1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
4
|
Honzel E, Hernandez-Morato I, Joshi A, Pennington-Fitzgerald W, Moayedi Y, Pitman MJ. Temporal Expression of Hox Genes and Phox2b in the Rat Nucleus Ambiguus During Development: Implications on Laryngeal Innervation. Laryngoscope 2023; 133:3462-3471. [PMID: 37350386 PMCID: PMC10907063 DOI: 10.1002/lary.30826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVES Recurrent laryngeal nerve (RLN) injury results in synkinetic reinnervation and vocal fold paralysis. Investigation of cues expressed in the developing brainstem that influence correct selective targeting of intrinsic laryngeal muscles may elucidate post-injury abnormalities contributing to non-functional reinnervation. Primary targets of interest were Hoxb1 and Hoxb2, members of the Hox family that create overlapping gradients in the developing brain, and their target Phox2b, a transcription factor necessary for cranial nerve branchio- and visceromotoneuron survival. METHODS Rat embryos at developmental days E14, E16, E18, and E20 (4 animals/age) were sectioned for RNA in situ hybridization to detect Hoxb1, Hoxb2, and Phox2b mRNA within the brainstem. Slides were costained with Islet1 antibody for identification of the nucleus ambiguus. Results were confirmed using immunohistochemistry. Sections were imaged on a confocal microscope. RNA and protein expressions were quantified using QuPath. Statistical analyses were performed using R. RESULTS Hoxb1, Hoxb2, and Phox2b expressions varied according to embryologic age. Hoxb1 and Hoxb2 expression peaked at E16, with significant decreases at E18 and E20 (one-way ANOVA p = 0.001 for both). Phox2b expression was highest at E14 and trended downward with increased embryologic age (one-way ANOVA p = 0.005). CONCLUSION Peak expression of Hoxb1 and Hoxb2 is observed at time points when the RLN arrives at the larynx and begins to branch toward individual muscles, positioning these gene products to be involved in cueing laryngeal motoneuron identity and target identification. Higher expression of Phox2b earlier in development suggests a role in laryngeal motoneuron formation. LEVEL OF EVIDENCE NA Laryngoscope, 133:3462-3471, 2023.
Collapse
Affiliation(s)
- Emily Honzel
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
| | - Ignacio Hernandez-Morato
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
| | - Abhinav Joshi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
| | - William Pennington-Fitzgerald
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
| | - Yalda Moayedi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
- Department of Neurology, Columbia University, New York, New York, U.S.A
| | - Michael J Pitman
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, New York, U.S.A
- Department of Neurology, Columbia University, New York, New York, U.S.A
| |
Collapse
|
5
|
Breton TS, Fike S, Francis M, Patnaude M, Murray CA, DiMaggio MA. Characterizing the SREB G protein-coupled receptor family in fish: Brain gene expression and genomic differences in upstream transcription factor binding sites. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111507. [PMID: 37611891 PMCID: PMC10529039 DOI: 10.1016/j.cbpa.2023.111507] [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: 06/07/2023] [Revised: 07/12/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
The SREB (Super-conserved Receptors Expressed in Brain) family of orphan G protein-coupled receptors is highly conserved in vertebrates and consists of three members: SREB1 (orphan designation GPR27), SREB2 (GPR85), and SREB3 (GPR173). SREBs are associated with processes ranging from neuronal plasticity to reproductive control. Relatively little is known about similarities across the entire family, or how mammalian gene expression patterns compare to non-mammalian vertebrates. In fish, this system may be particularly complex, as some species have gained a fourth member (SREB3B) while others have lost genes. To better understand the system, the present study aimed to: 1) use qPCR to characterize sreb and related gene expression patterns in the brains of three fish species with different systems, and 2) identify possible differences in transcriptional regulation among the receptors, using upstream transcription factor binding sites across 70 ray-finned fish genomes. Overall, regional patterns of sreb expression were abundant in forebrain-related areas. However, some species-specific patterns were detected, such as abundant expression of receptors in zebrafish (Danio rerio) hypothalamic-containing sections, and divergence between sreb3a and sreb3b in pufferfish (Dichotomyctere nigroviridis). In addition, a gene possibly related to the system (dkk3a) was spatially correlated with the receptors in all three species. Genomic regions upstream of sreb2 and sreb3b, but largely not sreb1 or sreb3a, contained many highly conserved transcription factor binding sites. These results provide novel information about expression differences and transcriptional regulation across fish that may inform future research to better understand these receptors.
Collapse
Affiliation(s)
- Timothy S Breton
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA.
| | - Samantha Fike
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Mullein Francis
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Michael Patnaude
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Casey A Murray
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
| | - Matthew A DiMaggio
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Feng W, Destain H, Smith JJ, Kratsios P. Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism. Nat Commun 2022; 13:6097. [PMID: 36243871 PMCID: PMC9569373 DOI: 10.1038/s41467-022-33781-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously, from embryonic stages through adulthood, in the nervous system. However, the functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component design principle for homeostatic control of Hox gene expression in adult MNs: Hox transcriptional autoregulation is counterbalanced by negative UNC-3 feedback. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.
Collapse
Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- University of Chicago Neuroscience Institute, Chicago, IL, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jayson J Smith
- Department of Neurobiology, 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.
- University of Chicago Neuroscience Institute, Chicago, IL, USA.
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
9
|
Perdomo-Sabogal A, Trakooljul N, Hadlich F, Murani E, Wimmers K, Ponsuksili S. DNA methylation landscapes from pig's limbic structures underline regulatory mechanisms relevant for brain plasticity. Sci Rep 2022; 12:16293. [PMID: 36175587 PMCID: PMC9522933 DOI: 10.1038/s41598-022-20682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
Epigenetic dynamics are essential for reconciling stress-induced responses in neuro-endocrine routes between the limbic brain and adrenal gland. CpG methylation associates with the initiation and end of regulatory mechanisms underlying responses critical for survival, and learning. Using Reduced Representation Bisulfite Sequencing, we identified methylation changes of functional relevance for mediating tissue-specific responses in the hippocampus, amygdala, hypothalamus, and adrenal gland in pigs. We identified 4186 differentially methylated CpGs across all tissues, remarkably, enriched for promoters of transcription factors (TFs) of the homeo domain and zinc finger classes. We also detected 5190 differentially methylated regions (DMRs, 748 Mb), with about half unique to a single pairwise. Two structures, the hypothalamus and the hippocampus, displayed 860 unique brain-DMRs, with many linked to regulation of chromatin, nervous development, neurogenesis, and cell-to-cell communication. TF binding motifs for TFAP2A and TFAP2C are enriched amount DMRs on promoters of other TFs, suggesting their role as master regulators, especially for pathways essential in long-term brain plasticity, memory, and stress responses. Our results reveal sets of TF that, together with CpG methylation, may serve as regulatory switches to modulate limbic brain plasticity and brain-specific molecular genetics in pigs.
Collapse
Affiliation(s)
- Alvaro Perdomo-Sabogal
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Murani
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.,University Rostock, Faculty of Agricultural and Environmental Sciences, 18059, Rostock, Germany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
| |
Collapse
|
10
|
Catela C, Chen Y, Weng Y, Wen K, Kratsios P. Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity. eLife 2022; 11:70766. [PMID: 35315772 PMCID: PMC8940177 DOI: 10.7554/elife.70766] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/12/2022] [Indexed: 12/30/2022] Open
Abstract
Spinal motor neurons (MNs) constitute cellular substrates for several movement disorders. Although their early development has received much attention, how spinal MNs become and remain terminally differentiated is poorly understood. Here, we determined the transcriptome of mouse MNs located at the brachial domain of the spinal cord at embryonic and postnatal stages. We identified novel transcription factors (TFs) and terminal differentiation genes (e.g. ion channels, neurotransmitter receptors, adhesion molecules) with continuous expression in MNs. Interestingly, genes encoding homeodomain TFs (e.g. HOX, LIM), previously implicated in early MN development, continue to be expressed postnatally, suggesting later functions. To test this idea, we inactivated Hoxc8 at successive stages of mouse MN development and observed motor deficits. Our in vivo findings suggest that Hoxc8 is not only required to establish, but also maintain expression of several MN terminal differentiation markers. Data from in vitro generated MNs indicate Hoxc8 acts directly and is sufficient to induce expression of terminal differentiation genes. Our findings dovetail recent observations in Caenorhabditis elegans MNs, pointing toward an evolutionarily conserved role for Hox in neuronal terminal differentiation.
Collapse
Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Yifei Weng
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Kailong Wen
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,University of Chicago Neuroscience Institute, Chicago, United States
| |
Collapse
|
11
|
Feng W, Li Y, Kratsios P. Emerging Roles for Hox Proteins in the Last Steps of Neuronal Development in Worms, Flies, and Mice. Front Neurosci 2022; 15:801791. [PMID: 35185450 PMCID: PMC8855150 DOI: 10.3389/fnins.2021.801791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022] Open
Abstract
A remarkable diversity of cell types characterizes every animal nervous system. Previous studies provided important insights into how neurons commit to a particular fate, migrate to the right place and form precise axodendritic patterns. However, the mechanisms controlling later steps of neuronal development remain poorly understood. Hox proteins represent a conserved family of homeodomain transcription factors with well-established roles in anterior-posterior (A-P) patterning and the early steps of nervous system development, including progenitor cell specification, neuronal migration, cell survival, axon guidance and dendrite morphogenesis. This review highlights recent studies in Caenorhabditis elegans, Drosophila melanogaster and mice that suggest new roles for Hox proteins in processes occurring during later steps of neuronal development, such as synapse formation and acquisition of neuronal terminal identity features (e.g., expression of ion channels, neurotransmitter receptors, and neuropeptides). Moreover, we focus on exciting findings suggesting Hox proteins are required to maintain synaptic structures and neuronal terminal identity during post-embryonic life. Altogether, these studies, in three model systems, support the hypothesis that certain Hox proteins are continuously required, from early development throughout post-embryonic life, to build and maintain a functional nervous system, significantly expanding their functional repertoire beyond the control of early A-P patterning.
Collapse
Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL, United States
| | - Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- Committee on Neurobiology, University of Chicago, Chicago, IL, United States
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, United States
- University of Chicago Neuroscience Institute, Chicago, IL, United States
- *Correspondence: Paschalis Kratsios,
| |
Collapse
|
12
|
OUP accepted manuscript. Brain 2022; 145:3214-3224. [DOI: 10.1093/brain/awac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/11/2022] [Accepted: 03/04/2022] [Indexed: 11/15/2022] Open
|
13
|
Watanabe N, Nakano M, Mitsuishi Y, Hara N, Mano T, Iwata A, Murayama S, Suzuki T, Ikeuchi T, Nishimura M. Transcriptional downregulation of FAM3C/ILEI in the Alzheimer's brain. Hum Mol Genet 2021; 31:122-132. [PMID: 34378027 DOI: 10.1093/hmg/ddab226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 11/14/2022] Open
Abstract
Amyloid-β (Aβ) accumulation in the brain triggers the pathogenic cascade for Alzheimer's disease (AD) development. The secretory protein FAM3C (also named ILEI) is a candidate for an endogenous suppressor of Aβ production. In this study, we found that FAM3C expression was transcriptionally downregulated in the AD brain. To determine the transcriptional mechanism of the human FAM3C gene, we delineated the minimal 5'-flanking sequence required for basal promoter activity. From a database search for DNA-binding motifs, expression analysis using cultured cells, and promoter DNA-binding assays, we identified SP1 and EBF1 as candidate basal transcription factors for FAM3C, and found that SMAD1 was a putative inducible transcription factor and KLF6 was a transcription repressor for FAM3C. Genomic deletion of the basal promoter sequence from HEK293 and Neuro-2a cells markedly reduced endogenous expression of FAM3C and abrogated SP1- or EBF1-mediated induction of FAM3C. Nuclear protein extracts from AD brains contained lower levels of SP1 and EBF1 than did those from control brains, although the relative mRNA levels of these factors did not differ significantly between the groups. Additionally, the ability of nuclear SP1 and EBF1 in AD brains to bind with the basal promoter sequence-containing DNA probe was reduced compared with the binding ability of these factors in control brains. Thus, the transcriptional downregulation of FAM3C in the AD brain is attributable to the reduced nuclear levels and genomic DNA binding of SP1 and EBF1. An expressional decline in FAM3C may be a risk factor for Aβ accumulation and eventually AD development.
Collapse
Affiliation(s)
- Naoki Watanabe
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Masaki Nakano
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Yachiyo Mitsuishi
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Atsushi Iwata
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.,Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Shigeo Murayama
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - Toshiharu Suzuki
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Masaki Nishimura
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga 520-2192, Japan
| |
Collapse
|
14
|
Yu D, Febbo IG, Maroteaux MJ, Wang H, Song Y, Han X, Sun C, Meyer EE, Rowe S, Chen Y, Canavier CC, Schrader LA. The Transcription Factor Shox2 Shapes Neuron Firing Properties and Suppresses Seizures by Regulation of Key Ion Channels in Thalamocortical Neurons. Cereb Cortex 2021; 31:3194-3212. [PMID: 33675359 DOI: 10.1093/cercor/bhaa414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Thalamocortical neurons (TCNs) play a critical role in the maintenance of thalamocortical oscillations, dysregulation of which can result in certain types of seizures. Precise control over firing rates of TCNs is foundational to these oscillations, yet the transcriptional mechanisms that constrain these firing rates remain elusive. We hypothesized that Shox2 is a transcriptional regulator of ion channels important for TCN function and that loss of Shox2 alters firing frequency and activity, ultimately perturbing thalamocortical oscillations into an epilepsy-prone state. In this study, we used RNA sequencing and quantitative PCR of control and Shox2 knockout mice to determine Shox2-affected genes and revealed a network of ion channel genes important for neuronal firing properties. Protein regulation was confirmed by Western blotting, and electrophysiological recordings showed that Shox2 KO impacted the firing properties of a subpopulation of TCNs. Computational modeling showed that disruption of these conductances in a manner similar to Shox2's effects modulated frequency of oscillations and could convert sleep spindles to near spike and wave activity, which are a hallmark for absence epilepsy. Finally, Shox2 KO mice were more susceptible to pilocarpine-induced seizures. Overall, these results reveal Shox2 as a transcription factor important for TCN function in adult mouse thalamus.
Collapse
Affiliation(s)
- Diankun Yu
- Neuroscience Program, Brain Institute, Tulane University, USA
| | | | | | - Hanyun Wang
- Neuroscience Program, Brain Institute, Tulane University, USA
| | - Yingnan Song
- Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Xiao Han
- Neuroscience Program, Brain Institute, Tulane University, USA
| | - Cheng Sun
- Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Emily E Meyer
- Neuroscience Program, Brain Institute, Tulane University, USA
| | - Stuart Rowe
- Neuroscience Program, Brain Institute, Tulane University, USA
| | - Yiping Chen
- Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Carmen C Canavier
- Cell Biology and Anatomy, LSU Health Sciences Center, New Orleans, LA 70112, USA
| | - Laura A Schrader
- Neuroscience Program, Brain Institute, Tulane University, USA.,Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| |
Collapse
|
15
|
Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
Collapse
Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| |
Collapse
|
16
|
Li Y, Osuma A, Correa E, Okebalama MA, Dao P, Gaylord O, Aburas J, Islam P, Brown AE, Kratsios P. Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function. eLife 2020; 9:59464. [PMID: 33001031 PMCID: PMC7529460 DOI: 10.7554/elife.59464] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023] Open
Abstract
Terminal selectors are transcription factors (TFs) that establish during development and maintain throughout life post-mitotic neuronal identity. We previously showed that UNC-3/Ebf, the terminal selector of C. elegans cholinergic motor neurons (MNs), acts indirectly to prevent alternative neuronal identities (Feng et al., 2020). Here, we globally identify the direct targets of UNC-3. Unexpectedly, we find that the suite of UNC-3 targets in MNs is modified across different life stages, revealing ‘temporal modularity’ in terminal selector function. In all larval and adult stages examined, UNC-3 is required for continuous expression of various protein classes (e.g. receptors, transporters) critical for MN function. However, only in late larvae and adults, UNC-3 is required to maintain expression of MN-specific TFs. Minimal disruption of UNC-3’s temporal modularity via genome engineering affects locomotion. Another C. elegans terminal selector (UNC-30/Pitx) also exhibits temporal modularity, supporting the potential generality of this mechanism for the control of neuronal identity.
Collapse
Affiliation(s)
- Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Anthony Osuma
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Edgar Correa
- Department of Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States
| | | | - Pauline Dao
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Olivia Gaylord
- Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States
| | - Jihad Aburas
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Priota Islam
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - André Ex Brown
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States.,Cell and Molecular Biology Program, University of Chicago, Chicago, United States.,Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States.,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, United States
| |
Collapse
|
17
|
Wang L, Gao Y, Zhao X, Guo C, Wang X, Yang Y, Han C, Zhao L, Qin Y, Liu L, Huang C, Wang W. HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress progression of hepatocellular carcinoma cells via ITGA2 pathway. Cell Prolif 2020; 53:e12835. [PMID: 32557953 PMCID: PMC7445403 DOI: 10.1111/cpr.12835] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/24/2022] Open
Abstract
Objectives HOXD3 is associated with progression of multiple types of cancer. This study aimed to identify the association of YY1 with HOXD3‐ITGA2 axis in the progression of hepatocellular carcinoma. Materials and Methods Bioinformatics assay was used to identify the effect of YY1, HOXD3 and ITGA2 expression in HCC tissues. The function of YY1 and HOXD3 in HCCs was determined by qRT‐PCR, MTT, apoptosis, Western blotting, colony formation, immunohistochemistry, and wound‐healing and transwell invasion assays. The relationship between YY1 and HOXD3 or HOXD3 and ITGA2 was explored by RNA‐Seq, ChIP‐PCR, dual luciferase reports and Pearson's assays. The interactions between YY1 and HDAC1 were determined by immunofluorescence microscopy and Co‐IP. Results Herein, we showed that the expression of YY1, HOXD3 and ITGA2 associated with the histologic and pathologic stages of HCC. Moreover, YY1, recruiting HDAC1, can directly target HOXD3 to regulate progression of HCCs. The relationship between YY1 and HOXD3 was unknown until uncovered by our present investigation. Furthermore, HOXD3 bound to promoter region of ITGA2 and up‐regulated the expression, thus activating the ERK1/2 signalling and inducing HCCs proliferation, metastasis and migration in the vitro and vivo. Conclusions Therefore, HOXD3, a target of YY1, facilitates HCC progression via activation of the ERK1/2 signalling by promoting ITGA2. This finding provides a new whole way to HCC therapy by serving YY1‐HOXD3‐ITGA2 regulatory axis as a potential therapeutic target for HCC therapy.
Collapse
Affiliation(s)
- Lumin Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yi Gao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Yan'an Key Laboratory of Chronic Disease Prevention and Research, Yan'an, China
| | - Xiaoge Zhao
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chen Guo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaofei Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yang Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Cong Han
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Lingyu Zhao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yannan Qin
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Liying Liu
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Cardiovascular Research Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenjing Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
18
|
Lin S, Zhuang J, Zhu L, Jiang Z. Matrine inhibits cell growth, migration, invasion and promotes autophagy in hepatocellular carcinoma by regulation of circ_0027345/miR-345-5p/HOXD3 axis. Cancer Cell Int 2020; 20:246. [PMID: 32549793 PMCID: PMC7296946 DOI: 10.1186/s12935-020-01293-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Background Matrine has been reported to exert anti-tumor effects in multiple types of cancers containing hepatocellular carcinoma (HCC). However, the anti-tumor molecular mechanisms of matrine in HCC is still not fully revealed. Methods Cell viability, apoptosis, cycle, migration and invasion were determined by Cell counting kit-8 (CCK-8), Flow cytometry and Transwell assays, respectively. Levels of all protein were analyzed by western blot analysis. The levels of circular RNA_0027345 (circ_0027345), microRNA-345-5p (miR-345-5p) and homeobox-containingD3 (HOXD3) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The interaction between circ_0027345 and circ_0027345 was identified using dual-luciferase reporter assay. The mouse xenograft model was constructed to explore the effect of matrine on tumor growth in vivo. Results Matrine suppressed cell growth, migration and invasion, while promoted apoptosis and autophagy in HCC cells. Matrine down-regulated the levels of circ_0027345 and HOXD3, and up-regulated miR-345-5p expression. Besides, circ_0027345 overexpression could reverse the inhibitory effect of matrine on cell progression. As the target gene of circ_0027345, miR-345-5p elevation counteracted the promotion effect of circ_0027345 overexpression on development of HCC cells. Moreover, miR-345-5p knockdown could facilitate cell growth, migration, invasion and repress cell apoptosis and autophagy by targeting HOXD3. Meanwhile, matrine restrained tumor growth of HCC by regulating circ_0027345/miR-345-5p/HOXD3 axis in vivo. Conclusion Matrine inhibited cell development and tumorigenesis in HCC by increasing miR-345-5p and decreasing circ_0027345 and HOXD3.
Collapse
Affiliation(s)
- Shaobing Lin
- Department of Pharmacy, Fujian Provincial Hospital, Fuzhou, China
| | - Jie Zhuang
- Department of Pharmacy, Fujian Provincial Hospital, Fuzhou, China
| | - Liping Zhu
- Department of Pharmacy, Fujian Provincial Hospital, Fuzhou, China
| | - Zongsheng Jiang
- Edinburgh University Joint Institute of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang China
| |
Collapse
|
19
|
Lozzi B, Huang TW, Sardar D, Huang AYS, Deneen B. Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain. Front Neurosci 2020; 14:61. [PMID: 32153350 PMCID: PMC7046629 DOI: 10.3389/fnins.2020.00061] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/15/2020] [Indexed: 12/19/2022] Open
Abstract
Astrocytes are the most abundant type of glial cell in the central nervous system and perform a myriad of vital functions, however, the nature of their diversity remains a longstanding question in neuroscience. Using transcription factor motif discovery analysis on region-specific gene signatures from astrocytes we uncovered universal and region-specific transcription factor expression profiles. This analysis revealed that motifs for Nuclear Factor-I (NFI) are present in genes enriched in astrocytes from all regions, with NFIB and NFIX exhibiting pan-astrocyte expression in the olfactory bulb, hippocampus, cortex, and brainstem. Further analysis into region-specific motif patterns, identified Nkx3-1, Stat4, Pgr, and Nkx6-1 as prospective region-specific transcription factors. Validation studies revealed that Nkx6-1 is exclusively expressed in astrocytes in the brainstem and associates with the promoters of several brainstem specific target genes. These studies illustrate the presence of multiple transcriptional layers in astrocytes across diverse brain regions and provide a new entry point for examining how astrocyte diversity is specified and maintained.
Collapse
Affiliation(s)
- Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States
| | - Teng-Wei Huang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States
| | - Debosmita Sardar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States
| | - Anna Yu-Szu Huang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States.,Department of Neurosurgery, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
20
|
Feng W, Li Y, Dao P, Aburas J, Islam P, Elbaz B, Kolarzyk A, Brown AE, Kratsios P. A terminal selector prevents a Hox transcriptional switch to safeguard motor neuron identity throughout life. eLife 2020; 9:50065. [PMID: 31902393 PMCID: PMC6944445 DOI: 10.7554/elife.50065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/08/2019] [Indexed: 01/01/2023] Open
Abstract
To become and remain functional, individual neuron types must select during development and maintain throughout life their distinct terminal identity features, such as expression of specific neurotransmitter receptors, ion channels and neuropeptides. Here, we report a molecular mechanism that enables cholinergic motor neurons (MNs) in the C. elegans ventral nerve cord to select and maintain their unique terminal identity. This mechanism relies on the dual function of the conserved terminal selector UNC-3 (Collier/Ebf). UNC-3 synergizes with LIN-39 (Scr/Dfd/Hox4-5) to directly co-activate multiple terminal identity traits specific to cholinergic MNs, but also antagonizes LIN-39’s ability to activate terminal features of alternative neuronal identities. Loss of unc-3 causes a switch in the transcriptional targets of LIN-39, thereby alternative, not cholinergic MN-specific, terminal features become activated and locomotion defects occur. The strategy of a terminal selector preventing a transcriptional switch may constitute a general principle for safeguarding neuronal identity throughout life.
Collapse
Affiliation(s)
- Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States
| | - Yinan Li
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States
| | - Pauline Dao
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Jihad Aburas
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Priota Islam
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Benayahu Elbaz
- Department of Neurology, Center for Peripheral Neuropathy, University of Chicago, Chicago, United States
| | - Anna Kolarzyk
- Department of Neurology, Center for Peripheral Neuropathy, University of Chicago, Chicago, United States
| | - André Ex Brown
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States.,Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, United States.,Committee on Neurobiology, University of Chicago, Chicago, United States.,The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, United States
| |
Collapse
|
21
|
Yang Z, Hu H, Zou Y, Luo W, Xie L, You Z. miR-7 Reduces High Glucose Induced-damage Via HoxB3 and PI3K/AKT/mTOR Signaling Pathways in Retinal Pigment Epithelial Cells. Curr Mol Med 2019; 20:372-378. [PMID: 31702491 DOI: 10.2174/1566524019666191023151137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 10/08/2019] [Accepted: 10/16/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Diabetic retinopathy (DR) is a common complication of diabetes. This study investigated the effect of miR-7 in the regulation of cell proliferation via the HoxB3 gene and PI3K/AKT/mTOR signaling pathways in DR. METHODS Human retinal pigment epithelial cell line (ARPE-19) cultured in normal medium (Control) and high glucose medium (25mM glucose, HG) was transfected with mimics NC (HG+ mimics NC), miR-7 mimics (HG+miR-7 mimics), inhibitor NC (HG+ inhibitor NC), and miR-inhibitor (HG+miR-7 inhibitor). The cells were assayed for viability, apoptosis, and expression of genes. RESULTS HG reduced cell viability and increased apoptosis. However, miR-7 mimics reduced the apoptosis. PCR results showed that miR-7 was significantly upregulated after transfection with miR-7 mimics. The expression of Hoxb3, mTOR, p-PI3K, and p- AKT was significantly downregulated at mRNA and protein levels after miR-7 mimics transfection, while no difference was observed for PI3K and AKT expression. CONCLUSION Our findings demonstrate that miR-7 regulates the growth of retinal epithelial cells through various pathways and is a potential therapeutic target for the prevention and treatment of diabetic retinopathy.
Collapse
Affiliation(s)
- Zhongyi Yang
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hanying Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuling Zou
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenbluo Luo
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lin Xie
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhipeng You
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| |
Collapse
|
22
|
Coughlan E, Garside VC, Wong SFL, Liang H, Kraus D, Karmakar K, Maheshwari U, Rijli FM, Bourne J, McGlinn E. A Hox Code Defines Spinocerebellar Neuron Subtype Regionalization. Cell Rep 2019; 29:2408-2421.e4. [DOI: 10.1016/j.celrep.2019.10.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/12/2019] [Accepted: 10/10/2019] [Indexed: 11/25/2022] Open
|
23
|
Homeobox B8 Targets Sterile Alpha Motif Domain-Containing Protein 9 and Drives Glioma Progression. Neurosci Bull 2019; 36:359-371. [PMID: 31646435 DOI: 10.1007/s12264-019-00436-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Gliomas are the most commonly occurring tumors of the central nervous system. Glioblastoma multiforme (GBM) is the most malignant and aggressive brain cancer in adults. Further understanding of the mechanisms underlying the aggressive nature of GBM is urgently needed. Here we identified homeobox B8 (HOXB8), a member of the homeobox family, as a crucial contributor to the aggressiveness of GBM. Data mining of publicly accessible RNA sequence datasets and our patient cohorts confirmed a higher expression of HOXB8 in the tumor tissue of GBM patients, and a strong positive correlation between the expression level and pathological grading of tumors and a negative correlation between the expression level and the overall survival rate. We next showed that HOXB8 promotes the proliferation and migration of glioblastoma cells and is crucial for the activation of the PI3K/AKT pathway and expression of epithelial-mesenchymal transition-related genes, possibly through direct binding to the promoter of SAMD9 (Sterile Alpha Motif Domain-Containing Protein 9) and activating its transcription. Collectively, we identified HOXB8 as a critical contributor to the aggressiveness of GBM, which provides insights into a potential therapeutic target for GBM and opens new avenues for improving its treatment outcome.
Collapse
|
24
|
Knapp B, Roedig J, Boldt K, Krzysko J, Horn N, Ueffing M, Wolfrum U. Affinity proteomics identifies novel functional modules related to adhesion GPCRs. Ann N Y Acad Sci 2019; 1456:144-167. [PMID: 31441075 DOI: 10.1111/nyas.14220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/08/2019] [Accepted: 07/25/2019] [Indexed: 01/04/2023]
Abstract
Adhesion G protein-coupled receptors (ADGRs) have recently become a target of intense research. Their unique protein structure, which consists of a G protein-coupled receptor combined with long adhesive extracellular domains, suggests a dual role in cell signaling and adhesion. Despite considerable progress in the understanding of ADGR signaling over the past years, the knowledge about ADGR protein networks is still limited. For most receptors, only a few interaction partners are known thus far. We aimed to identify novel ADGR-interacting partners to shed light on cellular protein networks that rely on ADGR function. For this, we applied affinity proteomics, utilizing tandem affinity purifications combined with mass spectrometry. Analysis of the acquired proteomics data provides evidence that ADGRs not only have functional roles at synapses but also at intracellular membranes, namely at the endoplasmic reticulum, the Golgi apparatus, mitochondria, and mitochondria-associated membranes (MAMs). Specifically, we found an association of ADGRs with several scaffold proteins of the membrane-associated guanylate kinases family, elementary units of the γ-secretase complex, the outer/inner mitochondrial membrane, MAMs, and regulators of the Wnt signaling pathways. Furthermore, the nuclear localization of ADGR domains together with their physical interaction with nuclear proteins and several transcription factors suggests a role of ADGRs in gene regulation.
Collapse
Affiliation(s)
- Barbara Knapp
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Jens Roedig
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Jacek Krzysko
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Nicola Horn
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research and Medical Bioanalytics, Centre for Ophthalmology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| |
Collapse
|
25
|
HOXA2 activity regulation by cytoplasmic relocation, protein stabilization and post-translational modification. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194404. [PMID: 31323436 DOI: 10.1016/j.bbagrm.2019.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/19/2019] [Accepted: 07/07/2019] [Indexed: 11/22/2022]
Abstract
HOX proteins are homeodomain transcription factors critically involved in patterning animal embryos and controlling organogenesis. While the functions of HOX proteins and the processes under their control begin to be well documented, the modalities of HOX protein activity regulation remain poorly understood. Here we show that HOXA2 interacts with PPP1CB, a catalytic subunit of the Ser/Thr PP1 phosphatase complex. This interaction co-localizes in the cytoplasm with a previously described HOXA2 interactor, KPC2, which belongs to the KPC E3 ubiquitin ligase complex. We provide evidence that HOXA2, PPP1CB and KPC2 define a molecularly and functionally interacting complex. Collectively, our experiments support that PPP1CB and KPC2 together inhibit the activity of HOXA2 by activating its nuclear export, but favored HOXA2 de-ubiquitination and stabilization thereby establishing a store of HOXA2 in the cytoplasm.
Collapse
|
26
|
Abdelhamed ZA, Abdelmottaleb DI, El-Asrag ME, Natarajan S, Wheway G, Inglehearn CF, Toomes C, Johnson CA. The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5. Sci Rep 2019; 9:5446. [PMID: 30931988 PMCID: PMC6445493 DOI: 10.1038/s41598-019-41940-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Primary cilia defects result in a group of related pleiotropic malformation syndromes known as ciliopathies, often characterised by cerebellar developmental and foliation defects. Here, we describe the cerebellar anatomical and signalling defects in the Tmem67tm1(Dgen)/H knockout mouse. At mid-gestation, Tmem67 mutant cerebella were hypoplastic and had aberrantly high canonical Wnt/β-catenin signalling, proliferation and apoptosis. Later in development, mutant cerebellar hemispheres had severe foliation defects and inferior lobe malformation, characterized by immature Purkinje cells (PCs). Early postnatal Tmem67 mutant cerebellum had disrupted ciliogenesis and reduced responsiveness to Shh signalling. Transcriptome profiling of Tmem67 mutant cerebella identified ectopic increased expression of homeobox-type transcription factors (Hoxa5, Hoxa4, Hoxb5 and Hoxd3), normally required for early rostral hindbrain patterning. HOXB5 protein levels were increased in the inferior lobe, and increased canonical Wnt signalling, following loss of TMEM67, was dependent on HOXB5. HOXB5 occupancy at the β-catenin promoter was significantly increased by activation of canonical Wnt signalling in Tmem67-/- mutant cerebellar neurones, suggesting that increased canonical Wnt signalling following mutation or loss of TMEM67 was directly dependent on HOXB5. Our results link dysregulated expression of Hox group genes with ciliary Wnt signalling defects in the developing cerebellum, providing new mechanistic insights into ciliopathy cerebellar hypoplasia phenotypes.
Collapse
Affiliation(s)
- Zakia A Abdelhamed
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Division of Human Genetics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Dina I Abdelmottaleb
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Mohammed E El-Asrag
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Subaashini Natarajan
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK
| | - Chris F Inglehearn
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Carmel Toomes
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK
| | - Colin A Johnson
- Divison of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, LS9 7TF, Leeds, UK.
| |
Collapse
|
27
|
Zakany J, Duboule D. Rescue of an aggressive female sexual courtship in mice by CRISPR/Cas9 secondary mutation in vivo. BMC Res Notes 2018; 11:193. [PMID: 29580290 PMCID: PMC5870235 DOI: 10.1186/s13104-018-3307-8] [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: 12/08/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE We had previously reported a mouse line carrying the Atypical female courtship (HoxD Afc ) allele, where an ectopic accumulation of Hoxd10 transcripts was observed in a sparse population of cells in the adult isocortex, as a result of a partial deletion of the HoxD gene cluster. Female mice carrying this allele displayed an exacerbated paracopulatory behavior, culminating in a severe mutilation of the studs' external genitals. To unequivocally demonstrate that this intriguing phenotype was indeed caused by an illegitimate function of the HOXD10 protein, we use CRISPR/Cas9 technology to induce a microdeletion into the homeobox of the Hoxd10 gene in cis with the HoxD Afc allele. RESULTS Females carrying this novel HoxDDel(1-9)d10hd allele no longer mutilate males. We conclude that a brain malfunction leading to a severe pathological behavior can be caused by the mere binding to DNA of a transcription factor expressed ectopically. We also show that in HoxD Afc mice, Hoxd10 was expressed in cells containing glutamate decarboxylase (Gad1) and Cholecystokinin (Cck) transcripts, corroborating our proposal that a small fraction of GABAergic neurons in adult hippocampus may participate to some aspects of female courtship.
Collapse
Affiliation(s)
- Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland. .,School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, Switzerland.
| |
Collapse
|
28
|
Russo D, Della Ragione F, Rizzo R, Sugiyama E, Scalabrì F, Hori K, Capasso S, Sticco L, Fioriniello S, De Gregorio R, Granata I, Guarracino MR, Maglione V, Johannes L, Bellenchi GC, Hoshino M, Setou M, D'Esposito M, Luini A, D'Angelo G. Glycosphingolipid metabolic reprogramming drives neural differentiation. EMBO J 2017; 37:embj.201797674. [PMID: 29282205 DOI: 10.15252/embj.201797674] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/17/2017] [Accepted: 11/24/2017] [Indexed: 01/13/2023] Open
Abstract
Neural development is accomplished by differentiation events leading to metabolic reprogramming. Glycosphingolipid metabolism is reprogrammed during neural development with a switch from globo- to ganglio-series glycosphingolipid production. Failure to execute this glycosphingolipid switch leads to neurodevelopmental disorders in humans, indicating that glycosphingolipids are key players in this process. Nevertheless, both the molecular mechanisms that control the glycosphingolipid switch and its function in neurodevelopment are poorly understood. Here, we describe a self-contained circuit that controls glycosphingolipid reprogramming and neural differentiation. We find that globo-series glycosphingolipids repress the epigenetic regulator of neuronal gene expression AUTS2. AUTS2 in turn binds and activates the promoter of the first and rate-limiting ganglioside-producing enzyme GM3 synthase, thus fostering the synthesis of gangliosides. By this mechanism, the globo-AUTS2 axis controls glycosphingolipid reprogramming and neural gene expression during neural differentiation, which involves this circuit in neurodevelopment and its defects in neuropathology.
Collapse
Affiliation(s)
- Domenico Russo
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy.,IRCCS INM, Neuromed, Pozzilli, Italy
| | - Riccardo Rizzo
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | - Eiji Sugiyama
- International Mass Imaging Center, Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu, Japan
| | - Francesco Scalabrì
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy.,IRCCS INM, Neuromed, Pozzilli, Italy
| | - Kei Hori
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Serena Capasso
- Institute of Protein Biochemistry, National Research Council, Naples, Italy.,Istituto di Ricovero e Cura a Carattere Scientifico-SDN, Naples, Italy
| | - Lucia Sticco
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | | | - Roberto De Gregorio
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Ilaria Granata
- High Performance Computing and Networking Institute, National Research Council, Naples, Italy
| | - Mario R Guarracino
- High Performance Computing and Networking Institute, National Research Council, Naples, Italy
| | | | - Ludger Johannes
- Chemical Biology of Membranes and Therapeutic Delivery Unit, Institut Curie, INSERM U 1143, CNRS, UMR 3666, PSL Research University, Paris Cedex 05, France
| | | | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Mitsutoshi Setou
- International Mass Imaging Center, Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu, Japan
| | - Maurizio D'Esposito
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy.,IRCCS INM, Neuromed, Pozzilli, Italy
| | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Naples, Italy.,Istituto di Ricovero e Cura a Carattere Scientifico-SDN, Naples, Italy
| | - Giovanni D'Angelo
- Institute of Protein Biochemistry, National Research Council, Naples, Italy .,Istituto di Ricovero e Cura a Carattere Scientifico-SDN, Naples, Italy
| |
Collapse
|
29
|
Lizen B, Moens C, Mouheiche J, Sacré T, Ahn MT, Jeannotte L, Salti A, Gofflot F. Conditional Loss of Hoxa5 Function Early after Birth Impacts on Expression of Genes with Synaptic Function. Front Mol Neurosci 2017; 10:369. [PMID: 29187810 PMCID: PMC5695161 DOI: 10.3389/fnmol.2017.00369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/26/2017] [Indexed: 12/24/2022] Open
Abstract
Hoxa5 is a member of the Hox gene family that plays critical roles in successive steps of the central nervous system formation during embryonic and fetal development. In the mouse, Hoxa5 was recently shown to be expressed in the medulla oblongata and the pons from fetal stages to adulthood. In these territories, Hoxa5 transcripts are enriched in many precerebellar neurons and several nuclei involved in autonomic functions, while the HOXA5 protein is detected mainly in glutamatergic and GABAergic neurons. However, whether HOXA5 is functionally required in these neurons after birth remains unknown. As a first approach to tackle this question, we aimed at determining the molecular programs downstream of the HOXA5 transcription factor in the context of the postnatal brainstem. A comparative transcriptomic analysis was performed in combination with gene expression localization, using a conditional postnatal Hoxa5 loss-of-function mouse model. After inactivation of Hoxa5 at postnatal days (P)1–P4, we established the transcriptome of the brainstem from P21 Hoxa5 conditional mutants using RNA-Seq analysis. One major finding was the downregulation of several genes associated with synaptic function in Hoxa5 mutant specimens including different actors involved in glutamatergic synapse, calcium signaling pathway, and GABAergic synapse. Data were confirmed and extended by reverse transcription quantitative polymerase chain reaction analysis, and the expression of several HOXA5 candidate targets was shown to co-localize with Hoxa5 transcripts in precerebellar nuclei. Together, these new results revealed that HOXA5, through the regulation of key actors of the glutamatergic/GABAergic synapses and calcium signaling, might be involved in synaptogenesis, synaptic transmission, and synaptic plasticity of the cortico-ponto-cerebellar circuitry in the postnatal brainstem.
Collapse
Affiliation(s)
- Benoit Lizen
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Charlotte Moens
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jinane Mouheiche
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Thomas Sacré
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marie-Thérèse Ahn
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec City, QC, Canada.,Centre de Recherche sur le Cancer, Université Laval, Quebec City, QC, Canada.,Centre de Recherche, Centre Hospitalier Universitaire de Québec, Université Laval, Quebec City, QC, Canada
| | - Ahmad Salti
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Françoise Gofflot
- Institut des Sciences de la Vie, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| |
Collapse
|
30
|
Bonfim-Silva R, Ferreira Melo FU, Thomé CH, Abraham KJ, De Souza FAL, Ramalho FS, Machado HR, De Oliveira RS, Cardoso AA, Covas DT, Fontes AM. Functional analysis of HOXA10 and HOXB4 in human medulloblastoma cell lines. Int J Oncol 2017; 51:1929-1940. [PMID: 29039487 DOI: 10.3892/ijo.2017.4151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 09/28/2017] [Indexed: 11/06/2022] Open
Abstract
Medulloblastoma (MB) is a malignant childhood brain tumor which at molecular level is classified into at least four major subtypes: WNT, SHH, group C and group D differing in response to treatment. Previous studies have associated changes in expression levels and activation of certain HOX genes with MB development. In the present study, we investigate the role of HOX genes in two attributes acquired by tumor cells: migration and proliferation potential, as well as, in vivo tumorigenic potential. We analyzed UW402, UW473, DAOY and ONS-76 human pediatric MB cell lines and cerebellum primary cultures. Two-color microarray-based gene expression analysis was used to identify differentially expressed HOX genes. Among the various HOX genes significantly overexpressed in DAOY and ONS-76 cell lines compared to UW402 and UW473 cell lines, HOXA10 and HOXB4 were selected for further analysis. The expression levels of these HOX genes were validated by real-time PCR. A mouse model was used to study the effect of the HOXA10 and HOXB4 genes on the in vivo tumorigenic potential and the in vitro proliferative and migration potential of MB cell lines. Our results show that the inhibition of HOXA10 in DAOY cell line led to increased in vitro cell migration while in vitro cell proliferation or in vivo tumorigenic potential were unaffected. We also observed that induced expression of HOXB4 in the UW473 cell line significantly reduced in vitro cell proliferation and migration capability of UW473 cells with no effect on the in vivo tumorigenicity. This suggests that HOXA10 plays a role in migration events and the HOXB4 gene is involved in proliferation and migration processes of medulloblastoma cells, however, it appears that these genes are not essential for the tumorigenic process of these cells.
Collapse
Affiliation(s)
- Ricardo Bonfim-Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Fernanda Ursoli Ferreira Melo
- Regional Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Carolina Hassibe Thomé
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Kuruvilla Joseph Abraham
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Fábio Augusto Labre De Souza
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Fernando Silva Ramalho
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Hélio Rubens Machado
- Division of Pediatric Neurosurgery of the Department of Surgery and Anatomy, University Hospital of Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Ricardo Santos De Oliveira
- Division of Pediatric Neurosurgery of the Department of Surgery and Anatomy, University Hospital of Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Angelo A Cardoso
- Center for Gene Therapy, City of Hope Alpha Stem Cell Clinic, Duarte, CA 91010, USA
| | - Dimas Tadeu Covas
- Department of Internal Medicine, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Aparecida Maria Fontes
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre 14049-900, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
31
|
Naruse M, Shibasaki K, Ishizaki Y. Temporal Changes in Transcription Factor Expression Associated with the Differentiation State of Cerebellar Neural Stem/Progenitor Cells During Development. Neurochem Res 2017; 43:205-211. [PMID: 28988404 DOI: 10.1007/s11064-017-2405-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 01/13/2023]
Abstract
During central nervous development, multi-potent neural stem/progenitor cells located in the ventricular/subventricular zones are temporally regulated to mostly produce neurons during early developmental stages and to produce glia during later developmental stages. After birth, the rodent cerebellum undergoes further dramatic development. It is also known that neural stem/progenitor cells are present in the white matter (WM) of the postnatal cerebellum until around P10, although the fate of these cells has yet to be determined. In the present study, it was revealed that primary neurospheres generated from cerebellar neural stem/progenitor cells at postnatal day 3 (P3) mainly differentiated into astrocytes and oligodendrocytes. In contrast, primary neurospheres generated from cerebellar neural stem/progenitor cells at P8 almost exclusively differentiated into astrocytes, but not oligodendrocytes. These results suggest that the differentiation potential of primary neurospheres changes depending on the timing of neural stem/progenitor cell isolation from the cerebellum. To identify the candidate transcription factors involved in regulating this temporal change, we utilized DNA microarray analysis to compare global gene-expression profiles of primary neurospheres generated from neural stem/progenitor cells isolated from either P3 or P8 cerebellum. The expression of zfp711, zfp618, barx1 and hoxb3 was higher in neurospheres generated from P3 cerebellum than from P8 by real-time quantitative PCR. Several precursor cells were found to express zfp618, barx1 or hoxb3 in the WM of the cerebellum at P3, but these transcription factors were absent from the WM of the P8 cerebellum.
Collapse
Affiliation(s)
- Masae Naruse
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Koji Shibasaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Yasuki Ishizaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan.
| |
Collapse
|
32
|
Lopes DM, Denk F, McMahon SB. The Molecular Fingerprint of Dorsal Root and Trigeminal Ganglion Neurons. Front Mol Neurosci 2017; 10:304. [PMID: 29018326 PMCID: PMC5623188 DOI: 10.3389/fnmol.2017.00304] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
The dorsal root ganglia (DRG) and trigeminal ganglia (TG) are clusters of cell bodies of highly specialized sensory neurons which are responsible for relaying information about our environment to the central nervous system. Despite previous efforts to characterize sensory neurons at the molecular level, it is still unknown whether those present in DRG and TG have distinct expression profiles and therefore a unique molecular fingerprint. To address this question, we isolated lumbar DRG and TG neurons using fluorescence-activated cell sorting from Advillin-GFP transgenic mice and performed RNA sequencing. Our transcriptome analyses showed that, despite being overwhelmingly similar, a number of genes are differentially expressed in DRG and TG neurons. Importantly, we identified 24 genes which were uniquely expressed in either ganglia, including an arginine vasopressin receptor and several homeobox genes, giving each population a distinct molecular fingerprint. We compared our findings with published studies to reveal that many genes previously reported to be present in neurons are in fact likely to originate from other cell types in the ganglia. Additionally, our neuron-specific results aligned well with a dataset examining whole human TG and DRG. We propose that the data can both improve our understanding of primary afferent biology and help contribute to the development of drug treatments and gene therapies which seek targets with unique or restricted expression patterns.
Collapse
Affiliation(s)
- Douglas M Lopes
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Franziska Denk
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Stephen B McMahon
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| |
Collapse
|
33
|
Parker HJ, Krumlauf R. Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28771970 DOI: 10.1002/wdev.286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Organization and development of the early vertebrate hindbrain are controlled by a cascade of regulatory interactions that govern the process of segmentation and patterning along the anterior-posterior axis via Hox genes. These interactions can be assembled into a gene regulatory network that provides a framework to interpret experimental data, generate hypotheses, and identify gaps in our understanding of the progressive process of hindbrain segmentation. The network can be broadly separated into a series of interconnected programs that govern early signaling, segmental subdivision, secondary signaling, segmentation, and ultimately specification of segmental identity. Hox genes play crucial roles in multiple programs within this network. Furthermore, the network reveals properties and principles that are likely to be general to other complex developmental systems. Data from vertebrate and invertebrate chordate models are shedding light on the origin and diversification of the network. Comprehensive cis-regulatory analyses of vertebrate Hox gene regulation have enabled powerful cross-species gene regulatory comparisons. Such an approach in the sea lamprey has revealed that the network mediating segmental Hox expression was present in ancestral vertebrates and has been maintained across diverse vertebrate lineages. Invertebrate chordates lack hindbrain segmentation but exhibit conservation of some aspects of the network, such as a role for retinoic acid in establishing nested Hox expression domains. These comparisons lead to a model in which early vertebrates underwent an elaboration of the network between anterior-posterior patterning and Hox gene expression, leading to the gene-regulatory programs for segmental subdivision and rhombomeric segmentation. WIREs Dev Biol 2017, 6:e286. doi: 10.1002/wdev.286 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| |
Collapse
|
34
|
Kratsios P, Kerk SY, Catela C, Liang J, Vidal B, Bayer EA, Feng W, De La Cruz ED, Croci L, Consalez GG, Mizumoto K, Hobert O. An intersectional gene regulatory strategy defines subclass diversity of C. elegans motor neurons. eLife 2017; 6. [PMID: 28677525 PMCID: PMC5498135 DOI: 10.7554/elife.25751] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/13/2017] [Indexed: 01/09/2023] Open
Abstract
A core principle of nervous system organization is the diversification of neuron classes into subclasses that share large sets of features but differ in select traits. We describe here a molecular mechanism necessary for motor neurons to acquire subclass-specific traits in the nematode Caenorhabditis elegans. Cholinergic motor neuron classes of the ventral nerve cord can be subdivided into subclasses along the anterior-posterior (A-P) axis based on synaptic connectivity patterns and molecular features. The conserved COE-type terminal selector UNC-3 not only controls the expression of traits shared by all members of a neuron class, but is also required for subclass-specific traits expressed along the A-P axis. UNC-3, which is not regionally restricted, requires region-specific cofactors in the form of Hox proteins to co-activate subclass-specific effector genes in post-mitotic motor neurons. This intersectional gene regulatory principle for neuronal subclass diversification may be conserved from nematodes to mice.
Collapse
Affiliation(s)
- Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Sze Yen Kerk
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Joseph Liang
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Berta Vidal
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Emily A Bayer
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Estanisla Daniel De La Cruz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| | - Laura Croci
- Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - G Giacomo Consalez
- Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele, Milan, Italy
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, United States
| |
Collapse
|
35
|
CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. Am J Hum Genet 2017; 100:773-788. [PMID: 28475860 PMCID: PMC5420353 DOI: 10.1016/j.ajhg.2017.04.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/06/2017] [Indexed: 01/13/2023] Open
Abstract
Epigenetic dysregulation has emerged as a recurring mechanism in the etiology of neurodevelopmental disorders. Two such disorders, CHARGE and Kabuki syndromes, result from loss of function mutations in chromodomain helicase DNA-binding protein 7 (CHD7LOF) and lysine (K) methyltransferase 2D (KMT2DLOF), respectively. Although these two syndromes are clinically distinct, there is significant phenotypic overlap. We therefore expected that epigenetically driven developmental pathways regulated by CHD7 and KMT2D would overlap and that DNA methylation (DNAm) alterations downstream of the mutations in these genes would identify common target genes, elucidating a mechanistic link between these two conditions, as well as specific target genes for each disorder. Genome-wide DNAm profiles in individuals with CHARGE and Kabuki syndromes with CHD7LOF or KMT2DLOF identified distinct sets of DNAm differences in each of the disorders, which were used to generate two unique, highly specific and sensitive DNAm signatures. These DNAm signatures were able to differentiate pathogenic mutations in these two genes from controls and from each other. Analysis of the DNAm targets in each gene-specific signature identified both common gene targets, including homeobox A5 (HOXA5), which could account for some of the clinical overlap in CHARGE and Kabuki syndromes, as well as distinct gene targets. Our findings demonstrate how characterization of the epigenome can contribute to our understanding of disease pathophysiology for epigenetic disorders, paving the way for explorations of novel therapeutics.
Collapse
|
36
|
Dunwell TL, Holland PWH. Diversity of human and mouse homeobox gene expression in development and adult tissues. BMC DEVELOPMENTAL BIOLOGY 2016; 16:40. [PMID: 27809766 PMCID: PMC5094009 DOI: 10.1186/s12861-016-0140-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
Background Homeobox genes encode a diverse set of transcription factors implicated in a vast range of biological processes including, but not limited to, embryonic cell fate specification and patterning. Although numerous studies report expression of particular sets of homeobox genes, a systematic analysis of the tissue specificity of homeobox genes is lacking. Results Here we analyse publicly-available transcriptome data from human and mouse developmental stages, and adult human tissues, to identify groups of homeobox genes with similar expression patterns. We calculate expression profiles for 242 human and 278 mouse homeobox loci across a combination of 59 human and 12 mouse adult tissues, early and late developmental stages. This revealed 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes. Most homeobox genes, however, have greater tissue-specificity, allowing us to compile homeobox gene expression lists for neural tissues, immune tissues, reproductive and developmental samples, and for numerous organ systems. In mouse development, we propose four distinct phases of homeobox gene expression: oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The final phase change is marked by expression of ANTP class genes. We also use these data to compare expression specificity between evolutionarily-based gene classes, revealing that ANTP, PRD, LIM and POU homeobox gene classes have highest tissue specificity while HNF, TALE, CUT and CERS are most widely expressed. Conclusions The homeobox genes comprise a large superclass and their expression patterns are correspondingly diverse, although in a broad sense related to an evolutionarily-based classification. The ubiquitous expression of some genes suggests roles in general cellular processes; in contrast, most human homeobox genes have greater tissue specificity and we compile useful homeobox datasets for particular tissues, organs and developmental stages. The identification of a set of eutherian-specific homeobox genes peaking from human 8-cell to morula stages suggests co-option of new genes to new developmental roles in evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0140-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
| |
Collapse
|
37
|
Lizen B, Hutlet B, Bissen D, Sauvegarde D, Hermant M, Ahn MT, Gofflot F. HOXA5 localization in postnatal and adult mouse brain is suggestive of regulatory roles in postmitotic neurons. J Comp Neurol 2016; 525:1155-1175. [PMID: 27650319 DOI: 10.1002/cne.24123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/08/2016] [Accepted: 09/15/2016] [Indexed: 01/13/2023]
Abstract
Hoxa5 is a member of the Hox gene family, which plays critical roles in successive steps of the central nervous system formation during embryonic and fetal development. Hoxa5 expression in the adult mouse brain has been reported, suggesting that this gene may be functionally required in the brain after birth. To provide further insight into the Hoxa5 expression pattern and potential functions in the brain, we have characterized its neuroanatomical profile from embryonic stages to adulthood. While most Hox mapping studies have been based solely on transcript analysis, we extended our analysis to HOXA5 protein localization in adulthood using specific antibodies. Our results show that Hoxa5 expression appears in the most caudal part of the hindbrain at fetal stages, where it is maintained until adulthood. In the medulla oblongata and pons, we detected Hoxa5 expression in many precerebellar neurons and in several nuclei implicated in the control of autonomic functions. In these territories, the HOXA5 protein is present solely in neurons, specifically in γ-aminobutyric acid (GABA)ergic, glutamatergic, and catecholaminergic neurons. Finally, we also detected Hoxa5 transcripts, but not the HOXA5 protein, in the thalamus and the cortex, from postnatal stages to adult stages, and in the cerebellum at adulthood. We provide evidence that some larger variants of Hoxa5 transcripts are present in these territories. Our mapping analysis allowed us to build hypotheses regarding HOXA5 functions in the nervous system after birth, such as a potential role in the establishment and refinement/plasticity of precerebellar circuits during postnatal and adult life. J. Comp. Neurol. 525:1155-1175, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Benoit Lizen
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Bertrand Hutlet
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Diane Bissen
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Deborah Sauvegarde
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Maryse Hermant
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Marie-Thérèse Ahn
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Françoise Gofflot
- Institute of Life Sciences, Catholic University of Louvain, 1348, Louvain-la-Neuve, Belgium
| |
Collapse
|
38
|
Chen F, Sun G, Peng J. RNAi-mediated HOXD3 knockdown inhibits growth in human RKO cells. Oncol Rep 2016; 36:1793-8. [PMID: 27499213 PMCID: PMC5022871 DOI: 10.3892/or.2016.4993] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/02/2016] [Indexed: 12/16/2022] Open
Abstract
Numerous studies have shown that the multifunctional Homeobox-containing (HOX) D3 gene is involved in various physiological and pathological processes. To elucidate the role and mechanism of HOXD3 in colorectal cancer (CRC), we measured its expression in five CRC cell lines. After determining that HOXD3 was highly expressed in the human RKO cancer cell line, we used lentiviral-mediated small interfering RNAs (siRNAs) to knock down HOXD3 expression and assessed proliferation, cell cycle distribution, apoptosis and colony formation using cell proliferation, flow cytometric, and colony formation assays. The expression of HOXD3 was strongly suppressed in the RKO cells infected with the lentiviruse expressing an HOXD3 short hairpin RNA (shRNA). The downregulation of HOXD3 expression in RKO cells significantly decreased proliferation and colony formation, and increased apoptosis in vitro, compared to the cells infected with the mock control (p<0.01). Moreover, specific downregulation of HOXD3 led to the accumulation of cells at the G2 phase of the cell cycle. Our findings revealed that the HOXD3 gene promotes CRC cell growth and plays a pivotal role in the development and survival of malignant human colorectal cancer cells.
Collapse
Affiliation(s)
- Fangjun Chen
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Guoping Sun
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jun Peng
- Department of Pathology, The Affiliated Anqing Municipal Hospital of Anhui Medical University, Anqing, Anhui 246003, P.R. China
| |
Collapse
|
39
|
Giunta M, Edvardson S, Xu Y, Schuelke M, Gomez-Duran A, Boczonadi V, Elpeleg O, Müller JS, Horvath R. Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy. Hum Mol Genet 2016; 25:2985-2996. [PMID: 27193168 PMCID: PMC5181591 DOI: 10.1093/hmg/ddw149] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/23/2022] Open
Abstract
The exosome complex is the most important RNA processing machinery within the cell. Mutations in its subunits EXOSC8 and EXOSC3 cause pontocerebellar hypoplasia, spinal muscular atrophy (SMA) and central nervous system demyelination. We present a patient with SMA-like phenotype carrying a homozygous mutation in RBM7—a subunit of the nuclear exosome targeting (NEXT) complex—which is known to bind and carry specific subtypes of coding and non-coding RNAs to the exosome. The NEXT complex with other protein complexes is responsible for the substrate specificity of the exosome. We performed RNA-sequencing (RNA-seq) analysis on primary fibroblasts of patients with mutations in EXOSC8 and RBM7 and gene knock-down experiments using zebrafish as a model system. RNA-seq analysis identified significantly altered expression of 62 transcripts shared by the two patient cell lines. Knock-down of rbm7, exosc8 and exosc3 in zebrafish showed a common pattern of defects in motor neurons and cerebellum. Our data indicate that impaired RNA metabolism may underlie the clinical phenotype by fine tuning gene expression which is essential for correct neuronal differentiation.
Collapse
Affiliation(s)
- Michele Giunta
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Shimon Edvardson
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel.,Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Markus Schuelke
- Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany
| | - Aurora Gomez-Duran
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Veronika Boczonadi
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Orly Elpeleg
- The Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Juliane S Müller
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK .,Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ, Newcastle upon Tyne, UK
| |
Collapse
|
40
|
Chojnowski JL, Trau HA, Masuda K, Manley NR. Temporal and spatial requirements for Hoxa3 in mouse embryonic development. Dev Biol 2016; 415:33-45. [PMID: 27178667 DOI: 10.1016/j.ydbio.2016.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 01/23/2023]
Abstract
Hoxa3(null) mice have severe defects in the development of pharyngeal organs including athymia, aparathyroidism, thyroid hypoplasia, and ultimobranchial body persistence, in addition to defects of the throat cartilages and cranial nerves. Some of the structures altered in the Hoxa3(null) mutant embryos are anterior to the described Hoxa3 gene expression boundary: the thyroid, soft palate, and lesser hyoid horn. All of these structures develop over time and through the interactions of multiple cell types. To investigate the specific cellular targets for HOXA3 function in these structures across developmental time, we performed a comprehensive analysis of the temporal and tissue-specific requirements for Hoxa3, including a lineage analysis using Hoxa3(Cre). The combination of these approaches showed that HOXA3 functions in both a cell autonomous and non-cell autonomous manner during development of the 3rd and 4th arch derivatives, and functions in a neural crest cell (NCC)-specific, non-cell autonomous manner for structures that were Hoxa3-negative by lineage tracing. Our data indicate that HOXA3 is required for tissue organization and organ differentiation in endodermal cells (in the tracheal epithelium, thymus, and parathyroid), and contributes to organ migration and morphogenesis in NCCs. These data provide a detailed picture of where and when HOXA3 acts to promote the development of the diverse structures that are altered in the Hoxa3(null) mutant. Data presented here, combined with our previous studies, indicate that the regionally restricted defects in Hoxa3 mutants do not reflect a role in positional identity (establishment of cell or tissue fate), but instead indicate a wider variety of functions including controlling distinct genetic programs for differentiation and morphogenesis in different cell types during development.
Collapse
Affiliation(s)
- Jena L Chojnowski
- Department of Genetics, Paul D. Coverdell Center, University of Georgia, 500 DW Brooks Drive, Athens, GA, 30602, USA
| | - Heidi A Trau
- Department of Genetics, Paul D. Coverdell Center, University of Georgia, 500 DW Brooks Drive, Athens, GA, 30602, USA
| | - Kyoko Masuda
- Department of Genetics, Paul D. Coverdell Center, University of Georgia, 500 DW Brooks Drive, Athens, GA, 30602, USA
| | - Nancy R Manley
- Department of Genetics, Paul D. Coverdell Center, University of Georgia, 500 DW Brooks Drive, Athens, GA, 30602, USA.
| |
Collapse
|
41
|
Bridoux L, Deneyer N, Bergiers I, Rezsohazy R. Molecular Analysis of the HOXA2-Dependent Degradation of RCHY1. PLoS One 2015; 10:e0141347. [PMID: 26496426 PMCID: PMC4619689 DOI: 10.1371/journal.pone.0141347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/07/2015] [Indexed: 01/19/2023] Open
Abstract
The homeodomain transcription factor Hoxa2 interacts with the RING-finger type E3 ubiquitin ligase RCHY1 and induces its proteasomal degradation. In this work, we dissected this non-transcriptional activity of Hoxa2 at the molecular level. The Hoxa2-mediated decay of RCHY1 involves both the 19S and 20S proteasome complexes. It relies on both the Hoxa2 homeodomain and C-terminal moiety although no single deletion in the Hoxa2 sequence could disrupt the RCHY1 interaction. That the Hoxa2 homeodomain alone could mediate RCHY1 binding is consistent with the shared ability all the Hox proteins we tested to interact with RCHY1. Nonetheless, the ability to induce RCHY1 degradation although critically relying on the homeodomain is not common to all Hox proteins. This identifies the homeodomain as necessary but not sufficient for what appears to be an almost generic Hox protein activity. Finally we provide evidence that the Hoxa2-induced degradation of RCHY1 is evolutionarily conserved among vertebrates. These data therefore support the hypothesis that the molecular and functional interaction between Hox proteins and RCHY1 is an ancestral Hox property.
Collapse
Affiliation(s)
- Laure Bridoux
- From the Animal Molecular and Cellular Biology group (AMCB), Life Sciences Institute (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Noémie Deneyer
- From the Animal Molecular and Cellular Biology group (AMCB), Life Sciences Institute (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Isabelle Bergiers
- From the Animal Molecular and Cellular Biology group (AMCB), Life Sciences Institute (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- From the Animal Molecular and Cellular Biology group (AMCB), Life Sciences Institute (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
- * E-mail:
| |
Collapse
|
42
|
Lizen B, Claus M, Jeannotte L, Rijli FM, Gofflot F. Perinatal induction of Cre recombination with tamoxifen. Transgenic Res 2015; 24:1065-77. [PMID: 26395370 DOI: 10.1007/s11248-015-9905-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/10/2015] [Indexed: 12/18/2022]
Abstract
Temporal control of site-specific recombination is commonly achieved by using a tamoxifen-inducible form of Cre or Flp recombinases. Although powerful protocols of induction have been developed for gene inactivation at adult stages or during embryonic development, induction of recombination at late gestational or early postnatal stages is still difficult to achieve. In this context, using the ubiquitous CMV-CreER(T2) transgenic mice, we have tested and validated two procedures to achieve recombination just before and just after birth. The efficiency of recombination was evaluated in the brain, which is known to be more problematic to target. For the late gestation treatment with tamoxifen, different protocols of complementary administration of progesterone and estrogen were tested. However, delayed delivery and/or mortality of pups due to difficult delivery were always observed. To circumvent this problem, pups were collected from tamoxifen-treated pregnant dams by caesarian section at E18.5 and given to foster mothers. For postnatal treatment, different dosages of tamoxifen were administered by intragastric injection to the pups during 3 or 4 days after birth. The efficiency of these treatments was analyzed at P7 using a transgenic reporter line. They were also validated with the Hoxa5 conditional allele. In conclusion, we have developed efficient procedures that allow achieving efficient recombination of floxed alleles at perinatal stages. These protocols will allow investigating the late/adult functions of many developmental genes, whose characterization has been so far restricted to embryonic development.
Collapse
Affiliation(s)
- Benoit Lizen
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Melissa Claus
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium.,Institut de Duve, Université catholique de Louvain, 1200, Woluwe-Saint-Lambert, Belgium
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, Canada.,CRHDQ, L'Hôtel-Dieu de Québec, Québec, Canada
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Françoise Gofflot
- Institut des Sciences de la Vie, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium.
| |
Collapse
|