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Trimbour R, Deutschmann IM, Cantini L. Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS. Bioinformatics 2024; 40:btae143. [PMID: 38460192 PMCID: PMC11065476 DOI: 10.1093/bioinformatics/btae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 03/11/2024] Open
Abstract
MOTIVATION The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation. We benchmarked HuMMuS with respect to the state-of-the-art on both paired and unpaired multi-omics datasets. Our results proved the improvements provided by HuMMuS in terms of transcription factor (TF) targets, TF binding motifs and regulatory regions prediction. Finally, once applied to snmC-seq, scATAC-seq and scRNA-seq data from mouse brain cortex, HuMMuS enabled to accurately cluster scRNA profiles and to identify potential driver TFs. AVAILABILITY AND IMPLEMENTATION HuMMuS is available at https://github.com/cantinilab/HuMMuS.
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Affiliation(s)
- Remi Trimbour
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Ina Maria Deutschmann
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
| | - Laura Cantini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, F-75015 Paris, France
- Institut de Biologie de l’Ecole Normale Supérieure, CNRS, INSERM, Ecole Normale Supérieure, Université PSL, 75005 Paris, France
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2
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Murphy KE, Duncan B, Sperringer JE, Zhang E, Haberman V, Wyatt EV, Maness P. Ankyrin B promotes developmental spine regulation in the mouse prefrontal cortex. Cereb Cortex 2023; 33:10634-10648. [PMID: 37642601 PMCID: PMC10560577 DOI: 10.1093/cercor/bhad311] [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: 03/17/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Postnatal regulation of dendritic spine formation and refinement in cortical pyramidal neurons is critical for excitatory/inhibitory balance in neocortical networks. Recent studies have identified a selective spine pruning mechanism in the mouse prefrontal cortex mediated by class 3 Semaphorins and the L1 cell adhesion molecules, neuron-glia related cell adhesion molecule, Close Homolog of L1, and L1. L1 cell adhesion molecules bind Ankyrin B, an actin-spectrin adaptor encoded by Ankyrin2, a high-confidence gene for autism spectrum disorder. In a new inducible mouse model (Nex1Cre-ERT2: Ank2flox: RCE), Ankyrin2 deletion in early postnatal pyramidal neurons increased spine density on apical dendrites in prefrontal cortex layer 2/3 of homozygous and heterozygous Ankyrin2-deficient mice. In contrast, Ankyrin2 deletion in adulthood had no effect on spine density. Sema3F-induced spine pruning was impaired in cortical neuron cultures from Ankyrin B-null mice and was rescued by re-expression of the 220 kDa Ankyrin B isoform but not 440 kDa Ankyrin B. Ankyrin B bound to neuron-glia related CAM at a cytoplasmic domain motif (FIGQY1231), and mutation to FIGQH inhibited binding, impairing Sema3F-induced spine pruning in neuronal cultures. Identification of a novel function for Ankyrin B in dendritic spine regulation provides insight into cortical circuit development, as well as potential molecular deficiencies in autism spectrum disorder.
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Affiliation(s)
- Kelsey E Murphy
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Bryce Duncan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Justin E Sperringer
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Erin Zhang
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Victoria Haberman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Elliott V Wyatt
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Patricia Maness
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
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3
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Murphy KE, Duncan BW, Sperringer JE, Zhang EY, Haberman VA, Wyatt EV, Maness PF. Ankyrin B Promotes Developmental Spine Regulation in the Mouse Prefrontal Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548527. [PMID: 37503187 PMCID: PMC10369899 DOI: 10.1101/2023.07.11.548527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Postnatal regulation of dendritic spine formation and refinement in cortical pyramidal neurons is critical for excitatory/inhibitory balance in neocortical networks. Recent studies have identified a selective spine pruning mechanism in the mouse prefrontal cortex (PFC) mediated by class 3 Semaphorins and the L1-CAM cell adhesion molecules Neuron-glia related CAM (NrCAM), Close Homolog of L1 (CHL1), and L1. L1-CAMs bind Ankyrin B (AnkB), an actin-spectrin adaptor encoded by Ankyrin2 ( ANK2 ), a high confidence gene for autism spectrum disorder (ASD). In a new inducible mouse model (Nex1Cre-ERT2: Ank2 flox : RCE), Ank2 deletion in early postnatal pyramidal neurons increased spine density on apical dendrites in PFC layer 2/3 of homozygous and heterozygous Ank2 -deficient mice. In contrast, Ank2 deletion in adulthood had no effect on spine density. Sema3F-induced spine pruning was impaired in cortical neuron cultures from AnkB-null mice and was rescued by re-expression of the 220 kDa AnkB isoform but not 440 kDa AnkB. AnkB bound to NrCAM at a cytoplasmic domain motif (FIGQY 1231 ), and mutation to FIGQH inhibited binding, impairing Sema3F-induced spine pruning in neuronal cultures. Identification of a novel function for AnkB in dendritic spine regulation provides insight into cortical circuit development, as well as potential molecular deficiencies in ASD.
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4
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [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: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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5
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Sekine K, Onoguchi M, Hamada M. Transposons contribute to the acquisition of cell type-specific cis-elements in the brain. Commun Biol 2023; 6:631. [PMID: 37301950 PMCID: PMC10257727 DOI: 10.1038/s42003-023-04989-7] [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: 01/28/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mammalian brains have evolved in stages over a long history to acquire higher functions. Recently, several transposable element (TE) families have been shown to evolve into cis-regulatory elements of brain-specific genes. However, it is not fully understood how TEs are important for gene regulatory networks. Here, we performed a single-cell level analysis using public data of scATAC-seq to discover TE-derived cis-elements that are important for specific cell types. Our results suggest that DNA elements derived from TEs, MER130 and MamRep434, can function as transcription factor-binding sites based on their internal motifs for Neurod2 and Lhx2, respectively, especially in glutamatergic neuronal progenitors. Furthermore, MER130- and MamRep434-derived cis-elements were amplified in the ancestors of Amniota and Eutheria, respectively. These results suggest that the acquisition of cis-elements with TEs occurred in different stages during evolution and may contribute to the acquisition of different functions or morphologies in the brain.
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Affiliation(s)
- Kotaro Sekine
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Masahiro Onoguchi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
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6
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Li C, Virgilio MC, Collins KL, Welch JD. Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction. Nat Biotechnol 2023; 41:387-398. [PMID: 36229609 PMCID: PMC10246490 DOI: 10.1038/s41587-022-01476-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/16/2022] [Indexed: 12/13/2022]
Abstract
Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the same cell, offer an opportunity to understand the temporal relationship between epigenome and transcriptome. To realize this potential, we developed MultiVelo, a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression and improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Application to multi-omic single-cell datasets from brain, skin and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. We also find four types of cell states: two states in which epigenome and transcriptome are coupled and two distinct decoupled states. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. MultiVelo is available on PyPI, Bioconda and GitHub ( https://github.com/welch-lab/MultiVelo ).
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Affiliation(s)
- Chen Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Maria C Virgilio
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen L Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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7
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Murphy KE, Zhang EY, Wyatt EV, Sperringer JE, Duncan BW, Maness PF. Doublecortin-Like Kinase 1 Facilitates Dendritic Spine Growth of Pyramidal Neurons in Mouse Prefrontal Cortex. Neuroscience 2023; 508:98-109. [PMID: 36064052 PMCID: PMC10317307 DOI: 10.1016/j.neuroscience.2022.08.020] [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: 02/17/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 01/17/2023]
Abstract
The L1 cell adhesion molecule NrCAM (Neuron-glia related cell adhesion molecule) functions as a co-receptor for secreted class 3 Semaphorins to prune subpopulations of dendritic spines on apical dendrites of pyramidal neurons in the developing mouse neocortex. The developing spine cytoskeleton is enriched in actin filaments, but a small number of microtubules have been shown to enter the spine apparently trafficking vesicles to the membrane. Doublecortin-like kinase 1 (DCLK1) is a member of the Doublecortin (DCX) family of microtubule-binding proteins with serine/threonine kinase activity. To determine if DCLK1 plays a role in spine remodeling, we generated a tamoxifen-inducible mouse line (Nex1Cre-ERT2: DCLK1flox/flox: RCE) to delete microtubule binding isoforms of DCLK1 from pyramidal neurons during postnatal stages of spine development. Homozygous DCLK1 conditional mutant mice exhibited decreased spine density on apical dendrites of pyramidal neurons in the prefrontal cortex (layer 2/3). Mature mushroom spines were selectively decreased upon DCLK1 deletion but dendritic arborization was unaltered. Mutagenesis and binding studies revealed that DCLK1 bound NrCAM at the conserved FIGQY1231 motif in the NrCAM cytoplasmic domain, a known interaction site for the actin-spectrin adaptor Ankyrin. These findings demonstrate in a novel mouse model that DCLK1 facilitates spine growth and maturation on cortical pyramidal neurons in the mouse prefrontal cortex.
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Affiliation(s)
- Kelsey E Murphy
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States
| | - Erin Y Zhang
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States
| | - Elliott V Wyatt
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States
| | - Justin E Sperringer
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States
| | - Bryce W Duncan
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States
| | - Patricia F Maness
- Department of Biochemistry and Biophysics, and Carolina Institute of Developmental Disabilities, University of North Carolina, School of Medicine at Chapel Hill, United States.
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8
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Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nat Commun 2022; 13:6747. [PMID: 36347848 PMCID: PMC9643508 DOI: 10.1038/s41467-022-34413-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.
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9
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Mary L, Leclerc D, Gilot D, Belaud-Rotureau MA, Jaillard S. The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects. Hum Mutat 2022; 43:1125-1148. [PMID: 35451537 DOI: 10.1002/humu.24388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
PBX1 is a highly conserved atypical homeodomain transcription factor (TF) belonging to the TALE (three amino acid loop extension) family. Dimerized with other TALE proteins, it can interact with numerous partners and reach dozens of regulating sequences, suggesting its role as a pioneer factor. PBX1 is expressed throughout the embryonic stages (as early as the blastula stage) in vertebrates. In human, PBX1 germline variations are linked to syndromic renal anomalies (CAKUTHED). In this review, we summarized available data on PBX1 functions, PBX1-deficient animal models, and PBX1 germline variations in humans. Two types of genetic alterations were identified in PBX1 gene. PBX1 missense variations generate a severe phenotype including lung hypoplasia, cardiac malformations, and sexual development defects (DSDs). Conversely, truncating variants generate milder phenotypes (mainly cryptorchidism and deafness). We suggest that defects in PBX1 interactions with various partners, including proteins from the HOX (HOXA7, HOXA10, etc.), WNT (WNT9B, WNT3), and Polycomb (BMI1, EED) families are responsible for abnormal proliferation and differentiation of the embryonic mesenchyme. These alterations could explain most of the defects observed in humans. However, some phenotype variability (especially DSDs) remains poorly understood. Further studies are needed to explore the TALE family in greater depth.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Delphine Leclerc
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - David Gilot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
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10
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Wang J, Wang A, Tian K, Hua X, Zhang B, Zheng Y, Kong X, Li W, Xu L, Wang J, Li Z, Liu Y, Zhou Y. A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors. Cell Discov 2022; 8:74. [PMID: 35915089 PMCID: PMC9343459 DOI: 10.1038/s41421-022-00421-2] [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: 02/27/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
β-catenin-dependent canonical Wnt signaling plays a plethora of roles in neocortex (Ncx) development, but its function in regulating the abundance of intermediate progenitors (IPs) is elusive. Here we identified neCtnnb1, an evolutionarily conserved cis-regulatory element with typical enhancer features in developing Ncx. neCtnnb1 locates 55 kilobase upstream of and spatially close to the promoter of Ctnnb1, the gene encoding β-catenin. CRISPR/Cas9-mediated activation or interference of the neCtnnb1 locus enhanced or inhibited transcription of Ctnnb1. neCtnnb1 drove transcription predominantly in the subventricular zone of developing Ncx. Knock-out of neCtnnb1 in mice resulted in compromised expression of Ctnnb1 and the Wnt reporter in developing Ncx. Importantly, knock-out of neCtnnb1 lead to reduced production and transit-amplification of IPs, which subsequently generated fewer upper-layer Ncx projection neurons (PNs). In contrast, enhancing the canonical Wnt signaling by stabilizing β-catenin in neCtnnb1-active cells promoted the production of IPs and upper-layer Ncx PNs. ASH2L was identified as the key trans-acting factor that associates with neCtnnb1 and Ctnnb1’s promoter to maintain Ctnnb1’s transcription in both mouse and human Ncx progenitors. These findings advance understanding of transcriptional regulation of Ctnnb1, and provide insights into mechanisms underlying Ncx expansion during development.
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Affiliation(s)
- Junbao Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Andi Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Kuan Tian
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Xiaojiao Hua
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Bo Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Yue Zheng
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Xiangfei Kong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Wei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Lichao Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Juan Wang
- Department of Neurology, Wuhan Central Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China
| | - Ying Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China.
| | - Yan Zhou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, Medical Research Institute at School of Medicine; The RNA Institute, College of Life Sciences; Wuhan University, Wuhan, Hubei, China.
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Ruscitti F, Cerminara M, Iascone M, Pezzoli L, Rosti G, Romano F, Ronchetto P, Martucciello G, Buratti S, Buffelli F, Bocciardi R, Puliti A, Divizia MT. An example of parenchymal renal sparing in the context of complex malformations due to a novel mutation in the PBX1 gene. Birth Defects Res 2022; 114:674-681. [PMID: 35751431 DOI: 10.1002/bdr2.2065] [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: 03/30/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022]
Abstract
INTRODUCTION PBX1 encodes the pre-B cell leukemia factor 1, a Three Amino acid Loop Extension (TALE) transcription factor crucial to regulate basic developmental processes. PBX1 loss-of-function variants have been initially described in association with renal malformations in both isolated and syndromic forms. CASE REPORT Herein, we report a male infant presenting multiple organ malformations (cleidosternal dysostosis, micrognathia, left lung hypoplasia, wide interatrial defect, pulmonary hypertension, total anomalous pulmonary venous return, intestinal malrotation) and carrying the heterozygous de novo c.868C > T (p.Arg290Trp) variant in PBX1. This novel variant affects the highly conserved homeodomain of the protein, leading to a non-conservative substitution and consequently altering its tridimensional structure and DNA-binding capacity. CONCLUSION So far, PBX1 has been reported in association with a broad spectrum of renal anomalies. However, given the role of this gene in many different developing processes, whole-exome sequencing can detect mutations in PBX1 even in patients with different phenotypes, not necessarily involving the renal primordium. This report presents a novel PBX1 variant with a predicted strong deleterious effect. The mutation leads to a non-conservative substitution in a very highly conserved domain of the protein, thus altering its tertiary structure and DNA-binding capacity.
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Affiliation(s)
| | - Maria Cerminara
- DINOGMI, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Laura Pezzoli
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giulia Rosti
- DINOGMI, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Patrizia Ronchetto
- UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giuseppe Martucciello
- DINOGMI, University of Genoa, Genoa, Italy
- UOC Chirurgia Pediatrica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Buratti
- UOC Terapia Intensiva Neonatale e Pediatrica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Buffelli
- Fetal-Perinatal Pathology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Renata Bocciardi
- DINOGMI, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Aldamaria Puliti
- DINOGMI, University of Genoa, Genoa, Italy
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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12
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Thalamocortical axons regulate neurogenesis and laminar fates in the early sensory cortex. Proc Natl Acad Sci U S A 2022; 119:e2201355119. [PMID: 35613048 PMCID: PMC9295754 DOI: 10.1073/pnas.2201355119] [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] [Indexed: 12/03/2022] Open
Abstract
This study addresses how the cerebral cortex is partitioned into specialized areas during development. Although both early embryonic patterning and postnatal synaptic input from sensory thalamic nuclei are known to be critical, early roles of thalamic axons in area-specific regulation of cortical neurogenesis are poorly understood. We examined this by developing a genetic mouse model in which thalamocortical projections fail to properly form during embryogenesis, and found these axons are required not only for an enhanced production of superficial layer neurons but also for promoting the layer 4 cell fate, a hallmark of the primary sensory cortex. These findings provide a mechanism by which thalamocortical axons complement the intrinsic programs of neurogenesis and early fate specification. Area-specific axonal projections from the mammalian thalamus shape unique cellular organization in target areas in the adult neocortex. How these axons control neurogenesis and early neuronal fate specification is poorly understood. By using mutant mice lacking the majority of thalamocortical axons, we show that these axons are required for the production and specification of the proper number of layer 4 neurons in primary sensory areas by the neonatal stage. Part of these area-specific roles is played by the thalamus-derived molecule, VGF. Our work reveals that extrinsic cues from sensory thalamic projections have an early role in the formation of cortical cytoarchitecture by enhancing the production and specification of layer 4 neurons.
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13
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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14
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Su Z, Wang Z, Lindtner S, Yang L, Shang Z, Tian Y, Guo R, You Y, Zhou W, Rubenstein JL, Yang Z, Zhang Z. Dlx1/2-dependent expression of Meis2 promotes neuronal fate determination in the mammalian striatum. Development 2022; 149:dev200035. [PMID: 35156680 PMCID: PMC8918808 DOI: 10.1242/dev.200035] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022]
Abstract
The striatum is a central regulator of behavior and motor function through the actions of D1 and D2 medium-sized spiny neurons (MSNs), which arise from a common lateral ganglionic eminence (LGE) progenitor. The molecular mechanisms of cell fate specification of these two neuronal subtypes are incompletely understood. Here, we found that deletion of murine Meis2, which is highly expressed in the LGE and derivatives, led to a large reduction in striatal MSNs due to a block in their differentiation. Meis2 directly binds to the Zfp503 and Six3 promoters and is required for their expression and specification of D1 and D2 MSNs, respectively. Finally, Meis2 expression is regulated by Dlx1/2 at least partially through the enhancer hs599 in the LGE subventricular zone. Overall, our findings define a pathway in the LGE whereby Dlx1/2 drives expression of Meis2, which subsequently promotes the fate determination of striatal D1 and D2 MSNs via Zfp503 and Six3.
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Affiliation(s)
- Zihao Su
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Ziwu Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Susan Lindtner
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Lin Yang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Zicong Shang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Yu Tian
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Rongliang Guo
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Yan You
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - John L. Rubenstein
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Zhengang Yang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Zhuangzhi Zhang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
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15
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Tocco C, Bertacchi M, Studer M. Structural and Functional Aspects of the Neurodevelopmental Gene NR2F1: From Animal Models to Human Pathology. Front Mol Neurosci 2022; 14:767965. [PMID: 34975398 PMCID: PMC8715095 DOI: 10.3389/fnmol.2021.767965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
The assembly and maturation of the mammalian brain result from an intricate cascade of highly coordinated developmental events, such as cell proliferation, migration, and differentiation. Any impairment of this delicate multi-factorial process can lead to complex neurodevelopmental diseases, sharing common pathogenic mechanisms and molecular pathways resulting in multiple clinical signs. A recently described monogenic neurodevelopmental syndrome named Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is caused by NR2F1 haploinsufficiency. The NR2F1 gene, coding for a transcriptional regulator belonging to the steroid/thyroid hormone receptor superfamily, is known to play key roles in several brain developmental processes, from proliferation and differentiation of neural progenitors to migration and identity acquisition of neocortical neurons. In a clinical context, the disruption of these cellular processes could underlie the pathogenesis of several symptoms affecting BBSOAS patients, such as intellectual disability, visual impairment, epilepsy, and autistic traits. In this review, we will introduce NR2F1 protein structure, molecular functioning, and expression profile in the developing mouse brain. Then, we will focus on Nr2f1 several functions during cortical development, from neocortical area and cell-type specification to maturation of network activity, hippocampal development governing learning behaviors, assembly of the visual system, and finally establishment of cortico-spinal descending tracts regulating motor execution. Whenever possible, we will link experimental findings in animal or cellular models to corresponding features of the human pathology. Finally, we will highlight some of the unresolved questions on the diverse functions played by Nr2f1 during brain development, in order to propose future research directions. All in all, we believe that understanding BBSOAS mechanisms will contribute to further unveiling pathophysiological mechanisms shared by several neurodevelopmental disorders and eventually lead to effective treatments.
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Affiliation(s)
- Chiara Tocco
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
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16
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Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. Proc Natl Acad Sci U S A 2021; 118:e2024795118. [PMID: 34921112 PMCID: PMC8713794 DOI: 10.1073/pnas.2024795118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.
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Affiliation(s)
- Athéna R Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
| | - Kartik Pattabiraman
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - Olga Golonzhka
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- School of Natural Sciences, University of California, Merced, CA 95343
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
| | - Len A Pennachio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Iros Barozzi
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, United Kingdom
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - John L Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
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17
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Hau AC, Mommaerts E, Laub V, Müller T, Dittmar G, Schulte D. Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells. Sci Rep 2021; 11:21013. [PMID: 34697387 PMCID: PMC8545929 DOI: 10.1038/s41598-021-99968-5] [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: 05/17/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
PAX6 is a highly conserved transcription factor and key regulator of several neurogenic processes, including the continuous generation of dopaminergic/GABAergic interneurons in the adult ventricular-subventricular (V-SVZ) neurogenic system in mice. Here we report that PAX6 cooperates with the TALE-homeodomain transcription factor PBX1 in this context. Chromatin-immunoprecipitation showed that PBX1 and PAX6 co-occupy shared genomic binding sites in adult V-SVZ stem- and progenitor cell cultures and mouse embryonic stem cells, while depletion of Pbx1 revealed that association of PAX6 with these sites requires the presence of PBX1. Expression profiling together with viral overexpression or knockdown of Pax6 or Pbx1 identified novel PBX1-PAX6 co-regulated genes, including several transcription factors. Computational modeling of genome wide expression identified novel cross-regulatory networks among these very transcription factors. Taken together, the results presented here highlight the intimate link that exists between PAX6 and TALE-HD family proteins and contribute novel insights into how the orchestrated activity of transcription factors shapes adult V-SVZ neurogenesis.
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Affiliation(s)
- Ann-Christin Hau
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany. .,NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Strassen, Luxembourg. .,National Center of Pathology, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg.
| | - Elise Mommaerts
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Vera Laub
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Tamara Müller
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Gunnar Dittmar
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Dorothea Schulte
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany.
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18
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Chen Y, Ding X, Wang S, Ding P, Xu Z, Li J, Wang M, Xiang R, Wang X, Wang H, Feng Q, Qiu J, Wang F, Huang Z, Zhang X, Tang G, Tang S. A single-cell atlas of mouse olfactory bulb chromatin accessibility. J Genet Genomics 2021; 48:147-162. [PMID: 33926839 DOI: 10.1016/j.jgg.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 10/21/2022]
Abstract
Olfaction, the sense of smell, is a fundamental trait crucial to many species. The olfactory bulb (OB) plays pivotal roles in processing and transmitting odor information from the environment to the brain. The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing. However, the epigenetic landscape of the mOB remains mostly unexplored. Herein, we apply single-cell assay for transposase-accessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the mOB. Based on single-cell epigenetic signatures, mOB cells are classified into 21 clusters corresponding to 11 cell types. We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred. In addition, the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage. Our study provides a valuable epigenetic data set for the mOB at single-cell resolution, and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.
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Affiliation(s)
- Yin Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyou Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Zaoxu Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiankang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Mingyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Rong Xiang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoling Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Qikai Feng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Feiyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhen Huang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Xingliang Zhang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China.
| | - Gen Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China.
| | - Shengping Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Zunyi Medical University, Zunyi, Guizhou 563099, China; China Medical University, Shenyang, Liaoning 110122, China.
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19
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Xu L, Zheng Y, Li X, Wang A, Huo D, Li Q, Wang S, Luo Z, Liu Y, Xu F, Wu X, Wu M, Zhou Y. Abnormal neocortex arealization and Sotos-like syndrome-associated behavior in Setd2 mutant mice. SCIENCE ADVANCES 2021; 7:7/1/eaba1180. [PMID: 33523829 PMCID: PMC7775761 DOI: 10.1126/sciadv.aba1180] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Proper formation of area identities of the cerebral cortex is crucial for cognitive functions and social behaviors of the brain. It remains largely unknown whether epigenetic mechanisms, including histone methylation, regulate cortical arealization. Here, we removed SETD2, the methyltransferase for histone 3 lysine-36 trimethylation (H3K36me3), in the developing dorsal forebrain in mice and showed that Setd2 is required for proper cortical arealization and the formation of cortico-thalamo-cortical circuits. Moreover, Setd2 conditional knockout mice exhibit defects in social interaction, motor learning, and spatial memory, reminiscent of patients with the Sotos-like syndrome bearing SETD2 mutations. SETD2 maintains the expression of clustered protocadherin (cPcdh) genes in an H3K36me3 methyltransferase-dependent manner. Aberrant cortical arealization was recapitulated in cPcdh heterozygous mice. Together, our study emphasizes epigenetic mechanisms underlying cortical arealization and pathogenesis of the Sotos-like syndrome.
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Affiliation(s)
- Lichao Xu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Yue Zheng
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Xuejing Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Andi Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Dawei Huo
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Qinglan Li
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Shikang Wang
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Zhiyuan Luo
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Ying Liu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xudong Wu
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China
| | - Min Wu
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
| | - Yan Zhou
- College of Life Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University; Frontier Science Center for Immunology and Metabolism, and Medical Research Institute at School of Medicine, Wuhan University, Wuhan 430071, China.
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China
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20
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García-Moreno F, Molnár Z. Variations of telencephalic development that paved the way for neocortical evolution. Prog Neurobiol 2020; 194:101865. [PMID: 32526253 PMCID: PMC7656292 DOI: 10.1016/j.pneurobio.2020.101865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
Charles Darwin stated, "community in embryonic structure reveals community of descent". Thus, to understand how the neocortex emerged during mammalian evolution we need to understand the evolution of the development of the pallium, the source of the neocortex. In this article, we review the variations in the development of the pallium that enabled the production of the six-layered neocortex. We propose that an accumulation of subtle modifications from very early brain development accounted for the diversification of vertebrate pallia and the origin of the neocortex. Initially, faint differences of expression of secretable morphogens promote a wide variety in the proportions and organization of sectors of the early pallium in different vertebrates. It prompted different sectors to host varied progenitors and distinct germinative zones. These cells and germinative compartments generate diverse neuronal populations that migrate and mix with each other through radial and tangential migrations in a taxon-specific fashion. Together, these early variations had a profound influence on neurogenetic gradients, lamination, positioning, and connectivity. Gene expression, hodology, and physiological properties of pallial neurons are important features to suggest homologies, but the origin of cells and their developmental trajectory are fundamental to understand evolutionary changes. Our review compares the development of the homologous pallial sectors in sauropsids and mammals, with a particular focus on cell lineage, in search of the key changes that led to the appearance of the mammalian neocortex.
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Affiliation(s)
- Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013, Bilbao, Spain; Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Bizkaia, Spain.
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, Sherrington Building, University of Oxford, Oxford, OX1 3QX, UK.
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21
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Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell 2020; 182:754-769.e18. [PMID: 32610082 PMCID: PMC7415678 DOI: 10.1016/j.cell.2020.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/16/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from nine dissected regions of the mid-gestation human telencephalon, as well as microdissected upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed temporal, regional, and laminar differences in chromatin accessibility and were correlated with gene expression differences across regions and gestational ages. We identified two functional de novo variants in a pRE for autism risk gene SLC6A1, and using CRISPRa, demonstrated that this pRE regulates SCL6A1. Additionally, mouse transgenic experiments validated enhancer activity for pREs proximal to FEZF2 and BCL11A. Thus, this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
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Affiliation(s)
- Eirene Markenscoff-Papadimitriou
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | | | | | - Fadya Binyameen
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephan J Sanders
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - John L Rubenstein
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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22
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Zhang L, Song NN, Zhang Q, Mei WY, He CH, Ma P, Huang Y, Chen JY, Mao B, Lang B, Ding YQ. Satb2 is required for the regionalization of retrosplenial cortex. Cell Death Differ 2020; 27:1604-1617. [PMID: 31666685 PMCID: PMC7206047 DOI: 10.1038/s41418-019-0443-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 02/08/2023] Open
Abstract
The retrosplenial cortex (Rsp) is a transitional cortex located between the neocortex and archicortex, but the molecular mechanism specifying Rsp from the archicortex remains elusive. We here report that the transcription factor Satb2 is required for specifying Rsp identity during its morphogenesis. In Satb2 CKO mice, the boundary between the Rsp and archicortex [i.e., subiculum (SubC)] disappears as early as E17.5, and Rsp efferent projection is aberrant. Rsp-specific genes are lost, whereas SubC-specific genes are ectopically expressed in Rsp of Satb2 CKO mice. Furthermore, cell-autonomous role of Satb2 in maintaining Rsp neuron identity is revealed by inactivation of Satb2 in Rsp neurons. Finally, Satb2 represses the transcription of Nr4a2. The misexpression of Nr4a2 together with Ctip2 induces expression of SubC-specific genes in wild-type Rsp, and simultaneous knockdown of these two genes in Rsp Satb2-mutant cells prevents their fate transition to SubC identity. Thus, Satb2 serves as a determinant gene in the Rsp regionalization by repressing Nr4a2 and Ctip2 during cortical development.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China.
| | - Ning-Ning Song
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Qiong Zhang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Wan-Ying Mei
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Chun-Hui He
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ying Huang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Jia-Yin Chen
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bing Lang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China
- Mental Health Institute of the Second Xiangya Hospital, National Clinical Research Center on Mental Disorders, National Technology Institute on Mental Disorders, Key Laboratory of Psychiatry and Mental Health of Hunan Province, Central South University, Changsha, 410011, Hunan, China
| | - Yu-Qiang Ding
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, and Department of Anatomy and Neurobiology, Collaborative Innovation Center for Brain Science, Tongji University School of Medicine, Shanghai, 200092, China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
- Department of Laboratory Animal Science, Fudan University, Shanghai, 200032, China.
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23
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Ambeskovic M, Ilnytskyy Y, Kiss D, Currie C, Montina T, Kovalchuk I, Metz GAS. Ancestral stress programs sex-specific biological aging trajectories and non-communicable disease risk. Aging (Albany NY) 2020; 12:3828-3847. [PMID: 32087063 PMCID: PMC7066928 DOI: 10.18632/aging.102848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/05/2020] [Indexed: 12/18/2022]
Abstract
The incidence of non-communicable diseases (NCDs) is rising globally but their causes are generally not understood. Here we show that cumulative ancestral stress leads to premature aging and raises NCD risk in a rat population. This longitudinal study revealed that cumulative multigenerational prenatal stress (MPS) across four generations (F0-F3) raises age- and sex-dependent adverse health outcomes in F4 offspring. MPS accelerated biological aging processes and exacerbated sex-specific incidences of respiratory and kidney diseases, inflammatory processes and tumors. Unbiased deep sequencing of frontal cortex revealed that MPS altered expression of microRNAs and their target genes involved in synaptic plasticity, stress regulation, immune function and longevity. Multi-layer top-down deep learning metabolite enrichment analysis of urine markers revealed altered metabolic homeodynamics in MPS males. Thus, peripheral metabolic signatures may provide sensitive biomarkers of stress vulnerability and disease risk. Programming by MPS appears to be a significant determinant of lifetime mental health trajectories, physical wellbeing and vulnerability to NCDs through altered epigenetic regulation.
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Affiliation(s)
- Mirela Ambeskovic
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Douglas Kiss
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Cheryl Currie
- Faculty of Health Sciences, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Tony Montina
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
| | - Gerlinde A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
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24
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Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2. Sci Rep 2019; 9:19697. [PMID: 31873146 PMCID: PMC6927953 DOI: 10.1038/s41598-019-56171-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Excitatory neurons of the mammalian cerebral cortex are organized into six functional layers characterized by unique patterns of connectivity, as well as distinctive physiological and morphological properties. Cortical layers appear after a highly regulated migration process in which cells move from the deeper, proliferative zone toward the superficial layers. Importantly, defects in this radial migration process have been implicated in neurodevelopmental and psychiatric diseases. Here we report that during the final stages of migration, transcription factor Neurogenic Differentiation 2 (Neurod2) contributes to terminal cellular localization within the cortical plate. In mice, in utero knockdown of Neurod2 resulted in reduced numbers of neurons localized to the uppermost region of the developing cortex, also termed the primitive cortical zone. Our ChIP-Seq and RNA-Seq analyses of genes regulated by NEUROD2 in the developing cortex identified a number of key target genes with known roles in Reelin signaling, a critical regulator of neuronal migration. Our focused analysis of regulation of the Reln gene, encoding the extracellular ligand REELIN, uncovered NEUROD2 binding to conserved E-box elements in multiple introns. Furthermore, we demonstrate that knockdown of NEUROD2 in primary cortical neurons resulted in a strong increase in Reln gene expression at the mRNA level, as well as a slight upregulation at the protein level. These data reveal a new role for NEUROD2 during the late stages of neuronal migration, and our analysis of its genomic targets offers new genes with potential roles in cortical lamination.
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25
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Davila RA, Harkins D, Currey L, Fraser J, Bowles J, Piper M. A simple, web-based repository for the management, access and analysis of micrographic images. J Mol Histol 2019; 50:573-580. [PMID: 31667690 DOI: 10.1007/s10735-019-09850-y] [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: 09/28/2019] [Accepted: 10/18/2019] [Indexed: 11/25/2022]
Abstract
Microscopy is advancing at a rapid pace, enabling high-speed, high-resolution analyses to be conducted in a wide range of cellular contexts. For example, the capacity to quickly capture high-resolution images from multiple optical sections over multiple channels with confocal microscopy has allowed researchers to gain deeper understanding of tissue morphology via techniques such as three-dimensional rendering, as have more recent advances such as lattice light sheet microscopy and superresolution structured illumination microscopy. With this, though, comes the challenge of storing, curating, analysing and sharing data. While there are ways in which this has been attempted previously, few approaches have provided a central repository in which all of these different aspects of microscopy can be seamlessly integrated. Here, we describe a web-based storage and analysis platform called Microndata, that enables relatively straightforward storage, annotation, tracking, analysis and multi-user access to micrographs. This easy to use tool will simplify and harmonise laboratory work flows, and, importantly, will provide a central storage repository that is readily accessed, even after the researcher responsible for capturing the images has left the laboratory. Microndata is open-source software, available at http://www.microndata.net/.
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Affiliation(s)
- Raul Ayala Davila
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Danyon Harkins
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Laura Currey
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, 4111, Australia
| | - James Fraser
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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26
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Saito K, Okamoto M, Watanabe Y, Noguchi N, Nagasaka A, Nishina Y, Shinoda T, Sakakibara A, Miyata T. Dorsal-to-Ventral Cortical Expansion Is Physically Primed by Ventral Streaming of Early Embryonic Preplate Neurons. Cell Rep 2019; 29:1555-1567.e5. [DOI: 10.1016/j.celrep.2019.09.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/11/2019] [Accepted: 09/25/2019] [Indexed: 01/08/2023] Open
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27
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Arai Y, Cwetsch AW, Coppola E, Cipriani S, Nishihara H, Kanki H, Saillour Y, Freret-Hodara B, Dutriaux A, Okada N, Okano H, Dehay C, Nardelli J, Gressens P, Shimogori T, D’Onofrio G, Pierani A. Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex. Cell Rep 2019; 29:645-658.e5. [DOI: 10.1016/j.celrep.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/12/2019] [Accepted: 09/04/2019] [Indexed: 10/25/2022] Open
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28
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Lin HC, Ko CY, Lee KH, Chen IH, Kao TJ, Chang WC, Hsu TI, Lee YC. E2f1 regulates the induction of promyelocytic leukemia zinc finger transcription in neuronal differentiation of pluripotent P19 embryonal carcinoma cells. Biochem Biophys Res Commun 2019; 512:629-634. [PMID: 30914194 DOI: 10.1016/j.bbrc.2019.03.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/10/2019] [Indexed: 10/27/2022]
Abstract
During brain development, the expression of promyelocytic leukemia zinc finger (Plzf) in neural stem cells is precisely controlled to maintain the balance between neural stem cell self-renewal and differentiation. However, the mechanism underlying transcriptional regulation of Plzf in neural stem cell is still unclear. Herein, using P19 embryonal carcinoma cells as a model, we observed that Plzf expression was induced in the P19-derived embryonic bodies, which enrich neural stem-like cell populations, as demonstrated by the expression of neural stem cell markers, Nestin and Sox2. We then characterized the Plzf promoter and identified two E2f1 binding sites (-755/-751 and -53/-49, the transcription start site was designated as +1) are important for the activation of Plzf promoter. Finally, we found that the induction of Plzf in the neural stem-like cells derived from pluripotent P19 cells is decrease by E2f1 knockdown. Taken together, we conclude that E2f1 is an important transcription factor that regulates Plzf transcription and may involve in maintaining the self-renewal ability of neural stem cells.
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Affiliation(s)
- Hsin-Chuan Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chiung-Yuan Ko
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - I-Han Chen
- Department of Chinese Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Tzu-Jen Kao
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chang Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-I Hsu
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
| | - Yi-Chao Lee
- PhD Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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29
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Ma CY, Madden P, Gontarz P, Wang T, Zhang B. FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. Front Genet 2019; 10:262. [PMID: 31001319 PMCID: PMC6454007 DOI: 10.3389/fgene.2019.00262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/08/2019] [Indexed: 11/23/2022] Open
Abstract
FeatSNP is an online tool and a curated database for exploring 81 million common SNPs’ potential functional impact on the human brain. FeatSNP uses the brain transcriptomes of the human population to improve functional annotation of human SNPs by integrating transcription factor binding prediction, public eQTL information, and brain specific epigenetic landscape, as well as information of Topologically Associating Domains (TADs). FeatSNP supports both single and batched SNP searching, and its interactive user interface enables users to explore the functional annotations and generate publication-quality visualization results. FeatSNP is freely available on the internet at FeatSNP.org with all major web browsers supported.
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Affiliation(s)
- Chun-Yu Ma
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Paul Gontarz
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Bo Zhang
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
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30
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Kast RJ, Levitt P. Precision in the development of neocortical architecture: From progenitors to cortical networks. Prog Neurobiol 2019; 175:77-95. [PMID: 30677429 PMCID: PMC6402587 DOI: 10.1016/j.pneurobio.2019.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 02/07/2023]
Abstract
Of all brain regions, the 6-layered neocortex has undergone the most dramatic changes in size and complexity during mammalian brain evolution. These changes, occurring in the context of a conserved set of organizational features that emerge through stereotypical developmental processes, are considered responsible for the cognitive capacities and sensory specializations represented within the mammalian clade. The modern experimental era of developmental neurobiology, spanning 6 decades, has deciphered a number of mechanisms responsible for producing the diversity of cortical neuron types, their precise connectivity and the role of gene by environment interactions. Here, experiments providing insight into the development of cortical projection neuron differentiation and connectivity are reviewed. This current perspective integrates discussion of classic studies and new findings, based on recent technical advances, to highlight an improved understanding of the neuronal complexity and precise connectivity of cortical circuitry. These descriptive advances bring new opportunities for studies related to the developmental origins of cortical circuits that will, in turn, improve the prospects of identifying pathogenic targets of neurodevelopmental disorders.
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Affiliation(s)
- Ryan J Kast
- Department of Pediatrics and Program in Developmental Neuroscience and Developmental Neurogenetics, The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90027, USA
| | - Pat Levitt
- Department of Pediatrics and Program in Developmental Neuroscience and Developmental Neurogenetics, The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90027, USA.
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31
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Selleri L, Zappavigna V, Ferretti E. 'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networks. Genes Dev 2019; 33:258-275. [PMID: 30824532 PMCID: PMC6411007 DOI: 10.1101/gad.318774.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pbx genes encode transcription factors that belong to the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. We have witnessed a surge in information about the roles of this gene family as leading actors in the transcriptional control of development. PBX proteins represent a clear example of how transcription factors can regulate developmental processes by combinatorial properties, acting within multimeric complexes to implement activation or repression of transcription depending on their interaction partners. Here, we revisit long-emphasized functions of PBX transcription factors as cofactors for HOX proteins, major architects of the body plan. We further discuss new knowledge on roles of PBX proteins in different developmental contexts as upstream regulators of Hox genes-as factors that interact with non-HOX proteins and can work independently of HOX-as well as potential pioneer factors. Committed to building a perfect body, PBX proteins govern regulatory networks that direct essential morphogenetic processes and organogenesis in vertebrate development. Perturbations of PBX-dependent networks can cause human congenital disease and cancer.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, University of California at San Francisco, San Francisco, California 94143, USA.,Institute of Human Genetics, University of California at San Francisco, San Francisco, California 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Orofacial Sciences, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elisabetta Ferretti
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Young M, Selleri L, Capellini TD. Genetics of scapula and pelvis development: An evolutionary perspective. Curr Top Dev Biol 2019; 132:311-349. [PMID: 30797513 PMCID: PMC6430119 DOI: 10.1016/bs.ctdb.2018.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
In tetrapods, the scapular and pelvic girdles perform the important function of anchoring the limbs to the trunk of the body and facilitating the movement of each appendage. This shared function, however, is one of relatively few similarities between the scapula and pelvis, which have significantly different morphologies, evolutionary histories, embryonic origins, and underlying genetic pathways. The scapula evolved in jawless fish prior to the pelvis, and its embryonic development is unique among bones in that it is derived from multiple progenitor cell populations, including the dermomyotome, somatopleure, and neural crest. Conversely, the pelvis evolved several million years later in jawed fish, and it develops from an embryonic somatopleuric cell population. The genetic networks controlling the formation of the pelvis and scapula also share similarities and differences, with a number of genes shaping only one or the other, while other gene products such as PBX transcription factors act as hierarchical developmental regulators of both girdle structures. Here, we provide a detailed review of the cellular processes and genetic networks underlying pelvis and scapula formation in tetrapods, while also highlighting unanswered questions about girdle evolution and development.
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Affiliation(s)
- Mariel Young
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California, Institute of Human Genetics, San Francisco, CA, United States; Program in Craniofacial Biology, Department of Anatomy, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California, Institute of Human Genetics, San Francisco, CA, United States.
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States; Broad Institute of Harvard and MIT, Cambridge, MA, United States.
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Ma CY, Madden P, Gontarz P, Wang T, Zhang B. FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. Front Genet 2019. [PMID: 31001319 DOI: 10.3389/fgene.2019.00262/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
FeatSNP is an online tool and a curated database for exploring 81 million common SNPs' potential functional impact on the human brain. FeatSNP uses the brain transcriptomes of the human population to improve functional annotation of human SNPs by integrating transcription factor binding prediction, public eQTL information, and brain specific epigenetic landscape, as well as information of Topologically Associating Domains (TADs). FeatSNP supports both single and batched SNP searching, and its interactive user interface enables users to explore the functional annotations and generate publication-quality visualization results. FeatSNP is freely available on the internet at FeatSNP.org with all major web browsers supported.
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Affiliation(s)
- Chun-Yu Ma
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Paul Gontarz
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Bo Zhang
- Center of Regenerative Medicine, Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
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Welsh IC, Hart J, Brown JM, Hansen K, Rocha Marques M, Aho RJ, Grishina I, Hurtado R, Herzlinger D, Ferretti E, Garcia-Garcia MJ, Selleri L. Pbx loss in cranial neural crest, unlike in epithelium, results in cleft palate only and a broader midface. J Anat 2018; 233:222-242. [PMID: 29797482 PMCID: PMC6036936 DOI: 10.1111/joa.12821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 01/21/2023] Open
Abstract
Orofacial clefting represents the most common craniofacial birth defect. Cleft lip with or without cleft palate (CL/P) is genetically distinct from cleft palate only (CPO). Numerous transcription factors (TFs) regulate normal development of the midface, comprising the premaxilla, maxilla and palatine bones, through control of basic cellular behaviors. Within the Pbx family of genes encoding Three Amino-acid Loop Extension (TALE) homeodomain-containing TFs, we previously established that in the mouse, Pbx1 plays a preeminent role in midfacial morphogenesis, and Pbx2 and Pbx3 execute collaborative functions in domains of coexpression. We also reported that Pbx1 loss from cephalic epithelial domains, on a Pbx2- or Pbx3-deficient background, results in CL/P via disruption of a regulatory network that controls apoptosis at the seam of frontonasal and maxillary process fusion. Conversely, Pbx1 loss in cranial neural crest cell (CNCC)-derived mesenchyme on a Pbx2-deficient background results in CPO, a phenotype not yet characterized. In this study, we provide in-depth analysis of PBX1 and PBX2 protein localization from early stages of midfacial morphogenesis throughout development of the secondary palate. We further establish CNCC-specific roles of PBX TFs and describe the developmental abnormalities resulting from their loss in the murine embryonic secondary palate. Additionally, we compare and contrast the phenotypes arising from PBX1 loss in CNCC with those caused by its loss in the epithelium and show that CNCC-specific Pbx1 deletion affects only later secondary palate morphogenesis. Moreover, CNCC mutants exhibit perturbed rostro-caudal organization and broadening of the midfacial complex. Proliferation defects are pronounced in CNCC mutants at gestational day (E)12.5, suggesting altered proliferation of mutant palatal progenitor cells, consistent with roles of PBX factors in maintaining progenitor cell state. Although the craniofacial skeletal abnormalities in CNCC mutants do not result from overt patterning defects, osteogenesis is delayed, underscoring a critical role of PBX factors in CNCC morphogenesis and differentiation. Overall, the characterization of tissue-specific Pbx loss-of-function mouse models with orofacial clefting establishes these strains as unique tools to further dissect the complexities of this congenital craniofacial malformation. This study closely links PBX TALE homeodomain proteins to the variation in maxillary shape and size that occurs in pathological settings and during evolution of midfacial morphology.
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Affiliation(s)
- Ian C Welsh
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - James Hart
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Joel M Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marcelo Rocha Marques
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Robert J Aho
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Irina Grishina
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Romulo Hurtado
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Doris Herzlinger
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Elisabetta Ferretti
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | | | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
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Bertacchi M, Parisot J, Studer M. The pleiotropic transcriptional regulator COUP-TFI plays multiple roles in neural development and disease. Brain Res 2018; 1705:75-94. [PMID: 29709504 DOI: 10.1016/j.brainres.2018.04.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 12/23/2022]
Abstract
Transcription factors are expressed in a dynamic fashion both in time and space during brain development, and exert their roles by activating a cascade of multiple target genes. This implies that understanding the precise function of a transcription factor becomes a challenging task. In this review, we will focus on COUP-TFI (or NR2F1), a nuclear receptor belonging to the superfamily of the steroid/thyroid hormone receptors, and considered to be one of the major transcriptional regulators orchestrating cortical arealization, cell-type specification and maturation. Recent data have unraveled the multi-faceted functions of COUP-TFI in the development of several mouse brain structures, including the neocortex, hippocampus and ganglionic eminences. Despite NR2F1 mutations and deletions in humans have been linked to a complex neurodevelopmental disease mainly associated to optic atrophy and intellectual disability, its role during the formation of the retina and optic nerve remains unclear. In light of its major influence in cortical development, we predict that its haploinsufficiency might be the cause of other cognitive diseases, not identified so far. Mouse models offer a unique opportunity of dissecting COUP-TFI function in different regions during brain assembly; hence, the importance of comparing and discussing common points linking mouse models to human patients' symptoms.
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Affiliation(s)
- Michele Bertacchi
- Université Côte d'Azur, CNRS, Inserm, iBV - Institut de Biologie Valrose, 06108 Nice, France.
| | - Josephine Parisot
- Université Côte d'Azur, CNRS, Inserm, iBV - Institut de Biologie Valrose, 06108 Nice, France
| | - Michèle Studer
- Université Côte d'Azur, CNRS, Inserm, iBV - Institut de Biologie Valrose, 06108 Nice, France.
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Slavotinek A, Risolino M, Losa M, Cho MT, Monaghan KG, Schneidman-Duhovny D, Parisotto S, Herkert JC, Stegmann APA, Miller K, Shur N, Chui J, Muller E, DeBrosse S, Szot JO, Chapman G, Pachter NS, Winlaw DS, Mendelsohn BA, Dalton J, Sarafoglou K, Karachunski PI, Lewis JM, Pedro H, Dunwoodie SL, Selleri L, Shieh J. De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects. Hum Mol Genet 2017; 26:4849-4860. [PMID: 29036646 PMCID: PMC6455034 DOI: 10.1093/hmg/ddx363] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads. Clinical findings similar to those in Pbx mutant mice were observed in all patients with varying expressivity and severity, including external ear anomalies, abnormal branchial arch derivatives, heart malformations, diaphragmatic hernia, renal hypoplasia and ambiguous genitalia. All patients but one had developmental delays. Previously reported patients with congenital anomalies affecting the kidney and urinary tract exhibited deletions and loss of function variants in PBX1. The sequence variants in our cases included missense substitutions adjacent to the PBX1 homeodomain (p.Arg184Pro, p.Met224Lys, and p.Arg227Pro) or within the homeodomain (p.Arg234Pro, and p.Arg235Gln), whereas p.Ser262Glnfs*2, and p.Arg288* yielded truncated PBX1 proteins. Functional studies on five PBX1 sequence variants revealed perturbation of intrinsic, PBX-dependent transactivation ability and altered nuclear translocation, suggesting abnormal interactions between mutant PBX1 proteins and wild-type TALE or HOX cofactors. It is likely that the mutations directly affect the transcription of PBX1 target genes to impact embryonic development. We conclude that deleterious sequence variants in PBX1 cause intellectual disability and pleiotropic malformations resembling those in Pbx1 mutant mice, arguing for strong conservation of gene function between these two species.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Maurizio Risolino
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Marta Losa
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biochemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarah Parisotto
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Johanna C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Jacqueline Chui
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Eric Muller
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Suzanne DeBrosse
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Justin O Szot
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Gavin Chapman
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - David S Winlaw
- University of Sydney, Medical School, Sydney, NSW, Australia
- Heart Centre for Children, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Joline Dalton
- Paul and Shelia Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Kyriakie Sarafoglou
- Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | | | - Jane M Lewis
- Department of Urology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Helio Pedro
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
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de Juan Romero C, Borrell V. Genetic maps and patterns of cerebral cortex folding. Curr Opin Cell Biol 2017; 49:31-37. [PMID: 29227862 DOI: 10.1016/j.ceb.2017.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/17/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Folding of the cerebral cortex during brain development is a complex process that depends on the orchestrated action of a number of factors, including generation and proliferation of basal progenitor cells, and the radial migration of neurons. Patterns of primary cortical folding are stereotyped between individuals and across phylogeny, reflecting a strong genetic regulation of the underlying cellular mechanisms. Here we summarize recent findings on cellular and genetic mechanisms regulating this fascinating process that underlies expansion and functional complexification of the mammalian cerebral cortex.
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Affiliation(s)
- Camino de Juan Romero
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain.
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38
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Artegiani B, Lyubimova A, Muraro M, van Es JH, van Oudenaarden A, Clevers H. A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche. Cell Rep 2017; 21:3271-3284. [DOI: 10.1016/j.celrep.2017.11.050] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/09/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
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Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. Neuron 2017; 92:59-74. [PMID: 27710791 DOI: 10.1016/j.neuron.2016.09.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/22/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
Elucidating the transcriptional circuitry controlling forebrain development requires an understanding of enhancer activity and regulation. We generated stable transgenic mouse lines that express CreERT2 and GFP from ten different enhancer elements with activity in distinct domains within the embryonic basal ganglia. We used these unique tools to generate a comprehensive regional fate map of the mouse subpallium, including sources for specific subtypes of amygdala neurons. We then focused on deciphering transcriptional mechanisms that control enhancer activity. Using machine-learning computations, in vivo chromosomal occupancy of 13 transcription factors that regulate subpallial patterning and differentiation and analysis of enhancer activity in Dlx1/2 and Lhx6 mutants, we elucidated novel molecular mechanisms that regulate region-specific enhancer activity in the developing brain. Thus, these subpallial enhancer transgenic lines are data and tool resources to study transcriptional regulation of GABAergic cell fate.
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40
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Hau AC, Grebbin BM, Agoston Z, Anders-Maurer M, Müller T, Groß A, Kolb J, Langer JD, Döring C, Schulte D. MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1. J Cell Biol 2017; 216:2715-2729. [PMID: 28739678 PMCID: PMC5584172 DOI: 10.1083/jcb.201701154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/08/2017] [Accepted: 06/14/2017] [Indexed: 11/22/2022] Open
Abstract
PARP1/ARTD1 induces chromatin opening by posttranslational modification of the linker histone H1, but how PARP1 is targeted to physiologically correct gene loci is poorly understood. Hau et al. show that in differentiating neurons, PARP1 is rapidly and specifically recruited to a neuron-specific promoter by the atypical homeodomain protein MEIS2. Pre–B-cell leukemia homeobox (PBX) and myeloid ecotropic viral integration site (MEIS) proteins control cell fate decisions in many physiological and pathophysiological contexts, but how these proteins function mechanistically remains poorly defined. Focusing on the first hours of neuronal differentiation of adult subventricular zone–derived stem/progenitor cells, we describe a sequence of events by which PBX-MEIS facilitates chromatin accessibility of transcriptionally inactive genes: In undifferentiated cells, PBX1 is bound to the H1-compacted promoter/proximal enhancer of the neuron-specific gene doublecortin (Dcx). Once differentiation is induced, MEIS associates with chromatin-bound PBX1, recruits PARP1/ARTD1, and initiates PARP1-mediated eviction of H1 from the chromatin fiber. These results for the first time link MEIS proteins to PARP-regulated chromatin dynamics and provide a mechanistic basis to explain the profound cellular changes elicited by these proteins.
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Affiliation(s)
- Ann-Christin Hau
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Britta Moyo Grebbin
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Zsuzsa Agoston
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Marie Anders-Maurer
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Tamara Müller
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Anja Groß
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Jasmine Kolb
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Claudia Döring
- Senckenberg Institute of Pathology, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology, Edinger Institute, University Hospital Frankfurt, J.W. Goethe University, Frankfurt, Germany
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41
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Le Tanno P, Breton J, Bidart M, Satre V, Harbuz R, Ray PF, Bosson C, Dieterich K, Jaillard S, Odent S, Poke G, Beddow R, Digilio MC, Novelli A, Bernardini L, Pisanti MA, Mackenroth L, Hackmann K, Vogel I, Christensen R, Fokstuen S, Béna F, Amblard F, Devillard F, Vieville G, Apostolou A, Jouk PS, Guebre-Egziabher F, Sartelet H, Coutton C. PBX1 haploinsufficiency leads to syndromic congenital anomalies of the kidney and urinary tract (CAKUT) in humans. J Med Genet 2017; 54:502-510. [PMID: 28270404 DOI: 10.1136/jmedgenet-2016-104435] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/03/2017] [Accepted: 01/17/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) represent a significant healthcare burden since it is the primary cause of chronic kidney in children. CNVs represent a recurrent molecular cause of CAKUT but the culprit gene remains often elusive. Our study aimed to define the gene responsible for CAKUT in patients with an 1q23.3q24.1 microdeletion. METHODS We describe eight patients presenting with CAKUT carrying an 1q23.3q24.1 microdeletion as identified by chromosomal microarray analysis (CMA). Clinical features were collected, especially the renal and urinary tract phenotype, and extrarenal features. We characterised PBX1 expression and localisation in fetal and adult kidneys using quantitative RT-PCR and immunohistochemistry. RESULTS We defined a 276-kb minimal common region (MCR) that only overlaps with the PBX1 gene. All eight patients presented with syndromic CAKUT. CAKUT were mostly bilateral renal hypoplasia (75%). The most frequent extrarenal symptoms were developmental delay and ear malformations. We demonstrate that PBX1 is strongly expressed in fetal kidneys and brain and expression levels decreased in adult samples. In control fetal kidneys, PBX1 was localised in nuclei of medullary, interstitial and mesenchymal cells, whereas it was present in endothelial cells in adult kidneys. CONCLUSIONS Our results indicate that PBX1 haploinsufficiency leads to syndromic CAKUT as supported by the Pbx1-null mice model. Correct PBX1 dosage appears to be critical for normal nephrogenesis and seems important for brain development in humans. CMA should be recommended in cases of fetal renal anomalies to improve genetic counselling and pregnancy management.
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Affiliation(s)
- Pauline Le Tanno
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Julie Breton
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Marie Bidart
- Université Grenoble Alpes, Grenoble, France
- UF Clinatec, Pôle Recherche, CHU Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
| | - Radu Harbuz
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Pierre F Ray
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Caroline Bosson
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Klaus Dieterich
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Sylvie Jaillard
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, Université de Rennes, Rennes, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du Développement CLAD-Ouest, Hôpital Sud, Rennes, France
| | - Gemma Poke
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | - Rachel Beddow
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | | | - Antonio Novelli
- Department of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Laura Bernardini
- Mendel Laboratory IRCCS "Casa Sollievo della Sofferenza" Hospital, Foggia, Italy
| | | | - Luisa Mackenroth
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Siv Fokstuen
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Frédérique Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Florence Amblard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Francoise Devillard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Gaelle Vieville
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Alexia Apostolou
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | | | - Hervé Sartelet
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Charles Coutton
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Université Grenoble Alpes, Grenoble, France
- Génétique et Procréation, Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
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Niu Y, Sengupta M, Titov AA, Choi SC, Morel L. The PBX1 lupus susceptibility gene regulates CD44 expression. Mol Immunol 2017; 85:148-154. [PMID: 28257976 PMCID: PMC5389453 DOI: 10.1016/j.molimm.2017.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/22/2017] [Indexed: 11/17/2022]
Abstract
PBX1-d is novel splice isoform of pre-B-cell leukemia homeobox 1 (PBX1) that lacks its DNA-binding and Hox-binding domains, and functions as a dominant negative. We have shown that PBX1-d expression in CD4+ T cells is associated with systemic lupus erythematosus (SLE) in a mouse model as well as in human subjects. More specifically, PBX1-d expression leads to the production of autoreactive activated CD4+ T cells, a reduced frequency and function of Foxp3+ regulatory T (Treg) cells and an expansion of follicular helper T (Tfh) cells. Very little is known about the function of PBX1 in T cells, except that it directly regulates the expression of miRNAs associated with Treg and Tfh homeostasis. In the present study, we show that PBX1 directly regulated the expression of CD44, a marker of T cell activation. Two PBX1 binding sites in the promoter directly regulated CD44 expression, with PBX1-d driving a higher expression than the normal isoform PBX1-b. In addition, mutations in each of the two binding sites had different effects of PBX1-b and PBX1-d. Finally, we showed that an enhanced recruitment of co-factor MEIS by PBX1-d over PBX1-b, while there was no difference for co-factor PREP1 recruitment. Therefore, this study demonstrates that the lupus-associated PBX1-d isoform directly transactivates CD44, a marker of CD44 activation and memory, and that it has different DNA binding and co-factor recruitment relative to the normal isoform. Taken together, these results confirm that PBX1 directly regulates genes related to T cell activation and shows that the lupus-associated isoform PBX1-d has unique molecular functions.
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Affiliation(s)
- Yuxin Niu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610-0275, USA
| | - Mayami Sengupta
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610-0275, USA
| | - Anton A Titov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610-0275, USA
| | - Seung-Chul Choi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610-0275, USA
| | - Laurence Morel
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610-0275, USA.
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Riedhammer KM, Siegel C, Alhaddad B, Montoya C, Kovacs-Nagy R, Wagner M, Meitinger T, Hoefele J. Identification of a Novel Heterozygous De Novo 7-bp Frameshift Deletion in PBX1 by Whole-Exome Sequencing Causing a Multi-Organ Syndrome Including Bilateral Dysplastic Kidneys and Hypoplastic Clavicles. Front Pediatr 2017; 5:251. [PMID: 29226118 PMCID: PMC5705563 DOI: 10.3389/fped.2017.00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/07/2017] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Congenital anomalies of the kidney and urinary tract (CAKUT) represent the primary cause of chronic kidney disease in children. Many genes have been attributed to the genesis of this disorder. Recently, haploinsufficiency of PBX1 caused by microdeletions has been shown to result in bilateral renal hypoplasia and other organ malformations. MATERIALS AND METHODS Here, we report on a 14-year-old male patient with congenital bilateral dysplastic kidneys, cryptorchidism, hypoplastic clavicles, developmental delay, impaired intelligence, and minor dysmorphic features. Presuming a syndromic origin, we performed SNP array analysis to scan for large copy number variations (CNVs) followed by whole-exome sequencing (WES). Sanger sequencing was done to confirm the variant's de novo status. RESULTS SNP array analysis did not reveal any microdeletions or -duplications larger than 50 or 100 kb, respectively. WES identified a novel heterozygous 7-bp frameshift deletion in PBX1 (c.413_419del, p.Gly138Valfs*40) resulting in a loss-of-function. The de novo status could be confirmed by Sanger sequencing. DISCUSSION By WES, we identified a novel heterozygous de novo 7-bp frameshift deletion in PBX1. Our findings expand the spectrum of causative variants in PBX1-related CAKUT. In this case, WES proved to be the apt technique to detect the variant responsible for the patient's phenotype, as single gene testing is not feasible given the multitude of genes involved in CAKUT and SNP array analysis misses rare single-nucleotide variants and small Indels.
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Affiliation(s)
- Korbinian Maria Riedhammer
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Corinna Siegel
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carmen Montoya
- KfH Center of Pediatric Nephrology, Children's Hospital Munich Schwabing, Munich, Germany
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
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Hanley O, Zewdu R, Cohen LJ, Jung H, Lacombe J, Philippidou P, Lee DH, Selleri L, Dasen JS. Parallel Pbx-Dependent Pathways Govern the Coalescence and Fate of Motor Columns. Neuron 2016; 91:1005-1020. [PMID: 27568519 DOI: 10.1016/j.neuron.2016.07.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/20/2016] [Accepted: 07/14/2016] [Indexed: 01/08/2023]
Abstract
The clustering of neurons sharing similar functional properties and connectivity is a common organizational feature of vertebrate nervous systems. Within motor networks, spinal motor neurons (MNs) segregate into longitudinally arrayed subtypes, establishing a central somatotopic map of peripheral target innervation. MN organization and connectivity relies on Hox transcription factors expressed along the rostrocaudal axis; however, the developmental mechanisms governing the orderly arrangement of MNs are largely unknown. We show that Pbx genes, which encode Hox cofactors, are essential for the segregation and clustering of neurons within motor columns. In the absence of Pbx1 and Pbx3 function, Hox-dependent programs are lost and the remaining MN subtypes are unclustered and disordered. Identification of Pbx gene targets revealed an unexpected and apparently Hox-independent role in defining molecular features of dorsally projecting medial motor column (MMC) neurons. These results indicate Pbx genes act in parallel genetic pathways to orchestrate neuronal subtype differentiation, connectivity, and organization.
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Affiliation(s)
- Olivia Hanley
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Rediet Zewdu
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Lisa J Cohen
- Genome Technology Center, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Heekyung Jung
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Julie Lacombe
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Polyxeni Philippidou
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - David H Lee
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jeremy S Dasen
- Neuroscience Institute and Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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Grebbin BM, Hau AC, Groß A, Anders-Maurer M, Schramm J, Koss M, Wille C, Mittelbronn M, Selleri L, Schulte D. Pbx1 is required for adult subventricular zone neurogenesis. Development 2016; 143:2281-91. [PMID: 27226325 DOI: 10.1242/dev.128033] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 05/15/2016] [Indexed: 12/22/2022]
Abstract
TALE-homeodomain proteins function as components of heteromeric complexes that contain one member each of the PBC and MEIS/PREP subclasses. We recently showed that MEIS2 cooperates with the neurogenic transcription factor PAX6 in the control of adult subventricular zone (SVZ) neurogenesis in rodents. Expression of the PBC protein PBX1 in the SVZ has been reported, but its functional role(s) has not been investigated. Using a genetic loss-of-function mouse model, we now show that Pbx1 is an early regulator of SVZ neurogenesis. Targeted deletion of Pbx1 by retroviral transduction of Cre recombinase into Pbx2-deficient SVZ stem and progenitor cells carrying floxed alleles of Pbx1 significantly reduced the production of neurons and increased the generation of oligodendrocytes. Loss of Pbx1 expression in neuronally committed neuroblasts in the rostral migratory stream in a Pbx2 null background, by contrast, severely compromised cell survival. By chromatin immunoprecipitation from endogenous tissues or isolated cells, we further detected PBX1 binding to known regulatory regions of the neuron-specific genes Dcx and Th days or even weeks before the respective genes are expressed during the normal program of SVZ neurogenesis, suggesting that PBX1 might act as a priming factor to mark these genes for subsequent activation. Collectively, our results establish that PBX1 regulates adult neural cell fate determination in a manner beyond that of its heterodimerization partner MEIS2.
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Affiliation(s)
- Britta Moyo Grebbin
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Ann-Christin Hau
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Anja Groß
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Marie Anders-Maurer
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Jasmine Schramm
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Matthew Koss
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Christoph Wille
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Michel Mittelbronn
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), J. W. Goethe University Medical School, German Cancer Consortium (DKTK), Heinrich-Hoffmann Str. 7, Frankfurt D-60528, Germany
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Dennis D, Picketts D, Slack RS, Schuurmans C. Forebrain neurogenesis: From embryo to adult. TRENDS IN DEVELOPMENTAL BIOLOGY 2016; 9:77-90. [PMID: 28367004 PMCID: PMC5373848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A satellite symposium to the Canadian Developmental Biology Conference 2016 was held on March 16-17, 2016 in Banff, Alberta, Canada, entitled Forebrain Neurogenesis: From embryo to adult. The Forebrain Neurogenesis symposium was a focused, high-intensity meeting, bringing together the top Canadian and international researchers in the field. This symposium reported the latest breaking news, along with 'state of the art' techniques to answer fundamental questions in developmental neurobiology. Topics covered ranged from stem cell regulation to neurocircuitry development, culminating with a session focused on neuropsychiatric disorders. Understanding the underlying causes of neurodevelopmental disorders such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD) is of great interest as diagnoses of these conditions are climbing at alarming rates. For instance, in 2012, the Centers for Disease Control reported that the prevalence rate of ASD in the U.S. was 1 in 88; while more recent data indicate that the number is as high as 1 in 68 (Centers for Disease Control and Prevention MMWR Surveillance Summaries. Vol. 63. No. 2). Similarly, the incidence of ASD is on the rise in Canada, increasing from 1 in 150 in 2000 to 1 in 63 in 2012 in southeastern Ontario (Centers for Disease Control and Prevention). Currently very little is known regarding the deficits underlying these neurodevelopmental conditions. Moreover, the development of effective therapies is further limited by major gaps in our understanding of the fundamental processes that regulate forebrain development and adult neurogenesis. The Forebrain Neurogenesis satellite symposium was thus timely, and it played a key role in advancing research in this important field, while also fostering collaborations between international leaders, and inspiring young researchers.
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Affiliation(s)
- Daniel Dennis
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute (HBI), Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta
| | - David Picketts
- Ottawa Hospital Research Institute, Ottawa, Ontario; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario
| | - Ruth S Slack
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario
| | - Carol Schuurmans
- Department of Biochemistry and Molecular Biology, Hotchkiss Brain Institute (HBI), Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, Alberta; Sunnybrook Research Institute, Biological Sciences, Toronto, Ontario, Canada
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