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Gauberg J, Moreno KB, Jayaraman K, Abumeri S, Jenkins S, Salazar AM, Meharena HS, Glasgow SM. Spinal motor neuron development and metabolism are transcriptionally regulated by Nuclear Factor IA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600888. [PMID: 38979382 PMCID: PMC11230388 DOI: 10.1101/2024.06.26.600888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Neural circuits governing all motor behaviors in vertebrates rely on the proper development of motor neurons and their precise targeting of limb muscles. Transcription factors are essential for motor neuron development, regulating their specification, migration, and axonal targeting. While transcriptional regulation of the early stages of motor neuron specification is well-established, much less is known about the role of transcription factors in the later stages of maturation and terminal arborization. Defining the molecular mechanisms of these later stages is critical for elucidating how motor circuits are constructed. Here, we demonstrate that the transcription factor Nuclear Factor-IA (NFIA) is required for motor neuron positioning, axonal branching, and neuromuscular junction formation. Moreover, we find that NFIA is required for proper mitochondrial function and ATP production, providing a new and important link between transcription factors and metabolism during motor neuron development. Together, these findings underscore the critical role of NFIA in instructing the assembly of spinal circuits for movement.
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Kulakova MA, Maslakov GP, Poliushkevich LO. Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:987-1001. [PMID: 38981695 DOI: 10.1134/s0006297924060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 07/11/2024]
Abstract
The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.
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Affiliation(s)
- Milana A Kulakova
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | - Georgy P Maslakov
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Liudmila O Poliushkevich
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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Swindell WR. Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords. Front Genet 2024; 15:1385114. [PMID: 38689650 PMCID: PMC11059082 DOI: 10.3389/fgene.2024.1385114] [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: 02/11/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction ALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs). Methods This study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified. Results The analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < -0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037). Conclusion This study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.
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Affiliation(s)
- William R. Swindell
- Department of Internal Medicine, Division of Hospital Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
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5
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Wellik DM. Hox genes and patterning the vertebrate body. Curr Top Dev Biol 2024; 159:1-27. [PMID: 38729674 DOI: 10.1016/bs.ctdb.2024.02.011] [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: 05/12/2024]
Abstract
The diversity of vertebrate body plans is dizzying, yet stunning for the many things they have in common. Vertebrates have inhabited virtually every part of the earth from its coldest to warmest climates. They locomote by swimming, flying, walking, slithering, or climbing, or combinations of these behaviors. And they exist in many different sizes, from the smallest of frogs, fish and lizards to giraffes, elephants, and blue whales. Despite these differences, vertebrates follow a remarkably similar blueprint for the establishment of their body plan. Within the relatively small amount of time required to complete gastrulation, the process through which the three germ layers, ectoderm, mesoderm, and endoderm are created, the embryo also generates its body axis and is simultaneously patterned. For the length of this axis, the genes that distinguish the neck from the rib cage or the trunk from the sacrum are the Hox genes. In vertebrates, there was evolutionary pressure to maintain this set of genes in the organism. Over the past decades, much has been learned regarding the regulatory mechanisms that ensure the appropriate expression of these genes along the main body axes. Genetic functions continue to be explored though much has been learned. Much less has been discerned on the identity of co-factors used by Hox proteins for the specificity of transcriptional regulation or what downstream targets and pathways are critical for patterning events, though there are notable exceptions. Current work in the field is demonstrating that Hox genes continue to function in many organs long after directing early patterning events. It is hopeful continued research will shed light on remaining questions regarding mechanisms used by this important and conserved set of transcriptional regulators.
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Affiliation(s)
- Deneen M Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States.
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6
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Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024; 43:113857. [PMID: 38421866 PMCID: PMC11091551 DOI: 10.1016/j.celrep.2024.113857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
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 generate a comprehensive molecular atlas of adult Caenorhabditis elegans MNs and a searchable database. Single-cell RNA sequencing of 13,200 cells reveals that ventral nerve cord MNs cluster into 29 molecularly distinct subclasses. Extending C. elegans Neuronal Gene Expression Map and Network (CeNGEN) findings, all MN subclasses are delineated by distinct expression codes of either neuropeptide or transcription factor gene families. Strikingly, combinatorial codes of homeodomain transcription factor genes succinctly delineate adult MN diversity in both 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
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; University of Chicago Neuroscience Institute, Chicago, IL 60637, USA
| | - Rebecca Collings
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, 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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7
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Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol 2024; 154:35-47. [PMID: 37438210 PMCID: PMC10592372 DOI: 10.1016/j.semcdb.2023.07.001] [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: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Neurons are remarkably long-lived, non-dividing cells that must maintain their functional features (e.g., electrical properties, chemical signaling) for extended periods of time - decades in humans. How neurons accomplish this incredible feat is poorly understood. Here, we review recent advances, primarily in the nematode C. elegans, that have enhanced our understanding of the molecular mechanisms that enable post-mitotic neurons to maintain their functionality across different life stages. We begin with "terminal selectors" - transcription factors necessary for the establishment and maintenance of neuronal identity. We highlight new findings on five terminal selectors (CHE-1 [Glass], UNC-3 [Collier/Ebf1-4], LIN-39 [Scr/Dfd/Hox4-5], UNC-86 [Acj6/Brn3a-c], AST-1 [Etv1/ER81]) from different transcription factor families (ZNF, COE, HOX, POU, ETS). We compare the functions of these factors in specific neuron types of C. elegans with the actions of their orthologs in other invertebrate (D. melanogaster) and vertebrate (M. musculus) systems, highlighting remarkable functional conservation. Finally, we reflect on recent findings implicating chromatin-modifying proteins, such as histone methyltransferases and Polycomb proteins, in the control of neuronal terminal identity. Altogether, these new studies on transcription factors and chromatin modifiers not only shed light on the fundamental problem of neuronal identity maintenance, but also outline mechanistic principles of gene regulation that may operate in other long-lived, post-mitotic cell types.
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Affiliation(s)
- Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Manasa Prahlad
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA.
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8
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Ritesh KC, de Boer RL, Lin M, Jeannotte L, Philippidou P. Multimodal Hox5 activity generates motor neuron diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579338. [PMID: 38370781 PMCID: PMC10871347 DOI: 10.1101/2024.02.08.579338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 controls chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.
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Affiliation(s)
- K C Ritesh
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raquel López de Boer
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Minshan Lin
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Centre Recherche sur le Cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology), Québec, Canada
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
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Bothe MS, Kohl T, Felmy F, Gallant J, Chagnaud BP. Timing and precision of rattlesnake spinal motoneurons are determined by the KV7 2/3 potassium channel. Curr Biol 2024; 34:286-297.e5. [PMID: 38157862 DOI: 10.1016/j.cub.2023.11.062] [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: 07/19/2023] [Revised: 10/11/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
The evolution of novel motor behaviors requires modifications in the central pattern generators (CPGs) controlling muscle activity. How such changes gradually lead to novel behaviors remains enigmatic due to the long time course of evolution. Rattlesnakes provide a unique opportunity to investigate how a locomotor CPG was evolutionarily modified to generate a novel behavior-in this case, acoustic signaling. We show that motoneurons (MNs) in the body and tail spinal cord of rattlesnakes possess fundamentally different physiological characteristics, which allow MNs in the tail to integrate and transmit CPG output for controlling superfast muscles with high temporal precision. Using patch-clamp electrophysiology, we demonstrate that these differences in locomotor and rattle MNs are mainly determined by KV72/3 potassium channels. However, although KV72/3 exerted a significantly different influence on locomotor and rattle MN physiology, single-cell RNA-seq unexpectedly did not reveal any differences in KV72/3 channels' expression. VIDEO ABSTRACT.
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Affiliation(s)
| | - Tobias Kohl
- TUM School of Life Science, Technical University of Munich, 85354 Munich, Germany
| | - Felix Felmy
- Institute of Zoology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Jason Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Boris P Chagnaud
- Institute of Biology, University of Graz, 8010 Graz, Austria; Department of Biology II, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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10
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Roman A, Huntemer-Silveira A, Waldron MA, Khalid Z, Blake J, Parr AM, Low WC. Cell Transplantation for Repair of the Spinal Cord and Prospects for Generating Region-Specific Exogenic Neuronal Cells. Cell Transplant 2024; 33:9636897241241998. [PMID: 38590295 PMCID: PMC11005494 DOI: 10.1177/09636897241241998] [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: 09/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Spinal cord injury (SCI) is associated with currently irreversible consequences in several functional components of the central nervous system. Despite the severity of injury, there remains no approved treatment to restore function. However, with a growing number of preclinical studies and clinical trials, cell transplantation has gained significant potential as a treatment for SCI. Researchers have identified several cell types as potential candidates for transplantation. To optimize successful functional outcomes after transplantation, one key factor concerns generating neuronal cells with regional and subtype specificity, thus calling on the developmental transcriptome patterning of spinal cord cells. A potential source of spinal cord cells for transplantation is the generation of exogenic neuronal progenitor cells via the emerging technologies of gene editing and blastocyst complementation. This review highlights the use of cell transplantation to treat SCI in the context of relevant developmental gene expression patterns useful for producing regionally specific exogenic spinal cells via in vitro differentiation and blastocyst complementation.
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Affiliation(s)
- Alex Roman
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Anne Huntemer-Silveira
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Madison A. Waldron
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Zainab Khalid
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey Blake
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Ann M. Parr
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Walter C. Low
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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12
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Lee Y, Yeo IS, Kim N, Lee DK, Kim KT, Yoon J, Yi J, Hong YB, Choi BO, Kosodo Y, Kim D, Park J, Song MR. Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2. eLife 2023; 12:e84596. [PMID: 37869988 PMCID: PMC10637776 DOI: 10.7554/elife.84596] [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: 10/31/2022] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
The fidelity of motor control requires the precise positional arrangement of motor pools and the establishment of synaptic connections between them. During neural development in the spinal cord, motor nerves project to specific target muscles and receive proprioceptive input from these muscles via the sensorimotor circuit. LIM-homeodomain transcription factors are known to play a crucial role in successively restricting specific motor neuronal fates. However, their exact contribution to limb-based motor pools and locomotor circuits has not been fully understood. To address this, we conducted an investigation into the role of Isl2, a LIM-homeodomain transcription factor, in motor pool organization. We found that deletion of Isl2 led to the dispersion of motor pools, primarily affecting the median motor column (MMC) and lateral motor column (LMC) populations. Additionally, hindlimb motor pools lacked Etv4 expression, and we observed reduced terminal axon branching and disorganized neuromuscular junctions in Isl2-deficient mice. Furthermore, we performed transcriptomic analysis on the spinal cords of Isl2-deficient mice and identified a variety of downregulated genes associated with motor neuron (MN) differentiation, axon development, and synapse organization in hindlimb motor pools. As a consequence of these disruptions, sensorimotor connectivity and hindlimb locomotion were impaired in Isl2-deficient mice. Taken together, our findings highlight the critical role of Isl2 in organizing motor pool position and sensorimotor circuits in hindlimb motor pools. This research provides valuable insights into the molecular mechanisms governing motor control and its potential implications for understanding motor-related disorders in humans.
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Affiliation(s)
- Yunjeong Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - In Seo Yeo
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - Namhee Kim
- Fermentation Regulation Technology Research Group, World Institute of KimchiGwangjuRepublic of Korea
| | - Dong-Keun Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - Kyung-Tai Kim
- Jeonbuk Department of Inhalation Research, Korea Institute of ToxicologyJeongeup-siRepublic of Korea
| | - Jiyoung Yoon
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - Jawoon Yi
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - Young Bin Hong
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of MedicineSeoulRepublic of Korea
- Department of Biochemistry, College of Medicine, Dong-A UniversityBusanRepublic of Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of MedicineSeoulRepublic of Korea
| | - Yoichi Kosodo
- Korea Brain Research InstituteDaeguRepublic of Korea
| | - Daesoo Kim
- Department of Brain and Cognitive Sciences, Korea Advanced Institute of Science and Technology (KAIST)DaejeonRepublic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
| | - Mi-Ryoung Song
- School of Life Sciences, Gwangju Institute of Science and Technology, Oryong-dong, Buk-guGwangjuRepublic of Korea
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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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14
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Bohic M, Upadhyay A, Eisdorfer JT, Keating J, Simon RC, Briones BA, Azadegan C, Nacht HD, Oputa O, Martinez AM, Bethell BN, Gradwell MA, Romanienko P, Ramer MS, Stuber GD, Abraira VE. A new Hoxb8FlpO mouse line for intersectional approaches to dissect developmentally defined adult sensorimotor circuits. Front Mol Neurosci 2023; 16:1176823. [PMID: 37603775 PMCID: PMC10437123 DOI: 10.3389/fnmol.2023.1176823] [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: 02/28/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023] Open
Abstract
Improvements in the speed and cost of expression profiling of neuronal tissues offer an unprecedented opportunity to define ever finer subgroups of neurons for functional studies. In the spinal cord, single cell RNA sequencing studies support decades of work on spinal cord lineage studies, offering a unique opportunity to probe adult function based on developmental lineage. While Cre/Flp recombinase intersectional strategies remain a powerful tool to manipulate spinal neurons, the field lacks genetic tools and strategies to restrict manipulations to the adult mouse spinal cord at the speed at which new tools develop. This study establishes a new workflow for intersectional mouse-viral strategies to dissect adult spinal function based on developmental lineages in a modular fashion. To restrict manipulations to the spinal cord, we generate a brain-sparing Hoxb8FlpO mouse line restricting Flp recombinase expression to caudal tissue. Recapitulating endogenous Hoxb8 gene expression, Flp-dependent reporter expression is present in the caudal embryo starting day 9.5. This expression restricts Flp activity in the adult to the caudal brainstem and below. Hoxb8FlpO heterozygous and homozygous mice do not develop any of the sensory or locomotor phenotypes evident in Hoxb8 heterozygous or mutant animals, suggesting normal developmental function of the Hoxb8 gene and protein in Hoxb8FlpO mice. Compared to the variability of brain recombination in available caudal Cre and Flp lines, Hoxb8FlpO activity is not present in the brain above the caudal brainstem, independent of mouse genetic background. Lastly, we combine the Hoxb8FlpO mouse line with dorsal horn developmental lineage Cre mouse lines to express GFP in developmentally determined dorsal horn populations. Using GFP-dependent Cre recombinase viruses and Cre recombinase-dependent inhibitory chemogenetics, we target developmentally defined lineages in the adult. We show how developmental knock-out versus transient adult silencing of the same ROR𝛃 lineage neurons affects adult sensorimotor behavior. In summary, this new mouse line and viral approach provides a blueprint to dissect adult somatosensory circuit function using Cre/Flp genetic tools to target spinal cord interneurons based on genetic lineage.
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Affiliation(s)
- Manon Bohic
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Aman Upadhyay
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- Neuroscience PhD Program at Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States
| | - Jaclyn T. Eisdorfer
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Jessica Keating
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- School of Medicine, Oregon Health and Science University, Portland, OR, United States
- M.D./PhD Program in Neuroscience, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Rhiana C. Simon
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Brandy A. Briones
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Chloe Azadegan
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Hannah D. Nacht
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Olisemeka Oputa
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Alana M. Martinez
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Bridget N. Bethell
- International Collaboration on Repair Discoveries and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Gradwell
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
| | - Peter Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Matt S. Ramer
- International Collaboration on Repair Discoveries and Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Garret D. Stuber
- Center for the Neurobiology of Addiction, Pain, and Emotion, Department of Anesthesiology and Pain Medicine, Department of Pharmacology, University of Washington, Seattle, WA, United States
| | - Victoria E. Abraira
- Cell Biology and Neuroscience Department, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
- W.M. Keck Center for Collaborative Neuroscience, Rutgers University, The State University of New Jersey, Piscataway, NJ, United States
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15
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Vieira JR, Shah B, Dupraz S, Paredes I, Himmels P, Schermann G, Adler H, Motta A, Gärtner L, Navarro-Aragall A, Ioannou E, Dyukova E, Bonnavion R, Fischer A, Bonanomi D, Bradke F, Ruhrberg C, Ruiz de Almodóvar C. Endothelial PlexinD1 signaling instructs spinal cord vascularization and motor neuron development. Neuron 2022; 110:4074-4089.e6. [PMID: 36549270 PMCID: PMC9796814 DOI: 10.1016/j.neuron.2022.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/04/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022]
Abstract
How the vascular and neural compartment cooperate to achieve such a complex and highly specialized structure as the central nervous system is still unclear. Here, we reveal a crosstalk between motor neurons (MNs) and endothelial cells (ECs), necessary for the coordinated development of MNs. By analyzing cell-to-cell interaction profiles of the mouse developing spinal cord, we uncovered semaphorin 3C (Sema3C) and PlexinD1 as a communication axis between MNs and ECs. Using cell-specific knockout mice and in vitro assays, we demonstrate that removal of Sema3C in MNs, or its receptor PlexinD1 in ECs, results in premature and aberrant vascularization of MN columns. Those vascular defects impair MN axon exit from the spinal cord. Impaired PlexinD1 signaling in ECs also causes MN maturation defects at later stages. This study highlights the importance of a timely and spatially controlled communication between MNs and ECs for proper spinal cord development.
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Affiliation(s)
- José Ricardo Vieira
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany; Faculty of Biosciences, Heidelberg University, Im Neuenheimer 234, 69120 Heidelberg, Germany
| | - Bhavin Shah
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany
| | - Sebastian Dupraz
- Institute for Neurovascular Cell Biology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Isidora Paredes
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany; Faculty of Biosciences, Heidelberg University, Im Neuenheimer 234, 69120 Heidelberg, Germany
| | - Patricia Himmels
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer 234, 69120 Heidelberg, Germany
| | - Géza Schermann
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany; Institute for Neurovascular Cell Biology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Heike Adler
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany
| | - Alessia Motta
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 60, 20132 Milan, Italy
| | - Lea Gärtner
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany
| | - Ariadna Navarro-Aragall
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, EC1V 9EL London, UK
| | - Elena Ioannou
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, EC1V 9EL London, UK
| | - Elena Dyukova
- Max-Planck-Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Remy Bonnavion
- Max-Planck-Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Andreas Fischer
- Department of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany; Division Vascular Signaling and Cancer, German Cancer Research Center Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dario Bonanomi
- San Raffaele Scientific Institute, Division of Neuroscience, via Olgettina 60, 20132 Milan, Italy
| | - Frank Bradke
- Laboratory of Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Venusberg Campus 1/99, 53127 Bonn, Germany
| | - Christiana Ruhrberg
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, EC1V 9EL London, UK
| | - Carmen Ruiz de Almodóvar
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Straße 13-17, 68167 Mannheim, Germany; Institute for Neurovascular Cell Biology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany; Schlegel Chair for Neurovascular Cell Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany.
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16
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Patel T, Hammelman J, Aziz S, Jang S, Closser M, Michaels TL, Blum JA, Gifford DK, Wichterle H. Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro. Nat Commun 2022; 13:5427. [PMID: 36109497 PMCID: PMC9477853 DOI: 10.1038/s41467-022-33022-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Neurons born in the embryo can undergo a protracted period of maturation lasting well into postnatal life. How gene expression changes are regulated during maturation and whether they can be recapitulated in cultured neurons remains poorly understood. Here, we show that mouse motor neurons exhibit pervasive changes in gene expression and accessibility of associated regulatory regions from embryonic till juvenile age. While motifs of selector transcription factors, ISL1 and LHX3, are enriched in nascent regulatory regions, motifs of NFI factors, activity-dependent factors, and hormone receptors become more prominent in maturation-dependent enhancers. Notably, stem cell-derived motor neurons recapitulate ~40% of the maturation expression program in vitro, with neural activity playing only a modest role as a late-stage modulator. Thus, the genetic maturation program consists of a core hardwired subprogram that is correctly executed in vitro and an extrinsically-controlled subprogram that is dependent on the in vivo context of the maturing organism.
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Affiliation(s)
- Tulsi Patel
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Jennifer Hammelman
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, 02139, USA
| | - Siaresh Aziz
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sumin Jang
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Michael Closser
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Theodore L Michaels
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, 02139, USA
| | - Hynek Wichterle
- Departments of Pathology & Cell Biology, Neuroscience, and Neurology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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