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1
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Lau F, Binacchi R, Brugnara S, Cumplido-Mayoral A, Savino SD, Khan I, Orso A, Sartori S, Bellosta P, Carl M, Poggi L, Provenzano G. Using Single-Cell RNA sequencing with Drosophila, Zebrafish, and mouse models for studying Alzheimer's and Parkinson's disease. Neuroscience 2025; 573:505-517. [PMID: 40154937 DOI: 10.1016/j.neuroscience.2025.03.042] [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: 02/19/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025]
Abstract
Alzheimer's and Parkinson's disease are the most common neurodegenerative diseases, significantly affecting the elderly with no current cure available. With the rapidly aging global population, advancing research on these diseases becomes increasingly critical. Both disorders are often studied using model organisms, which enable researchers to investigate disease phenotypes and their underlying molecular mechanisms. In this review, we critically discuss the strengths and limitations of using Drosophila, zebrafish, and mice as models for Alzheimer's and Parkinson's research. A focus is the application of single-cell RNA sequencing, which has revolutionized the field by providing novel insights into the cellular and transcriptomic landscapes characterizing these diseases. We assess how combining animal disease modeling with high-throughput sequencing and computational approaches has advanced the field of Alzheimer's and Parkinson's disease research. Thereby, we highlight the importance of integrative multidisciplinary approaches to further our understanding of disease mechanisms and thus accelerating the development of successful therapeutic interventions.
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Affiliation(s)
- Frederik Lau
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Rebecca Binacchi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Samuele Brugnara
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Alba Cumplido-Mayoral
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Serena Di Savino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Ihsanullah Khan
- Department of Civil, Environmental and Mechanical Engineering, University of Trento 38123 Trento, Italy
| | - Angela Orso
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Samuele Sartori
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy; Department of Medicine NYU Grossman School of Medicine, 550 First Avenue, 10016 NY, USA.
| | - Matthias Carl
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy.
| | - Lucia Poggi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy.
| | - Giovanni Provenzano
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento 38123 Trento, Italy.
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2
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Adameyko I, Bakken T, Bhaduri A, Chhatbar C, Filbin MG, Gate D, Hochgerner H, Kim CN, Krull J, La Manno G, Li Q, Linnarsson S, Ma Q, Mayer C, Menon V, Nano P, Prinz M, Quake S, Walsh CA, Yang J, Bayraktar OA, Gokce O, Habib N, Konopka G, Liddelow SA, Nowakowski TJ. Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system. Nat Neurosci 2024; 27:2278-2291. [PMID: 39627588 PMCID: PMC11949301 DOI: 10.1038/s41593-024-01827-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 10/22/2024] [Indexed: 12/13/2024]
Abstract
Single-cell and single-nucleus genomic approaches can provide unbiased and multimodal insights. Here, we discuss what constitutes a molecular cell atlas and how to leverage single-cell omics data to generate hypotheses and gain insights into cell transitions in development and disease of the nervous system. We share points of reflection on what to consider during study design and implementation as well as limitations and pitfalls.
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Affiliation(s)
- Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | | | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chintan Chhatbar
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA, USA
| | - David Gate
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hannah Hochgerner
- Faculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel
| | - Chang Nam Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jordan Krull
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, the James Comprehensive Cancer Center, the Ohio State University, Columbus, OH, USA
| | - Gioele La Manno
- Laboratory of Neurodevelopmental Systems Biology, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Qingyun Li
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, the James Comprehensive Cancer Center, the Ohio State University, Columbus, OH, USA
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
| | - Vilas Menon
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA
| | - Patricia Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Steve Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Jin Yang
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | - Ozgun Gokce
- Department of Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn, Bonn, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Naomi Habib
- The Edmond and Lily Safra Center for Brain Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA.
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
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4
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Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci 2024; 27:2292-2309. [PMID: 39627587 PMCID: PMC11999325 DOI: 10.1038/s41593-024-01806-0] [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: 11/22/2023] [Accepted: 09/23/2024] [Indexed: 12/13/2024]
Abstract
Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells. Here, we summarize the most promising and robust technologies in these areas, discuss their strengths and limitations and discuss key computational approaches for analysis of these complex datasets. We highlight how data sharing and integration, documentation, visualization and benchmarking of results contribute to transparency, reproducibility, collaboration and democratization in neuroscience, and discuss needs and opportunities for future technology development and analysis.
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Affiliation(s)
- Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fei Chen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Myriam Heiman
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
| | - Kenneth Harris
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Manolis Kellis
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ariel Levine
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Mo Lotfollahi
- Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vijay Ramani
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, San Francisco, CA, USA
| | - Rahul Satijia
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Lucas Schirmer
- Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yin Shen
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Na Sun
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gilad S Green
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Fabian Theis
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiao Wang
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ozgun Gokce
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Shane Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA.
| | - Evan Macosko
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
| | | | - Naomi Habib
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tomasz J Nowakowski
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
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