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Doe CQ, Thor S. 40 years of homeodomain transcription factors in the Drosophila nervous system. Development 2024; 151:dev202910. [PMID: 38819456 PMCID: PMC11190446 DOI: 10.1242/dev.202910] [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] [Indexed: 06/01/2024]
Abstract
Drosophila nervous system development progresses through a series of well-characterized steps in which homeodomain transcription factors (HDTFs) play key roles during most, if not all, phases. Strikingly, although some HDTFs have only one role, many others are involved in multiple steps of the developmental process. Most Drosophila HDTFs engaged in nervous system development are conserved in vertebrates and often play similar roles during vertebrate development. In this Spotlight, we focus on the role of HDTFs during embryogenesis, where they were first characterized.
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Affiliation(s)
- Chris Q. Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, Eugene, OR 97403, USA
| | - Stefan Thor
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
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Smith JJ, Taylor SR, Blum JA, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552048. [PMID: 37577463 PMCID: PMC10418256 DOI: 10.1101/2023.08.04.552048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Motor neurons (MNs) constitute an ancient cell type targeted by multiple adult-onset diseases. It is therefore important to define the molecular makeup of adult MNs in animal models and extract organizing principles. Here, we generated a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database (http://celegans.spinalcordatlas.org). Single-cell RNA-sequencing of 13,200 cells revealed that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. All subclasses are delineated by unique expression codes of either neuropeptide or transcription factor gene families. Strikingly, we found that combinatorial codes of homeodomain transcription factor genes define adult MN diversity both in C. elegans and mice. Further, molecularly defined MN subclasses in C. elegans display distinct patterns of connectivity. Hence, our study couples the connectivity map of the C. elegans motor circuit with a molecular atlas of its constituent MNs, and uncovers organizing principles and conserved molecular codes of adult MN diversity.
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Affiliation(s)
- Jayson J. Smith
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA
- University of Chicago Neuroscience Institute, Chicago, IL, 60637, USA
| | - Seth R. Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, 84602, USA
| | - Jacob A. Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M. Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
- Program in Neuroscience, Vanderbilt University, Nashville, TN, 37240, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, 60637, USA
- University of Chicago Neuroscience Institute, Chicago, IL, 60637, USA
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Fedoseyeva VB, Novosadova EV, Nenasheva VV, Novosadova LV, Grivennikov IA, Tarantul VZ. Transcription of HOX Genes Is Significantly Increased during Neuronal Differentiation of iPSCs Derived from Patients with Parkinson's Disease. J Dev Biol 2023; 11:23. [PMID: 37367477 DOI: 10.3390/jdb11020023] [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: 04/10/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Parkinson's disease (PD) is the most serious movement disorder, but the actual cause of this disease is still unknown. Induced pluripotent stem cell-derived neural cultures from PD patients carry the potential for experimental modeling of underlying molecular events. We analyzed the RNA-seq data of iPSC-derived neural precursor cells (NPCs) and terminally differentiated neurons (TDNs) from healthy donors (HD) and PD patients with mutations in PARK2 published previously. The high level of transcription of HOX family protein-coding genes and lncRNA transcribed from the HOX clusters was revealed in the neural cultures from PD patients, while in HD NPCs and TDNs, the majority of these genes were not expressed or slightly transcribed. The results of this analysis were generally confirmed by qPCR. The HOX paralogs in the 3' clusters were activated more strongly than the genes of the 5' cluster. The abnormal activation of the HOX gene program upon neuronal differentiation in the cells of PD patients raises the possibility that the abnormal expression of these key regulators of neuronal development impacts PD pathology. Further research is needed to investigate this hypothesis.
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Affiliation(s)
- Viya B Fedoseyeva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Ekaterina V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Lyudmila V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Igor A Grivennikov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Vyacheslav Z Tarantul
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
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Elder N, Fattahi F, McDevitt TC, Zholudeva LV. Diseased, differentiated and difficult: Strategies for improved engineering of in vitro neurological systems. Front Cell Neurosci 2022; 16:962103. [PMID: 36238834 PMCID: PMC9550918 DOI: 10.3389/fncel.2022.962103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/22/2022] [Indexed: 12/01/2022] Open
Abstract
The rapidly growing field of cellular engineering is enabling scientists to more effectively create in vitro models of disease and develop specific cell types that can be used to repair damaged tissue. In particular, the engineering of neurons and other components of the nervous system is at the forefront of this field. The methods used to engineer neural cells can be largely divided into systems that undergo directed differentiation through exogenous stimulation (i.e., via small molecules, arguably following developmental pathways) and those that undergo induced differentiation via protein overexpression (i.e., genetically induced and activated; arguably bypassing developmental pathways). Here, we highlight the differences between directed differentiation and induced differentiation strategies, how they can complement one another to generate specific cell phenotypes, and impacts of each strategy on downstream applications. Continued research in this nascent field will lead to the development of improved models of neurological circuits and novel treatments for those living with neurological injury and disease.
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Affiliation(s)
- Nicholas Elder
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Institutes, San Francisco, CA, United States
| | - Faranak Fattahi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Todd C. McDevitt
- Gladstone Institutes, San Francisco, CA, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
- Sana Biotechnology, Inc., South San Francisco, CA, United States
| | - Lyandysha V. Zholudeva
- Gladstone Institutes, San Francisco, CA, United States
- *Correspondence: Lyandysha V. Zholudeva,
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