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Nehme R, Pietiläinen O, Barrett LE. Genomic, molecular, and cellular divergence of the human brain. Trends Neurosci 2024:S0166-2236(24)00089-4. [PMID: 38897852 DOI: 10.1016/j.tins.2024.05.009] [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: 02/29/2024] [Revised: 04/29/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
While many core biological processes are conserved across species, the human brain has evolved with unique capacities. Current understanding of the neurobiological mechanisms that endow human traits as well as associated vulnerabilities remains limited. However, emerging data have illuminated species divergence in DNA elements and genome organization, in molecular, morphological, and functional features of conserved neural cell types, as well as temporal differences in brain development. Here, we summarize recent data on unique features of the human brain and their complex implications for the study and treatment of brain diseases. We also consider key outstanding questions in the field and discuss the technologies and foundational knowledge that will be required to accelerate understanding of human neurobiology.
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Affiliation(s)
- Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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Moakley DF, Campbell M, Anglada-Girotto M, Feng H, Califano A, Au E, Zhang C. Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.597128. [PMID: 38915499 PMCID: PMC11195221 DOI: 10.1101/2024.06.13.597128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes. This approach reliably inferred the regulons of 350 RBPs and their cell type-specific activities. Our analysis revealed driving factors delineating neuronal identities, among which we validated Elavl2 as a key RBP for MGE-specific splicing in GABAergic interneurons using an in vitro ESC differentiation system. We also identified a module of exons and candidate regulators specific for long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing regulatory programs that drive neuronal molecular diversity, including those that do not align with gene expression-based classifications.
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Affiliation(s)
- Daniel F Moakley
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Melissa Campbell
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Neurosciences, University of California, San Diego, USA
| | - Miquel Anglada-Girotto
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Present address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Huijuan Feng
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
- Columbia Translational Neuroscience Initiative Scholar, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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Choi YK, Feng L, Jeong WK, Kim J. Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity. Brain Inform 2024; 11:15. [PMID: 38833195 DOI: 10.1186/s40708-024-00228-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging and diseases. Developments in imaging technology, such as microscopy and labeling tools, have allowed researchers to visualize this connectivity through high-resolution brain-wide imaging. With this, image processing and analysis have become more crucial. However, despite the wealth of neural images generated, access to an integrated image processing and analysis pipeline to process these data is challenging due to scattered information on available tools and methods. To map the neural connections, registration to atlases and feature extraction through segmentation and signal detection are necessary. In this review, our goal is to provide an updated overview of recent advances in these image-processing methods, with a particular focus on fluorescent images of the mouse brain. Our goal is to outline a pathway toward an integrated image-processing pipeline tailored for connecto-informatics. An integrated workflow of these image processing will facilitate researchers' approach to mapping brain connectivity to better understand complex brain networks and their underlying brain functions. By highlighting the image-processing tools available for fluroscent imaging of the mouse brain, this review will contribute to a deeper grasp of connecto-informatics, paving the way for better comprehension of brain connectivity and its implications.
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Affiliation(s)
- Yoon Kyoung Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | | | - Won-Ki Jeong
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea.
- KIST-SKKU Brain Research Center, SKKU Institute for Convergence, Sungkyunkwan University, Suwon, South Korea.
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Shamir I, Assaf Y, Shamir R. Clustering the cortical laminae: in vivo parcellation. Brain Struct Funct 2024; 229:443-458. [PMID: 38193916 PMCID: PMC10917860 DOI: 10.1007/s00429-023-02748-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
The laminar microstructure of the cerebral cortex has distinct anatomical characteristics of the development, function, connectivity, and even various pathologies of the brain. In recent years, multiple neuroimaging studies have utilized magnetic resonance imaging (MRI) relaxometry to visualize and explore this intricate microstructure, successfully delineating the cortical laminar components. Despite this progress, T1 is still primarily considered a direct measure of myeloarchitecture (myelin content), rather than a probe of tissue cytoarchitecture (cellular composition). This study aims to offer a robust, whole-brain validation of T1 imaging as a practical and effective tool for exploring the laminar composition of the cortex. To do so, we cluster complex microstructural cortical datasets of both human (N = 30) and macaque (N = 1) brains using an adaptation of an algorithm for clustering cell omics profiles. The resulting cluster patterns are then compared to established atlases of cytoarchitectonic features, exhibiting significant correspondence in both species. Lastly, we demonstrate the expanded applicability of T1 imaging by exploring some of the cytoarchitectonic features behind various unique skillsets, such as musicality and athleticism.
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Affiliation(s)
- Ittai Shamir
- Department of Neurobiology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Yaniv Assaf
- Department of Neurobiology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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Peng H, Xie P, Xiong F. Meet the authors: Hanchuan Peng, Peng Xie, and Feng Xiong. PATTERNS (NEW YORK, N.Y.) 2024; 5:100912. [PMID: 38264723 PMCID: PMC10801219 DOI: 10.1016/j.patter.2023.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
In a recent paper at Patterns, Hanchuan Peng, Peng Xie, and Feng Xiong from Southeast University describe a deep learning method to characterize complete single-neuron morphologies, which can discover neuron projection patterns of diverse cells and learn neuronal morphology representation. In this interview, the authors shared the story behind the paper and their research experience. This interview is a companion to these authors' recent paper, "DSM: Deep sequential model for complete neuronal morphology representation and feature extraction."1.
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Affiliation(s)
- Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu 210096, China
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu 210096, China
| | - Feng Xiong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu 210096, China
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