptional state conversely orchestrate social competition and hierarchy. Neuron 2024; 112:611-627.e8. [PMID: 38086372 DOI: 10.1016/j.neuron.2023.11.012] [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: 02/05/2023] [Revised: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 02/24/2024]
Abstract
Social animals compete for limited resources, resulting in a social hierarchy. Although different neuronal subpopulations in the medial prefrontal cortex (mPFC), which has been mechanistically implicated in social dominance behavior, encode distinct social competition behaviors, their identities and associated molecular underpinnings have not yet been identified. In this study, we found that mPFC neurons projecting to the nucleus accumbens (mPFC-NAc) encode social winning behavior, whereas mPFC neurons projecting to the ventral tegmental area (mPFC-VTA) encode social losing behavior. High-throughput single-cell transcriptomic analysis and projection-specific genetic manipulation revealed that the expression level of POU domain, class 3, transcription factor 1 (Pou3f1) in mPFC-VTA neurons controls social hierarchy. Optogenetic activation of mPFC-VTA neurons increases Pou3f1 expression and lowers social rank. Together, these data demonstrate that discrete activity and gene expression in separate mPFC projections oppositely orchestrate social competition and hierarchy.
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Affiliation(s)
- Tae-Yong Choi
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sejin Jeong
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Eum Ji Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeongseop Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea
| | - Yun Ha Jeong
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Byungsoo Kang
- Sysoft R&D Center, Daegu 41065, Republic of Korea; Neurovascular Unit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Ja Wook Koo
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea.
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9
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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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10
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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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11
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Cheung G, Pauler FM, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Gutmann-Özgen N, Ivec AE, Bock C, Shigemoto R, Hippenmeyer S. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron 2024; 112:230-246.e11. [PMID: 38096816 DOI: 10.1016/j.neuron.2023.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/06/2023] [Accepted: 11/10/2023] [Indexed: 01/21/2024]
Abstract
The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.
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Affiliation(s)
- Giselle Cheung
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Florian M Pauler
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Peter Koppensteiner
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences; 1090 Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, 1090 Vienna, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Martin Schrammel
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Natalie Gutmann-Özgen
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Alexis E Ivec
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences; 1090 Vienna, Austria; Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, 1090 Vienna, Austria
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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de Ceglia R, Ledonne A, Litvin DG, Lind BL, Carriero G, Latagliata EC, Bindocci E, Di Castro MA, Savtchouk I, Vitali I, Ranjak A, Congiu M, Canonica T, Wisden W, Harris K, Mameli M, Mercuri N, Telley L, Volterra A. Specialized astrocytes mediate glutamatergic gliotransmission in the CNS. Nature 2023; 622:120-129. [PMID: 37674083 PMCID: PMC10550825 DOI: 10.1038/s41586-023-06502-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Multimodal astrocyte-neuron communications govern brain circuitry assembly and function1. For example, through rapid glutamate release, astrocytes can control excitability, plasticity and synchronous activity2,3 of synaptic networks, while also contributing to their dysregulation in neuropsychiatric conditions4-7. For astrocytes to communicate through fast focal glutamate release, they should possess an apparatus for Ca2+-dependent exocytosis similar to neurons8-10. However, the existence of this mechanism has been questioned11-13 owing to inconsistent data14-17 and a lack of direct supporting evidence. Here we revisited the astrocyte glutamate exocytosis hypothesis by considering the emerging molecular heterogeneity of astrocytes18-21 and using molecular, bioinformatic and imaging approaches, together with cell-specific genetic tools that interfere with glutamate exocytosis in vivo. By analysing existing single-cell RNA-sequencing databases and our patch-seq data, we identified nine molecularly distinct clusters of hippocampal astrocytes, among which we found a notable subpopulation that selectively expressed synaptic-like glutamate-release machinery and localized to discrete hippocampal sites. Using GluSnFR-based glutamate imaging22 in situ and in vivo, we identified a corresponding astrocyte subgroup that responds reliably to astrocyte-selective stimulations with subsecond glutamate release events at spatially precise hotspots, which were suppressed by astrocyte-targeted deletion of vesicular glutamate transporter 1 (VGLUT1). Furthermore, deletion of this transporter or its isoform VGLUT2 revealed specific contributions of glutamatergic astrocytes in cortico-hippocampal and nigrostriatal circuits during normal behaviour and pathological processes. By uncovering this atypical subpopulation of specialized astrocytes in the adult brain, we provide insights into the complex roles of astrocytes in central nervous system (CNS) physiology and diseases, and identify a potential therapeutic target.
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Affiliation(s)
- Roberta de Ceglia
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Ada Ledonne
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
- Department of Experimental Neuroscience, IRCCS Santa Lucia Foundation, Rome, Italy
| | - David Gregory Litvin
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
- Wyss Center for Bio and Neuro Engineering, Campus Biotech, Geneva, Switzerland
| | - Barbara Lykke Lind
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giovanni Carriero
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | | | - Erika Bindocci
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | | | - Iaroslav Savtchouk
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
- Department of Biomedical Sciences, Marquette University, Milwaukee, WI, USA
| | - Ilaria Vitali
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Anurag Ranjak
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Mauro Congiu
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Tara Canonica
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - William Wisden
- Department of Life Sciences and UK Dementia Research Institute, Imperial College London, London, UK
| | - Kenneth Harris
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Manuel Mameli
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland
| | - Nicola Mercuri
- Department of Experimental Neuroscience, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ludovic Telley
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland.
| | - Andrea Volterra
- Department of Fundamental Neuroscience, University of Lausanne, Lausanne, Switzerland.
- Wyss Center for Bio and Neuro Engineering, Campus Biotech, Geneva, Switzerland.
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18
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Arbabi K, Jiang Y, Howard D, Nigam A, Inoue W, Gonzalez-Burgos G, Felsky D, Tripathy SJ. Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse patch-seq datasets. iScience 2023; 26:107329. [PMID: 37520693 PMCID: PMC10374462 DOI: 10.1016/j.isci.2023.107329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/25/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Microglia are cells with diverse roles, including the regulation of neuronal excitability. We leveraged Patch-seq to assess the presence and effects of microglia in the local microenvironment of recorded neurons. We first quantified the amounts of microglial transcripts in three Patch-seq datasets of human and mouse neocortical neurons, observing extensive contamination. Variation in microglial contamination was explained foremost by donor identity, particularly in human samples, and additionally by neuronal cell type identity in mice. Gene set enrichment analysis suggests that microglial contamination is reflective of activated microglia, and that these transcriptional signatures are distinct from those captured via single-nucleus RNA-seq. Finally, neurons with greater microglial contamination differed markedly in their electrophysiological characteristics, including lowered input resistances and more depolarized action potential thresholds. Our results generalize beyond Patch-seq to suggest that activated microglia may be widely present across brain slice preparations and contribute to neuron- and donor-related electrophysiological variability in vitro.
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Affiliation(s)
- Keon Arbabi
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yiyue Jiang
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Derek Howard
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Anukrati Nigam
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Wataru Inoue
- Robarts Research Institute, Western University, London, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Guillermo Gonzalez-Burgos
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Shreejoy J. Tripathy
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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19
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Cao JW, Liu LY, Yu YC. Gap junctions regulate the development of neural circuits in the neocortex. Curr Opin Neurobiol 2023; 81:102735. [PMID: 37263136 DOI: 10.1016/j.conb.2023.102735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 05/07/2023] [Indexed: 06/03/2023]
Abstract
Gap junctions between cells are ubiquitously expressed in the developing brain. They are involved in major steps of neocortical development, including neurogenesis, cell migration, synaptogenesis, and neural circuit formation, and have been implicated in cortical column formation. Dysfunctional gap junctions can contribute to or even cause a variety of brain diseases. Although the role of gap junctions in neocortical development is better known, a comprehensive understanding of their functions is far from complete. Here we explore several critical open questions surrounding gap junctions and their involvement in neural circuit development. Addressing them will greatly impact our understanding of the fundamental mechanisms of neocortical structure and function as well as the etiology of brain disease.
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Affiliation(s)
- Jun-Wei Cao
- School of Basic Medical Sciences, Xiangnan University, Chenzhou, Hunan 423000, China
| | - Lin-Yun Liu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Shanghai 200032, China
| | - Yong-Chun Yu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Shanghai 200032, China.
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20
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Kilpatrick S, Irwin C, Singh KK. Human pluripotent stem cell (hPSC) and organoid models of autism: opportunities and limitations. Transl Psychiatry 2023; 13:217. [PMID: 37344450 DOI: 10.1038/s41398-023-02510-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder caused by genetic or environmental perturbations during early development. Diagnoses are dependent on the identification of behavioral abnormalities that likely emerge well after the disorder is established, leaving critical developmental windows uncharacterized. This is further complicated by the incredible clinical and genetic heterogeneity of the disorder that is not captured in most mammalian models. In recent years, advancements in stem cell technology have created the opportunity to model ASD in a human context through the use of pluripotent stem cells (hPSCs), which can be used to generate 2D cellular models as well as 3D unguided- and region-specific neural organoids. These models produce profoundly intricate systems, capable of modeling the developing brain spatiotemporally to reproduce key developmental milestones throughout early development. When complemented with multi-omics, genome editing, and electrophysiology analysis, they can be used as a powerful tool to profile the neurobiological mechanisms underlying this complex disorder. In this review, we will explore the recent advancements in hPSC-based modeling, discuss present and future applications of the model to ASD research, and finally consider the limitations and future directions within the field to make this system more robust and broadly applicable.
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Affiliation(s)
- Savannah Kilpatrick
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada
| | - Courtney Irwin
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karun K Singh
- Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
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21
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Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023:10.1038/s41582-023-00809-y. [PMID: 37198436 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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22
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Wei Y, Nandi A, Jia X, Siegle JH, Denman D, Lee SY, Buchin A, Van Geit W, Mosher CP, Olsen S, Anastassiou CA. Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex. Nat Commun 2023; 14:2344. [PMID: 37095130 PMCID: PMC10126114 DOI: 10.1038/s41467-023-37844-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties from experiments with in vivo recorded units via computational modeling and optotagging experiments. We found two one-channel and six multi-channel clusters in mouse visual cortex with distinct in vivo properties in terms of activity, cortical depth, and behavior. We used biophysical models to map the two one- and the six multi-channel clusters to specific in vitro classes with unique morphology, excitability and conductance properties that explain their distinct extracellular signatures and functional characteristics. These concepts were tested in ground-truth optotagging experiments with two inhibitory classes unveiling distinct in vivo properties. This multi-modal approach presents a powerful way to separate in vivo clusters and infer their cellular properties from first principles.
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Affiliation(s)
- Yina Wei
- Zhejiang Lab, Hangzhou, 311100, China.
- Allen Institute for Brain Science, Seattle, WA, 98109, USA.
| | - Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- School of Life Sciences/McGovern Institute for Brain Research, Tsinghua University, 100084, Beijing, China
| | | | | | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Cajal Neuroscience Inc, Seattle, WA, 98102, USA
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL) Campus Biotech, Geneva, 1202, Switzerland
| | - Clayton P Mosher
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Shawn Olsen
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Costas A Anastassiou
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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23
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Wei Y, Nandi A, Jia X, Siegle JH, Denman D, Lee SY, Buchin A, Geit WV, Mosher CP, Olsen S, Anastassiou CA. Associations between in vitro , in vivo and in silico cell classes in mouse primary visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.532851. [PMID: 37131710 PMCID: PMC10153154 DOI: 10.1101/2023.04.17.532851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties from experiments with in vivo recorded units via computational modeling and optotagging experiments. We found two one-channel and six multi-channel clusters in mouse visual cortex with distinct in vivo properties in terms of activity, cortical depth, and behavior. We used biophysical models to map the two one- and the six multi-channel clusters to specific in vitro classes with unique morphology, excitability and conductance properties that explain their distinct extracellular signatures and functional characteristics. These concepts were tested in ground-truth optotagging experiments with two inhibitory classes unveiling distinct in vivo properties. This multi-modal approach presents a powerful way to separate in vivo clusters and infer their cellular properties from first principles.
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Affiliation(s)
- Yina Wei
- Zhejiang Lab, Hangzhou 311100, China
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- School of Life Sciences, Tsinghua University, Beijing, 100084, China, IDG/McGovern Institute for Brain Research at Tsinghua University, Beijing, 100084, China
| | | | | | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Cajal Neuroscience Inc, Seattle, WA 98102, USA
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL) Campus Biotech, Geneva 1202, Switzerland
| | - Clayton P. Mosher
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shawn Olsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Costas A. Anastassiou
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Lead contact
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24
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Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor A, Brittain D, Buchanan J, Bumbarger D, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu S, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA. Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533857. [PMID: 36993629 PMCID: PMC10055412 DOI: 10.1101/2023.03.22.533857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types 1 . Neural cell types have previously been defined by morphology 2, 3 , electrophysiology 4, 5 , transcriptomic expression 6-8 , connectivity 9-13 , or even a combination of such modalities 14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21 . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25 , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.
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25
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Li Z, Gao E, Zhou J, Han W, Xu X, Gao X. Applications of deep learning in understanding gene regulation. CELL REPORTS METHODS 2023; 3:100384. [PMID: 36814848 PMCID: PMC9939384 DOI: 10.1016/j.crmeth.2022.100384] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gene regulation is a central topic in cell biology. Advances in omics technologies and the accumulation of omics data have provided better opportunities for gene regulation studies than ever before. For this reason deep learning, as a data-driven predictive modeling approach, has been successfully applied to this field during the past decade. In this article, we aim to give a brief yet comprehensive overview of representative deep-learning methods for gene regulation. Specifically, we discuss and compare the design principles and datasets used by each method, creating a reference for researchers who wish to replicate or improve existing methods. We also discuss the common problems of existing approaches and prospectively introduce the emerging deep-learning paradigms that will potentially alleviate them. We hope that this article will provide a rich and up-to-date resource and shed light on future research directions in this area.
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Affiliation(s)
- Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Elva Gao
- The KAUST School, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juexiao Zhou
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Wenkai Han
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Xiaopeng Xu
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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26
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Jihad M, Yet İ. Multiomics Integration at Single-Cell Resolution Using Bayesian Networks: A Case Study in Hepatocellular Carcinoma. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:24-33. [PMID: 36602810 DOI: 10.1089/omi.2022.0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multiomics data integration is one of the leading frontiers of complex disease research and integrative biology. The advances in single-cell sequencing technologies offer yet another crucial dimension in multiomics research. The single-cell studies enable the study and integration of multiomics data simultaneously in the same cell. We report in this study multiomics data integration in single-cell resolution using Bayesian networks (BNs) in a case study of hepatocellular carcinoma (HCC). A BN encodes the conditional dependencies/independencies of variables using a graphical model with an accompanying joint probability. RNA-seq and Reduced Representation Bisulfite Sequencing data were analyzed separately, and copy number variations were estimated by the hidden Markov model method. Several BN models were constructed to reveal omics' causal and associational relationships. These methods were subjected to a validation study using an independent data set. We show the heterogeneity of the multiple cellular layers of HCC at single-cell omics resolution by identifying best-fitted BN models of 295 genes. We also provide novel insights into the multiomics mechanistic relationships in the human lymphocyte antigen class I genes in HCC. To the best of our knowledge, this is the first study to focus on integrating omics data using a machine learning algorithm, BNs, at the single-cell resolution using a case study of HCC.
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Affiliation(s)
- Muntadher Jihad
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - İdil Yet
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
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27
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Royero P, Quatraccioni A, Früngel R, Silva MH, Bast A, Ulas T, Beyer M, Opitz T, Schultze JL, Graham ME, Oberlaender M, Becker A, Schoch S, Beck H. Circuit-selective cell-autonomous regulation of inhibition in pyramidal neurons by Ste20-like kinase. Cell Rep 2022; 41:111757. [PMID: 36476865 PMCID: PMC9756112 DOI: 10.1016/j.celrep.2022.111757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Maintaining an appropriate balance between excitation and inhibition is critical for neuronal information processing. Cortical neurons can cell-autonomously adjust the inhibition they receive to individual levels of excitatory input, but the underlying mechanisms are unclear. We describe that Ste20-like kinase (SLK) mediates cell-autonomous regulation of excitation-inhibition balance in the thalamocortical feedforward circuit, but not in the feedback circuit. This effect is due to regulation of inhibition originating from parvalbumin-expressing interneurons, while inhibition via somatostatin-expressing interneurons is unaffected. Computational modeling shows that this mechanism promotes stable excitatory-inhibitory ratios across pyramidal cells and ensures robust and sparse coding. Patch-clamp RNA sequencing yields genes differentially regulated by SLK knockdown, as well as genes associated with excitation-inhibition balance participating in transsynaptic communication and cytoskeletal dynamics. These data identify a mechanism for cell-autonomous regulation of a specific inhibitory circuit that is critical to ensure that a majority of cortical pyramidal cells participate in information coding.
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Affiliation(s)
- Pedro Royero
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Anne Quatraccioni
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Rieke Früngel
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Mariella Hurtado Silva
- Synapse Proteomics, Children’s Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Arco Bast
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany,International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Marc Beyer
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V., Bonn, Germany
| | - Thoralf Opitz
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany,Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Mark E. Graham
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany
| | - Marcel Oberlaender
- In Silico Brain Sciences Group, Max-Planck Institute for Neurobiology of Behavior – Caesar, Bonn, Germany
| | - Albert Becker
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany
| | - Susanne Schoch
- Department of Neuropathology, University Hospital Bonn, Section for Translational Epilepsy Research, 53127 Bonn, Germany
| | - Heinz Beck
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, University of Bonn Medical Center, Venusberg-Campus 1, 53105 Bonn, Germany,Deutsches Zentrum für Neurodegenerative Erkrankungen e.V., Bonn, Germany,Corresponding author
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28
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Lv X, Li S, Li J, Yu XY, Ge X, Li B, Hu S, Lin Y, Zhang S, Yang J, Zhang X, Yan J, Joyner AL, Shi H, Wu Q, Shi SH. Patterned cPCDH expression regulates the fine organization of the neocortex. Nature 2022; 612:503-511. [PMID: 36477535 DOI: 10.1038/s41586-022-05495-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/28/2022] [Indexed: 12/12/2022]
Abstract
The neocortex consists of a vast number of diverse neurons that form distinct layers and intricate circuits at the single-cell resolution to support complex brain functions1. Diverse cell-surface molecules are thought to be key for defining neuronal identity, and they mediate interneuronal interactions for structural and functional organization2-6. However, the precise mechanisms that control the fine neuronal organization of the neocortex remain largely unclear. Here, by integrating in-depth single-cell RNA-sequencing analysis, progenitor lineage labelling and mosaic functional analysis, we report that the diverse yet patterned expression of clustered protocadherins (cPCDHs)-the largest subgroup of the cadherin superfamily of cell-adhesion molecules7-regulates the precise spatial arrangement and synaptic connectivity of excitatory neurons in the mouse neocortex. The expression of cPcdh genes in individual neocortical excitatory neurons is diverse yet exhibits distinct composition patterns linked to their developmental origin and spatial positioning. A reduction in functional cPCDH expression causes a lateral clustering of clonally related excitatory neurons originating from the same neural progenitor and a significant increase in synaptic connectivity. By contrast, overexpression of a single cPCDH isoform leads to a lateral dispersion of clonally related excitatory neurons and a considerable decrease in synaptic connectivity. These results suggest that patterned cPCDH expression biases fine spatial and functional organization of individual neocortical excitatory neurons in the mammalian brain.
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Affiliation(s)
- Xiaohui Lv
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Centre, New York, NY, USA
| | - Shuo Li
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China
| | - Jingwei Li
- Centre for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang-Yu Yu
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China
| | - Xiao Ge
- Centre for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Li
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuhan Hu
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Lin
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China
| | - Songbo Zhang
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China
| | - Jiajun Yang
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China
| | - Xiuli Zhang
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Jie Yan
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Centre, New York, NY, USA
| | - Hang Shi
- School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Centre of Biological Structure, Beijing Advanced Innovation Centre for Structural Biology, Tsinghua University, Beijing, China
| | - Qiang Wu
- Centre for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Song-Hai Shi
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Centre for Life Sciences, Tsinghua University, Beijing, China. .,Beijing Frontier Research Centre of Biological Structure, Beijing Advanced Innovation Centre for Structural Biology, Tsinghua University, Beijing, China. .,Chinese Institute for Brain Research, Beijing, China.
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29
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Correlation Analysis of Molecularly-Defined Cortical Interneuron Populations with Morpho-Electric Properties in Layer V of Mouse Neocortex. Neurosci Bull 2022:10.1007/s12264-022-00983-x. [DOI: 10.1007/s12264-022-00983-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
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30
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Wei JR, Hao ZZ, Xu C, Huang M, Tang L, Xu N, Liu R, Shen Y, Teichmann SA, Miao Z, Liu S. Identification of visual cortex cell types and species differences using single-cell RNA sequencing. Nat Commun 2022; 13:6902. [PMID: 36371428 PMCID: PMC9653448 DOI: 10.1038/s41467-022-34590-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
The primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers including HPCAL1 and NXPH4, and also identified two cell types, an NPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependent OSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions.
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Affiliation(s)
- Jia-Ru Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 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, China
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lei Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 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, China
| | - Ruifeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Zhichao Miao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China.
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, UK.
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, China.
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31
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Moore H, Lega BC, Konopka G. Riding brain "waves" to identify human memory genes. Curr Opin Cell Biol 2022; 78:102118. [PMID: 35947942 DOI: 10.1016/j.ceb.2022.102118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
While there is extensive research on memory-related oscillations and brain gene expression, the relationship between oscillations and gene expression has rarely been studied. Recently, progress has been made to identify specific genes associated with oscillations that are correlated with episodic memory. Neocortical regions, in particular the temporal pole, have been examined in this line of research due to their accessibility during neurosurgical procedures. By harnessing this accessibility, a unique and powerful study design has allowed gene expression and intracranial oscillatory data to be sourced from the same human patients. These studies have identified a plethora of understudied gene targets that should be further characterized with respect to human brain function. Future work should extend to other brain regions to increase our understanding of the genetic signatures of oscillations and, ultimately, human cognition.
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Affiliation(s)
- Haley Moore
- Department of Neuroscience, UT Southwestern Medical Center, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA; Department of Neurosurgery, UT Southwestern Medical Center, USA
| | - Bradley C Lega
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA; Department of Neurosurgery, UT Southwestern Medical Center, USA.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA.
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32
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Huang W, Xu Q, Su J, Tang L, Hao ZZ, Xu C, Liu R, Shen Y, Sang X, Xu N, Tie X, Miao Z, Liu X, Xu Y, Liu F, Liu Y, Liu S. Linking transcriptomes with morphological and functional phenotypes in mammalian retinal ganglion cells. Cell Rep 2022; 40:111322. [PMID: 36103830 DOI: 10.1016/j.celrep.2022.111322] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/19/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Retinal ganglion cells (RGCs) are the brain's gateway to the visual world. They can be classified into different types on the basis of their electrophysiological, transcriptomic, or morphological characteristics. Here, we characterize the transcriptomic, morphological, and functional features of 472 high-quality RGCs using Patch sequencing (Patch-seq), providing functional and morphological annotation of many transcriptomic-defined cell types of a previously established RGC atlas. We show a convergence of different modalities in defining the RGC identity and reveal the degree of correspondence for well-characterized cell types across multimodal data. Moreover, we complement some RGC types with detailed morphological and functional properties. We also identify differentially expressed genes among ON, OFF, and ON-OFF RGCs such as Vat1l, Slitrk6, and Lmo7, providing candidate marker genes for functional studies. Our research suggests that the molecularly distinct clusters may also differ in their roles of encoding visual information.
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Affiliation(s)
- Wanjing 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
| | - Qiang 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
| | - Jing Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Lei Tang
- 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
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Ruifeng 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
| | - 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
| | - Xuan Sang
- 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
| | - Xiaoxiu Tie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhichao Miao
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Xialin 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
| | - Ying Xu
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China; Key Laboratory of CNS Regeneration (Jinan University), Ministry of Education, Guangzhou, 510632, China
| | - Feng 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.
| | - Yizhi 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; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing 100085, 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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Habibey R, Rojo Arias JE, Striebel J, Busskamp V. Microfluidics for Neuronal Cell and Circuit Engineering. Chem Rev 2022; 122:14842-14880. [PMID: 36070858 PMCID: PMC9523714 DOI: 10.1021/acs.chemrev.2c00212] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread adoption of microfluidic devices among the neuroscience and neurobiology communities has enabled addressing a broad range of questions at the molecular, cellular, circuit, and system levels. Here, we review biomedical engineering approaches that harness the power of microfluidics for bottom-up generation of neuronal cell types and for the assembly and analysis of neural circuits. Microfluidics-based approaches are instrumental to generate the knowledge necessary for the derivation of diverse neuronal cell types from human pluripotent stem cells, as they enable the isolation and subsequent examination of individual neurons of interest. Moreover, microfluidic devices allow to engineer neural circuits with specific orientations and directionality by providing control over neuronal cell polarity and permitting the isolation of axons in individual microchannels. Similarly, the use of microfluidic chips enables the construction not only of 2D but also of 3D brain, retinal, and peripheral nervous system model circuits. Such brain-on-a-chip and organoid-on-a-chip technologies are promising platforms for studying these organs as they closely recapitulate some aspects of in vivo biological processes. Microfluidic 3D neuronal models, together with 2D in vitro systems, are widely used in many applications ranging from drug development and toxicology studies to neurological disease modeling and personalized medicine. Altogether, microfluidics provide researchers with powerful systems that complement and partially replace animal models.
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Affiliation(s)
- Rouhollah Habibey
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Jesús Eduardo Rojo Arias
- Wellcome─MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Johannes Striebel
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
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Jiang SN, Cao JW, Liu LY, Zhou Y, Shan GY, Fu YH, Shao YC, Yu YC. Sncg, Mybpc1, and Parm1 Classify subpopulations of VIP-expressing interneurons in layers 2/3 of the somatosensory cortex. Cereb Cortex 2022; 33:4293-4304. [PMID: 36030380 DOI: 10.1093/cercor/bhac343] [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: 02/11/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Neocortical vasoactive intestinal polypeptide-expressing (VIP+) interneurons display highly diverse morpho-electrophysiological and molecular properties. To begin to understand the function of VIP+ interneurons in cortical circuits, they must be clearly and comprehensively classified into distinct subpopulations based on specific molecular markers. Here, we utilized patch-clamp RT-PCR (Patch-PCR) to simultaneously obtain the morpho-electric properties and mRNA profiles of 155 VIP+ interneurons in layers 2 and 3 (L2/3) of the mouse somatosensory cortex. Using an unsupervised clustering method, we identified 3 electrophysiological types (E-types) and 2 morphological types (M-types) of VIP+ interneurons. Joint clustering based on the combined electrophysiological and morphological features resulted in 3 morpho-electric types (ME-types). More importantly, we found these 3 ME-types expressed distinct marker genes: ~94% of Sncg+ cells were ME-type 1, 100% of Mybpc1+ cells were ME-type 2, and ~78% of Parm1+ were ME-type 3. By clarifying the properties of subpopulations of cortical L2/3 VIP+ interneurons, this study establishes a basis for future investigations aiming to elucidate their physiological roles.
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Affiliation(s)
- Shao-Na Jiang
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
| | - Jun-Wei Cao
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
| | - Lin-Yun Liu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
| | - Ying Zhou
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
| | - Guang-Yao Shan
- School of Clinical Medicine, Fudan University, Dong'an Road 131, Shanghai 200032, China
| | - Ying-Hui Fu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
| | - Yun-Chao Shao
- Orthopaedic Department of Zhongshan Hospital, Fudan University, Fenglin Road 180, Shanghai 200032, China
| | - Yong-Chun Yu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Dong'an Rold 131, Shanghai 200032, China
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Pavón Arocas O, Branco T. Preparation of acute midbrain slices containing the superior colliculus and periaqueductal Gray for patch-clamp recordings. PLoS One 2022; 17:e0271832. [PMID: 35951507 PMCID: PMC9371254 DOI: 10.1371/journal.pone.0271832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
This protocol is a practical guide for preparing acute coronal slices from the midbrain of young adult mice for electrophysiology experiments. It describes two different sets of solutions with their respective incubation strategies and two alternative procedures for brain extraction: decapitation under terminal isoflurane anaesthesia and intracardial perfusion with artificial cerebrospinal fluid under terminal isoflurane anaesthesia. Slices can be prepared from wild-type mice as well as from mice that have been genetically modified or transfected with viral constructs to label subsets of cells. The preparation can be used to investigate the electrophysiological properties of midbrain neurons in combination with pharmacology, opto- and chemogenetic manipulations, and calcium imaging; which can be followed by morphological reconstruction, immunohistochemistry, or single-cell transcriptomics. The protocol also provides a detailed list of materials and reagents including the design for a low-cost and easy to assemble 3D printed slice recovery chamber, general advice for troubleshooting common issues leading to suboptimal slice quality, and some suggestions to ensure good maintenance of a patch-clamp rig.
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Affiliation(s)
- Oriol Pavón Arocas
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, United Kingdom
- * E-mail:
| | - Tiago Branco
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, United Kingdom
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36
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Lewis CM, Griffith TN. The mechanisms of cold encoding. Curr Opin Neurobiol 2022; 75:102571. [DOI: 10.1016/j.conb.2022.102571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/15/2022]
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David CK, Sugimura YK, Kallurkar PS, Picardo MCD, Saha MS, Conradi Smith GD, Del Negro CA. Single cell transcriptome sequencing of inspiratory neurons of the preBötzinger complex in neonatal mice. Sci Data 2022; 9:457. [PMID: 35907922 PMCID: PMC9338969 DOI: 10.1038/s41597-022-01569-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
Neurons in the brainstem preBötzinger complex (preBötC) generate the rhythm and rudimentary motor pattern for inspiratory breathing movements. We performed whole-cell patch-clamp recordings from inspiratory neurons in the preBötC of neonatal mouse slices that retain breathing-related rhythmicity in vitro. We classified neurons based on their electrophysiological properties and genetic background, and then aspirated their cellular contents for single-cell RNA sequencing (scRNA-seq). This data set provides the raw nucleotide sequences (FASTQ files) and annotated files of nucleotide sequences mapped to the mouse genome (mm10 from Ensembl), which includes the fragment counts, gene lengths, and fragments per kilobase of transcript per million mapped reads (FPKM). These data reflect the transcriptomes of the neurons that generate the rhythm and pattern for inspiratory breathing movements.
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Affiliation(s)
- Caroline K David
- Department of Applied Science, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA
| | - Yae K Sugimura
- Department of Neuroscience, Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato, Tokyo, 105-8461, Japan
| | - Prajkta S Kallurkar
- Department of Applied Science, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA
| | - Maria Cristina D Picardo
- Department of Applied Science, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA
| | - Margaret S Saha
- Department of Biology, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA
| | - Gregory D Conradi Smith
- Department of Applied Science, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA
| | - Christopher A Del Negro
- Department of Applied Science, William & Mary, 540 Landrum Drive, Williamsburg, Virginia, 23185, USA.
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Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science 2022; 376:1441-1446. [PMID: 35587512 PMCID: PMC9233096 DOI: 10.1126/science.abm5224] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Progenitors of the developing human neocortex reside in the ventricular and outer subventricular zones (VZ and OSVZ, respectively). However, whether cells derived from these niches have similar developmental fates is unknown. By performing fate mapping in primary human tissue, we demonstrate that astrocytes derived from these niches populate anatomically distinct layers. Cortical plate astrocytes emerge from VZ progenitors and proliferate locally, while putative white matter astrocytes are morphologically heterogeneous and emerge from both VZ and OSVZ progenitors. Furthermore, via single-cell sequencing of morphologically defined astrocyte subtypes using Patch-seq, we identify molecular distinctions between VZ-derived cortical plate astrocytes and OSVZ-derived white matter astrocytes that persist into adulthood. Together, our study highlights a complex role for cell lineage in the diversification of human neocortical astrocytes.
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Affiliation(s)
- Denise E Allen
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Kevin C Donohue
- Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,School of Medicine, The University of California San Francisco, San Francisco, USA,Center for Integrative Neuroscience, The University of California San Francisco; San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Kavli Institute for Fundamental Neuroscience, The University of California San Francisco, San Francisco, USA
| | - Cathryn R Cadwell
- Department of Pathology, The University of California San Francisco, San Francisco, USA
| | - David Shin
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Matthew G Keefe
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Vikaas S Sohal
- Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Kavli Institute for Fundamental Neuroscience, The University of California San Francisco, San Francisco, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Corresponding author.
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Wu H, Dang D, Yang X, Wang J, Qi R, Yang W, Liang W. Accurate and Automatic Extraction of Cell Self-Rotation Speed in an ODEP Field Using an Area Change Algorithm. MICROMACHINES 2022; 13:mi13060818. [PMID: 35744432 PMCID: PMC9229272 DOI: 10.3390/mi13060818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022]
Abstract
Cells are complex biological units that can sense physicochemical stimuli from their surroundings and respond positively to them through characterization of the cell behavior. Thus, understanding the motions of cells is important for investigating their intrinsic properties and reflecting their various states. Computer-vision-based methods for elucidating cell behavior offer a novel approach to accurately extract cell motions. Here, we propose an algorithm based on area change to automatically extract the self-rotation of cells in an optically induced dielectrophoresis field. To obtain a clear and complete outline of the cell structure, dark corner removal and contrast stretching techniques are used in the pre-processing stage. The self-rotation speed is calculated by determining the frequency of the cell area changes in all of the captured images. The algorithm is suitable for calculating in-plane and out-of-plane rotations, while addressing the problem of identical images at different rotation angles when dealing with rotations of spherical and flat cells. In addition, the algorithm can be used to determine the motion trajectory of cells. The experimental results show that the algorithm can efficiently and accurately calculate cell rotation speeds of up to ~155 rpm. Potential applications of the proposed algorithm include cell morphology extraction, cell classification, and characterization of the cell mechanical properties. The algorithm can be very helpful for those who are interested in using computer vision and artificial-intelligence-based ideology in single-cell studies, drug treatment, and other bio-related fields.
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Affiliation(s)
- Haiyang Wu
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110168, China; (H.W.); (X.Y.); (J.W.)
| | - Dan Dang
- School of Science, Shenyang Jianzhu University, Shenyang 110168, China
- Correspondence: (D.D.); (R.Q.); (W.L.)
| | - Xieliu Yang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110168, China; (H.W.); (X.Y.); (J.W.)
| | - Junhai Wang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110168, China; (H.W.); (X.Y.); (J.W.)
| | - Ruolong Qi
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110168, China; (H.W.); (X.Y.); (J.W.)
- Correspondence: (D.D.); (R.Q.); (W.L.)
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China;
| | - Wenfeng Liang
- School of Mechanical Engineering, Shenyang Jianzhu University, Shenyang 110168, China; (H.W.); (X.Y.); (J.W.)
- Correspondence: (D.D.); (R.Q.); (W.L.)
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40
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Huang W, Xu Q, Liu F, Su J, Xiao D, Tang L, Hao ZZ, Liu R, Xiang K, Bi Y, Miao Z, Liu X, Liu Y, Liu S. Identification of TPBG-Expressing Amacrine Cells in DAT-tdTomato Mouse. Invest Ophthalmol Vis Sci 2022; 63:13. [PMID: 35551574 PMCID: PMC9123489 DOI: 10.1167/iovs.63.5.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose Neurons are the bricks of the neuronal system and experimental access to certain neuron subtypes will be of great help to decipher neuronal circuits. Here, we identified trophoblast glycoprotein (TPBG)-expressing GABAergic amacrine cells (ACs) that were selectively labeled in DAT-tdTomato transgenic mice. Methods Retina and brain sections were prepared for immunostaining with antibodies against various biomarkers. Patch-sequencing was performed to obtain the transcriptomes of tdTomato-positive cells in DAT-tdTomato mice. Whole-cell recordings were conducted to identify responses to light stimulation. Results Tyrosine hydroxylase immunoreactive cells were colocalized with tdTomato-positive cells in substantia nigra pars compacta, but not in the retina. Transcriptomes collected from tdTomato-positive cells in retinas via Patch-sequencing exhibited the expression of marker genes of ACs (Pax6 and Slc32a1) and marker genes of GABAergic neurons (Gad1, Gad2, and Slc6a1). Immunostaining with antibodies against relevant proteins (GAD67, GAD65, and GABA) also confirmed transcriptomic results. Furthermore, tdTomato-positive cells in retinas selectively expressed Tpbg, a marker gene for distinct clusters molecularly defined, which was proved with TPBG immunoreactivity in fluorescently labeled cells. Finally, tdTomato-positive cells recorded showed ON-OFF responses to light stimulation. Conclusions Ectopic expression occurs in the retina but not in the substantia nigra pars compacta in the DAT-tdTomato mouse, and fluorescently labeled cells in the retina are TPBG-expressing GABAergic ACs. This type of transgenic mice has been proved as an ideal tool to achieve efficient labeling of a distinct subset of ACs that selectively express Tpbg.
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Affiliation(s)
- Wanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qiang Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Feng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jing Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lei Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 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, China
| | - Ruifeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Kangjian Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yalan Bi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Xialin Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 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, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, China
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41
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Kabbara A, Robert G, Khalil M, Verin M, Benquet P, Hassan M. An electroencephalography connectome predictive model of major depressive disorder severity. Sci Rep 2022; 12:6816. [PMID: 35473962 PMCID: PMC9042869 DOI: 10.1038/s41598-022-10949-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 04/05/2022] [Indexed: 11/21/2022] Open
Abstract
Emerging evidence showed that major depressive disorder (MDD) is associated with disruptions of brain structural and functional networks, rather than impairment of isolated brain region. Thus, connectome-based models capable of predicting the depression severity at the individual level can be clinically useful. Here, we applied a machine-learning approach to predict the severity of depression using resting-state networks derived from source-reconstructed Electroencephalography (EEG) signals. Using regression models and three independent EEG datasets (N = 328), we tested whether resting state functional connectivity could predict individual depression score. On the first dataset, results showed that individuals scores could be reasonably predicted (r = 0.6, p = 4 × 10-18) using intrinsic functional connectivity in the EEG alpha band (8-13 Hz). In particular, the brain regions which contributed the most to the predictive network belong to the default mode network. We further tested the predictive potential of the established model by conducting two external validations on (N1 = 53, N2 = 154). Results showed statistically significant correlations between the predicted and the measured depression scale scores (r1 = 0.52, r2 = 0.44, p < 0.001). These findings lay the foundation for developing a generalizable and scientifically interpretable EEG network-based markers that can ultimately support clinicians in a biologically-based characterization of MDD.
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Affiliation(s)
- Aya Kabbara
- Lebanese Association for Scientific Research, Tripoli, Lebanon
- MINDig, F-35000, Rennes, France
| | - Gabriel Robert
- Academic Department of Psychiatry, Centre Hospitalier Guillaume Régnier, Rennes, France
- Empenn, U1228, IRISA, UMR 6074, Rennes, France
- Comportement et Noyaux Gris Centraux, EA 4712, CHU Rennes, Université de Rennes 1, 35000, Rennes, France
| | - Mohamad Khalil
- Azm Center for Research in Biotechnology and Its Applications, EDST, Tripoli, Lebanon
- CRSI Research Center, Faculty of Engineering, Lebanese University, Beirut, Lebanon
| | - Marc Verin
- Comportement et Noyaux Gris Centraux, EA 4712, CHU Rennes, Université de Rennes 1, 35000, Rennes, France
- Univ Rennes, Inserm, LTSI-U1099, F-35000, Rennes, France
| | - Pascal Benquet
- Univ Rennes, Inserm, LTSI-U1099, F-35000, Rennes, France
| | - Mahmoud Hassan
- MINDig, F-35000, Rennes, France.
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
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Muhtaseb AW, Duan J. Modeling common and rare genetic risk factors of neuropsychiatric disorders in human induced pluripotent stem cells. Schizophr Res 2022:S0920-9964(22)00156-6. [PMID: 35459617 PMCID: PMC9735430 DOI: 10.1016/j.schres.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Recent genome-wide association studies (GWAS) and whole-exome sequencing of neuropsychiatric disorders, especially schizophrenia, have identified a plethora of common and rare disease risk variants/genes. Translating the mounting human genetic discoveries into novel disease biology and more tailored clinical treatments is tied to our ability to causally connect genetic risk variants to molecular and cellular phenotypes. When combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) nuclease-mediated genome editing system, human induced pluripotent stem cell (hiPSC)-derived neural cultures (both 2D and 3D organoids) provide a promising tractable cellular model for bridging the gap between genetic findings and disease biology. In this review, we first conceptualize the advances in understanding the disease polygenicity and convergence from the past decade of iPSC modeling of different types of genetic risk factors of neuropsychiatric disorders. We then discuss the major cell types and cellular phenotypes that are most relevant to neuropsychiatric disorders in iPSC modeling. Finally, we critically review the limitations of iPSC modeling of neuropsychiatric disorders and outline the need for implementing and developing novel methods to scale up the number of iPSC lines and disease risk variants in a systematic manner. Sufficiently scaled-up iPSC modeling and a better functional interpretation of genetic risk variants, in combination with cutting-edge CRISPR/Cas9 gene editing and single-cell multi-omics methods, will enable the field to identify the specific and convergent molecular and cellular phenotypes in precision for neuropsychiatric disorders.
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Affiliation(s)
- Abdurrahman W Muhtaseb
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, United States of America
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, United States of America.
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Aceto G, Nardella L, Nanni S, Pecci V, Bertozzi A, Colussi C, D'Ascenzo M, Grassi C. Activation of histamine type 2 receptors enhances intrinsic excitability of medium spiny neurons in the nucleus accumbens. J Physiol 2022; 600:2225-2243. [PMID: 35343587 PMCID: PMC9325548 DOI: 10.1113/jp282962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract Histaminergic neurons are exclusively located in the hypothalamic tuberomammillary nucleus, from where they project to many brain areas including the nucleus accumbens (NAc), a brain area that integrates diverse monoaminergic inputs to coordinate motivated behaviours. While the NAc expresses various histamine receptor subtypes, the mechanisms by which histamine modulates NAc activity are still poorly understood. Using whole‐cell patch‐clamp recordings, we found that pharmacological activation of histamine 2 (H2) receptors elevates the excitability of NAc medium spiny neurons (MSNs), while activation of H1 receptors failed to significantly affect MSN excitability. The evoked firing of MSNs increased after seconds of local H2 agonist administration and remained elevated for minutes. H2 receptor (H2R) activation accelerated subthreshold depolarization in response to current injection, reduced the latency to fire, diminished action potential afterhyperpolarization and increased the action potential half‐width. The increased excitability was protein kinase A‐dependent and associated with decreased A‐type K+ currents. In addition, selective pharmacological inhibition of the Kv4.2 channel, the main molecular determinant of A‐type K+ currents in MSNs, mimicked and occluded the increased excitability induced by H2R activation. Our results indicate that histaminergic transmission in the NAc increases MSN intrinsic excitability through H2R‐dependent modulation of Kv4.2 channels. Activation of H2R will significantly alter spike firing in MSNs in vivo, and this effect could be an important mechanism by which these receptors mediate certain aspects of goal‐induced behaviours. Key points Histamine is synthesized and released by hypothalamic neurons of the tuberomammillary nucleus and serves as a general modulator for whole‐brain activity including the nucleus accumbens. Histamine receptors type 2 (HR2), which are expressed in the nucleus accumbens, couple to Gαs/off proteins which elevate cyclic adenosine monophosphate levels and activate protein kinase A. Whole‐cell patch‐clamp recordings revealed that H2R activation increased the evoked firing in medium spiny neurons of the nucleus accumbens via protein kinase A‐dependent mechanisms. HR2 activation accelerated subthreshold depolarization in response to current injection, reduced the latency to fire, diminished action potential medium after‐hyperpolarization and increased the action potential half‐width. HR2 activation also reduced A‐type potassium current. Selective pharmacological inhibition of the Kv4.2 channel mimicked and occluded the increased excitability induced by H2R activation.
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Affiliation(s)
- Giuseppe Aceto
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italia.,Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luca Nardella
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Simona Nanni
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italia.,Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Valeria Pecci
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessia Bertozzi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, Rome, Italy
| | - Claudia Colussi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, Rome, Italy
| | - Marcello D'Ascenzo
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italia.,Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Claudio Grassi
- Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, Roma, Italia.,Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
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44
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Degro CE, Bolduan F, Vida I, Booker SA. Interneuron diversity in the rat dentate gyrus: An unbiased in vitro classification. Hippocampus 2022; 32:310-331. [PMID: 35171512 PMCID: PMC9306941 DOI: 10.1002/hipo.23408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/08/2022]
Abstract
Information processing in cortical circuits, including the hippocampus, relies on the dynamic control of neuronal activity by GABAergic interneurons (INs). INs form a heterogenous population with defined types displaying distinct morphological, molecular, and physiological characteristics. In the major input region of the hippocampus, the dentate gyrus (DG), a number of IN types have been described which provide synaptic inhibition to distinct compartments of excitatory principal cells (PrCs) and other INs. In this study, we perform an unbiased classification of GABAergic INs in the DG by combining in vitro whole-cell patch-clamp recordings, intracellular labeling, morphological analysis, and supervised cluster analysis to better define IN type diversity in this region. This analysis reveals that DG INs divide into at least 13 distinct morpho-physiological types which reflect the complexity of the local IN network and serve as a basis for further network analyses.
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Affiliation(s)
- Claudius E Degro
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Felix Bolduan
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Imre Vida
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Sam A Booker
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
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45
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Luhmann HJ. Neurophysiology of the Developing Cerebral Cortex: What We Have Learned and What We Need to Know. Front Cell Neurosci 2022; 15:814012. [PMID: 35046777 PMCID: PMC8761895 DOI: 10.3389/fncel.2021.814012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/09/2021] [Indexed: 11/15/2022] Open
Abstract
This review article aims to give a brief summary on the novel technologies, the challenges, our current understanding, and the open questions in the field of the neurophysiology of the developing cerebral cortex in rodents. In the past, in vitro electrophysiological and calcium imaging studies on single neurons provided important insights into the function of cellular and subcellular mechanism during early postnatal development. In the past decade, neuronal activity in large cortical networks was recorded in pre- and neonatal rodents in vivo by the use of novel high-density multi-electrode arrays and genetically encoded calcium indicators. These studies demonstrated a surprisingly rich repertoire of spontaneous cortical and subcortical activity patterns, which are currently not completely understood in their functional roles in early development and their impact on cortical maturation. Technological progress in targeted genetic manipulations, optogenetics, and chemogenetics now allow the experimental manipulation of specific neuronal cell types to elucidate the function of early (transient) cortical circuits and their role in the generation of spontaneous and sensory evoked cortical activity patterns. Large-scale interactions between different cortical areas and subcortical regions, characterization of developmental shifts from synchronized to desynchronized activity patterns, identification of transient circuits and hub neurons, role of electrical activity in the control of glial cell differentiation and function are future key tasks to gain further insights into the neurophysiology of the developing cerebral cortex.
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Affiliation(s)
- Heiko J. Luhmann
- Institute of Physiology, University Medical Center Mainz, Mainz, Germany
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46
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Osorio D. Interpretable multi-modal data integration. NATURE COMPUTATIONAL SCIENCE 2022; 2:8-9. [PMID: 38177710 DOI: 10.1038/s43588-021-00186-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
- Daniel Osorio
- Norwegian Centre for Molecular Medicine, University of Oslo, Oslo, Norway.
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47
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A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data. NATURE COMPUTATIONAL SCIENCE 2022; 2:38-46. [PMID: 35480297 DOI: 10.1038/s43588-021-00185-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phenotypes of complex biological systems are fundamentally driven by various multi-scale mechanisms. Multi-modal data, such as single cell multi-omics data, enables a deeper understanding of underlying complex mechanisms across scales for phenotypes. We developed an interpretable regularized learning model, deepManReg, to predict phenotypes from multi-modal data. First, deepManReg employs deep neural networks to learn cross-modal manifolds and then to align multi-modal features onto a common latent space. Second, deepManReg uses cross-modal manifolds as a feature graph to regularize the classifiers for improving phenotype predictions and also for prioritizing the multi-modal features and cross-modal interactions for the phenotypes. We applied deepManReg to (1) an image dataset of handwritten digits with multi-features and (2) single cell multi-modal data (Patch-seq data) including transcriptomics and electrophysiology for neuronal cells in the mouse brain. We show that deepManReg improved phenotype prediction in both datasets, and also prioritized genes and electrophysiological features for the phenotypes of neuronal cells.
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48
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Nano PR, Nguyen CV, Mil J, Bhaduri A. Cortical Cartography: Mapping Arealization Using Single-Cell Omics Technology. Front Neural Circuits 2021; 15:788560. [PMID: 34955761 PMCID: PMC8707733 DOI: 10.3389/fncir.2021.788560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
The cerebral cortex derives its cognitive power from a modular network of specialized areas processing a multitude of information. The assembly and organization of these regions is vital for human behavior and perception, as evidenced by the prevalence of area-specific phenotypes that manifest in neurodevelopmental and psychiatric disorders. Generations of scientists have examined the architecture of the human cortex, but efforts to capture the gene networks which drive arealization have been hampered by the lack of tractable models of human neurodevelopment. Advancements in "omics" technologies, imaging, and computational power have enabled exciting breakthroughs into the molecular and structural characteristics of cortical areas, including transcriptomic, epigenomic, metabolomic, and proteomic profiles of mammalian models. Here we review the single-omics atlases that have shaped our current understanding of cortical areas, and their potential to fuel a new era of multi-omic single-cell endeavors to interrogate both the developing and adult human cortex.
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Affiliation(s)
| | | | | | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
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49
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Scala F, Kobak D, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Hartmanis L, Jiang X, Laturnus S, Miranda E, Mulherkar S, Tan ZH, Yao Z, Zeng H, Sandberg R, Berens P, Tolias AS. Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature 2021; 598:144-150. [PMID: 33184512 PMCID: PMC8113357 DOI: 10.1038/s41586-020-2907-3] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]
Abstract
Cortical neurons exhibit extreme diversity in gene expression as well as in morphological and electrophysiological properties1,2. Most existing neural taxonomies are based on either transcriptomic3,4 or morpho-electric5,6 criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells7. Here we used Patch-seq8 to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of more than 1,300 neurons in adult mouse primary motor cortex, providing a morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (those expressing Vip, Pvalb, Sst and so on) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neuronal types in the neocortex do not always form discrete entities. Instead, neurons form a hierarchy that consists of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
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Affiliation(s)
- Federico Scala
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Matteo Bernabucci
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Yves Bernaerts
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- International Max Planck Research School for Intelligent Systems, Tübingen, Germany
| | - Cathryn René Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Jesus Ramon Castro
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolong Jiang
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA
| | - Sophie Laturnus
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Elanine Miranda
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shalaka Mulherkar
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Zheng Huan Tan
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Philipp Berens
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
- Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
- Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany.
| | - Andreas S Tolias
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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50
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A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 DOI: 10.1101/2020.10.19.343129v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 05/26/2023]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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