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Tian Y, Wu X, Luo S, Xiong D, Liu R, Hu L, Yuan Y, Shi G, Yao J, Huang Z, Fu F, Yang X, Tang Z, Zhang J, Hu K. A multi-omic single-cell landscape of cellular diversification in the developing human cerebral cortex. Comput Struct Biotechnol J 2024; 23:2173-2189. [PMID: 38827229 PMCID: PMC11141146 DOI: 10.1016/j.csbj.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.
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Affiliation(s)
- Yuhan Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Songhao Luo
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiwei Huang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Fang Fu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Yang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Kunhua Hu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Public Platform Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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2
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An J, Yang H, Park SM, Chwae YJ, Joe EH. The LRRK2-G2019S mutation attenuates repair of brain injury partially by reducing the release of osteopontin-containing monocytic exosome-like vesicles. Neurobiol Dis 2024; 197:106528. [PMID: 38740348 DOI: 10.1016/j.nbd.2024.106528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Brain injury has been suggested as a risk factor for neurodegenerative diseases. Accordingly, defects in the brain's intrinsic capacity to repair injury may result in the accumulation of damage and a progressive loss of brain function. The G2019S (GS) mutation in LRRK2 (leucine rich repeat kinase 2) is the most prevalent genetic alteration in Parkinson's disease (PD). Here, we sought to investigate how this LRRK2-GS mutation affects repair of the injured brain. METHODS Brain injury was induced by stereotaxic injection of ATP, a damage-associated molecular pattern (DAMP) component, into the striatum of wild-type (WT) and LRRK2-GS mice. Effects of the LRRK2-GS mutation on brain injury and the recovery from injury were examined by analyzing the molecular and cellular behavior of neurons, astrocytes, and monocytes. RESULTS Damaged neurons express osteopontin (OPN), a factor associated with brain repair. Following ATP-induced damage, monocytes entered injured brains, phagocytosing damaged neurons and producing exosome-like vesicles (EVs) containing OPN through activation of the inflammasome and subsequent pyroptosis. Following EV production, neurons and astrocytes processes elongated towards injured cores. In LRRK2-GS mice, OPN expression and monocytic pyroptosis were decreased compared with that in WT mice, resulting in diminished release of OPN-containing EVs and attenuated elongation of neuron and astrocyte processes. In addition, exosomes prepared from injured LRRK2-GS brains induced neurite outgrowth less efficiently than those from injured WT brains. CONCLUSIONS The LRRK2-GS mutation delays repair of injured brains through reduced expression of OPN and diminished release of OPN-containing EVs from monocytes. These findings suggest that the LRRK2-GS mutation may promote the development of PD by delaying the repair of brain injury.
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Affiliation(s)
- Jiawei An
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Department of Pharmacology, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Center for Convergence Research of Neurological Disorders, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea
| | - Haijie Yang
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Department of Pharmacology, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Center for Convergence Research of Neurological Disorders, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea
| | - Sang Myun Park
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Department of Pharmacology, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Center for Convergence Research of Neurological Disorders, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea
| | - Yong-Joon Chwae
- Department of Microbiology, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea
| | - Eun-Hye Joe
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Department of Pharmacology, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea; Center for Convergence Research of Neurological Disorders, Ajou University School of Medicine, Suwon, Kyunggi-do 16499, Republic of Korea.
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3
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Poon JYY, Mok MTS, Ho SKL, Cheng SSW, Lo IFM, Luk HM. A de novo pathogenic variant in neuronal differentiation factor 2 in a Chinese patient with early infantile epileptic encephalopathy. Clin Dysmorphol 2024; 33:128-133. [PMID: 38818821 DOI: 10.1097/mcd.0000000000000498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
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4
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Frank CE, Sadeghi J, Heath DD, Semeniuk CAD. Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha). GENES, BRAIN, AND BEHAVIOR 2024; 23:e12898. [PMID: 38817102 PMCID: PMC11140169 DOI: 10.1111/gbb.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]
Abstract
Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g., improved immune response, growth, and metabolism), we explored probiotic supplementation (mixture of Bifidobacterium, Lactobacillus, and Lactococcus), to overcome drawbacks. We first examined fish gut bacterial community composition using 16S metabarcoding (via principal coordinate analyses and PERMANOVA) and determined probiotics significantly impacted gut bacteria composition (p = 0.001). Secondly, we examined how a genomic disruptor (triploidy) and diet supplements (probiotics) impact gene transcription and behavioral profiles of hatchery-reared Chinook salmon (Oncorhynchus tshawytscha). Juveniles from four treatment groups (diploid-regular feed, diploid-probiotic feed, triploid-regular feed, and triploid-probiotic feed; n = 360) underwent behavioral assays to test activity, exploration, neophobia, predator evasion, aggression/sociality, behavioral sensitivity, and flexibility. In these fish, transcriptional profiles for genes associated with neural functions (neurogenesis/synaptic plasticity) and biomarkers for stress response and development (growth/appetite) were (i) examined across treatments and (ii) used to describe behavioral phenotypes via principal component analyses and general linear mixed models. Triploids exhibited a more active behavioral profile (p = 0.002), and those on a regular diet had greater Neuropeptide Y transcription (p = 0.02). A growth gene (early growth response protein 1, p = 0.02) and long-term neural development genes (neurogenic differentiation factor, p = 0.003 and synaptysomal-associated protein 25-a, p = 0.005) impacted activity and reactionary profiles, respectively. Overall, our probiotic treatment did not compensate for triploidy. Our research highlights novel applications of behavioral transcriptomics for identifying candidate genes and dynamic, mechanistic associations with complex behavioral repertoires.
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Affiliation(s)
- Chelsea E. Frank
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
| | - Javad Sadeghi
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
| | - Daniel D. Heath
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
| | - Christina A. D. Semeniuk
- Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
- Great Lakes Institute for Environmental ResearchUniversity of WindsorWindsorOntarioCanada
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Kulatunga DCM, Ranaraja U, Kim EY, Kim RE, Kim DE, Ji KB, Kim MK. A novel APP splice variant-dependent marker system to precisely demarcate maturity in SH-SY5Y cell-derived neurons. Sci Rep 2024; 14:12113. [PMID: 38802572 PMCID: PMC11130256 DOI: 10.1038/s41598-024-63005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
SH-SY5Y, a neuroblastoma cell line, can be converted into mature neuronal phenotypes, characterized by the expression of mature neuronal and neurotransmitter markers. However, the mature phenotypes described across multiple studies appear inconsistent. As this cell line expresses common neuronal markers after a simple induction, there is a high chance of misinterpreting its maturity. Therefore, sole reliance on common neuronal markers is presumably inadequate. The Alzheimer's disease (AD) central gene, amyloid precursor protein (APP), has shown contrasting transcript variant dynamics in various cell types. We differentiated SH-SY5Y cells into mature neuron-like cells using a concise protocol and observed the upregulation of total APP throughout differentiation. However, APP transcript variant-1 was upregulated only during the early to middle stages of differentiation and declined in later stages. We identified the maturity state where this post-transcriptional shift occurs, terming it "true maturity." At this stage, we observed a predominant expression of mature neuronal and cholinergic markers, along with a distinct APP variant pattern. Our findings emphasize the necessity of using a differentiation state-sensitive marker system to precisely characterize SH-SY5Y differentiation. Moreover, this study offers an APP-guided, alternative neuronal marker system to enhance the accuracy of the conventional markers.
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Affiliation(s)
- D Chanuka M Kulatunga
- Laboratory of Animal Reproduction and Physiology, College of Agriculture and Life Sciences, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Umanthi Ranaraja
- Laboratory of Animal Reproduction and Physiology, College of Agriculture and Life Sciences, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | | | | | - Dong Ern Kim
- Laboratory of Animal Reproduction and Physiology, College of Agriculture and Life Sciences, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Kuk Bin Ji
- Laboratory of Animal Reproduction and Physiology, College of Agriculture and Life Sciences, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Min Kyu Kim
- Laboratory of Animal Reproduction and Physiology, College of Agriculture and Life Sciences, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea.
- MK Biotech Inc., Daejeon, Republic of Korea.
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Tian T, Zhang J, Lin X, Wei Z, Hakonarson H. Dependency-aware deep generative models for multitasking analysis of spatial omics data. Nat Methods 2024:10.1038/s41592-024-02257-y. [PMID: 38783067 DOI: 10.1038/s41592-024-02257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/25/2024] [Indexed: 05/25/2024]
Abstract
Spatially resolved transcriptomics (SRT) technologies have significantly advanced biomedical research, but their data analysis remains challenging due to the discrete nature of the data and the high levels of noise, compounded by complex spatial dependencies. Here, we propose spaVAE, a dependency-aware, deep generative spatial variational autoencoder model that probabilistically characterizes count data while capturing spatial correlations. spaVAE introduces a hybrid embedding combining a Gaussian process prior with a Gaussian prior to explicitly capture spatial correlations among spots. It then optimizes the parameters of deep neural networks to approximate the distributions underlying the SRT data. With the approximated distributions, spaVAE can contribute to several analytical tasks that are essential for SRT data analysis, including dimensionality reduction, visualization, clustering, batch integration, denoising, differential expression, spatial interpolation, resolution enhancement and identification of spatially variable genes. Moreover, we have extended spaVAE to spaPeakVAE and spaMultiVAE to characterize spatial ATAC-seq (assay for transposase-accessible chromatin using sequencing) data and spatial multi-omics data, respectively.
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Affiliation(s)
- Tian Tian
- School of Computer Science, National Engineering Research Center for Multimedia Software, Institute of Artificial Intelligence, and Hubei Key Laboratory of Multimedia and Network Communication Engineering, Wuhan University, Wuhan, Hubei, China
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jie Zhang
- National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, Jiangsu, China
| | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA.
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Ducza L, Gaál B. The Neglected Sibling: NLRP2 Inflammasome in the Nervous System. Aging Dis 2024; 15:1006-1028. [PMID: 38722788 PMCID: PMC11081174 DOI: 10.14336/ad.2023.0926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/26/2023] [Indexed: 05/13/2024] Open
Abstract
While classical NOD-like receptor pyrin domain containing protein 1 (NLRP1) and NLRP3 inflammasomal proteins have been extensively investigated, the contribution of NLRP2 is still ill-defined in the nervous system. Given the putative significance of NLRP2 in orchestrating neuroinflammation, further inquiry is needed to gain a better understanding of its connectome, hence its specific targeting may hold a promising therapeutic implication. Therefore, bioinformatical approach for extracting information, specifically in the context of neuropathologies, is also undoubtedly preferred. To the best of our knowledge, there is no review study selectively targeting only NLRP2. Increasing, but still fragmentary evidence should encourage researchers to thoroughly investigate this inflammasome in various animal- and human models. Taken together, herein we aimed to review the current literature focusing on the role of NLRP2 inflammasome in the nervous system and more importantly, we provide an algorithm-based protein network of human NLRP2 for elucidating potentially valuable molecular partnerships that can be the beginning of a new discourse and future therapeutic considerations.
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Affiliation(s)
- László Ducza
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Hungary, Hungary
| | - Botond Gaál
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Hungary, Hungary
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8
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Liu Y, Chen X, Ma Y, Song C, Ma J, Chen C, Su J, Ma L, Saiyin H. Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Mol Psychiatry 2024:10.1038/s41380-024-02562-0. [PMID: 38654124 DOI: 10.1038/s41380-024-02562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Pathogenic mutant huntingtin (mHTT) infiltrates the adult Huntington's disease (HD) brain and impairs fetal corticogenesis. However, most HD animal models rarely recapitulate neuroanatomical alterations in adult HD and developing brains. Thus, the human cortical organoid (hCO) is an alternative approach to decode mHTT pathogenesis precisely during human corticogenesis. Here, we replicated the altered corticogenesis in the HD fetal brain using HD patient-derived hCOs. Our HD-hCOs had pathological phenotypes, including deficient junctional complexes in the neural tubes, delayed postmitotic neuronal maturation, dysregulated fate specification of cortical neuron subtypes, and abnormalities in early HD subcortical projections during corticogenesis, revealing a causal link between impaired progenitor cells and chaotic cortical neuronal layering in the HD brain. We identified novel long, oriented, and enriched polyQ assemblies of HTTs that hold large flat Golgi stacks and scaffold clathrin+ vesicles in the neural tubes of hCOs. Flat Golgi stacks conjugated polyQ assemblies by ADP-ribosylation factor 1 (ARF1). Inhibiting ARF1 activation with Brefeldin A (BFA) disassociated polyQ assemblies from Golgi. PolyQ assembles with mHTT scaffolded fewer ARF1 and formed shorter polyQ assembles with fewer and shorter Golgi and clathrin vesicles in neural tubes of HD-hCOs compared with those in hCOs. Inhibiting the activation of ARF1 by BFA in healthy hCOs replicated impaired junctional complexes in the neural tubes. Together, endogenous polyQ assemblies with mHTT reduced the Golgi recruiting ARF1 in the neuroepithelium, impaired the Golgi structure and activities, and altered the corticogenesis in HD-hCO.
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Affiliation(s)
- Yang Liu
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinyu Chen
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yunlong Ma
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chenyun Song
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jixin Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cheng Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lixiang Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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Lin YC, Wuputra K, Kato K, Ku CC, Saito S, Noguchi M, Nakamura Y, Hsiao M, Lin CS, Wu DC, Kawaguchi A, Yu HS, Yokoyama KK. Di-n-butyl phthalate promotes the neural differentiation of mouse embryonic stem cells through neurogenic differentiation 1. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123722. [PMID: 38460589 DOI: 10.1016/j.envpol.2024.123722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
An understanding of the risk of gene deletion and mutation posed by endocrine-disrupting chemicals (EDCs) is necessary for the identification of etiological reagents for many human diseases. Therefore, the characterization of the genetic traits caused by developmental exposure to EDCs is an important research subject. A new regenerative approach using embryonic stem cells (ESCs) holds promise for the development of stem-cell-based therapies and the identification of novel therapeutic agents against human diseases. Here, we focused on the characterization of the genetic traits and alterations in pluripotency/stemness triggered by phthalate ester derivatives. Regarding their in vitro effects, we reported the abilities of ESCs regarding proliferation, cell-cycle control, and neural ectoderm differentiation. The expression of their stemness-related genes and their genetic changes toward neural differentiation were examined, which led to the observation that the tumor suppressor gene product p53/retinoblastoma protein 1 and its related cascades play critical functions in cell-cycle progression, cell death, and neural differentiation. In addition, the expression of neurogenic differentiation 1 was affected by exposure to di-n-butyl phthalate in the context of cell differentiation into neural lineages. The nervous system is one of the most sensitive tissues to exposure to phthalate ester derivatives. The present screening system provides a good tool for studying the mechanisms underlying the effects of EDCs on the developmental regulation of humans and rodents, especially on the neuronal development of ESCs.
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Affiliation(s)
- Ying-Chu Lin
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Kenly Wuputra
- Graduate Institute of Medicine, Kaohsiung Medical University, 807, Taiwan; Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung, 807, Taiwan; Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Chia-Chen Ku
- Graduate Institute of Medicine, Kaohsiung Medical University, 807, Taiwan; Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung, 807, Taiwan; Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Shigeo Saito
- Saito Laboratory of Cell Technology, Yaita, Tochigi, 329-1571, Japan
| | - Michiya Noguchi
- Cell Engineering Division, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yukio Nakamura
- Cell Engineering Division, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Michael Hsiao
- Genome Research Center, Academia Sinica, Nangan, Taipei, 115, Taiwan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, Kaohsiung Medical University, 807, Taiwan; Department of Biological Sciences, National Sun Yan-Sen University, Kaohsiung, 80424, Taiwan
| | - Deng-Chyang Wu
- Graduate Institute of Medicine, Kaohsiung Medical University, 807, Taiwan; Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung, 807, Taiwan; Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan; Department of Gastroenterology, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Hsin-Su Yu
- Emeritus Professor in College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Kazunari K Yokoyama
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, 807, Taiwan; Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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10
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Alamin M, Humaira Sultana M, Babarinde IA, Azad AKM, Moni MA, Xu H. Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs). Brief Bioinform 2024; 25:bbae230. [PMID: 38739758 PMCID: PMC11089419 DOI: 10.1093/bib/bbae230] [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: 12/22/2023] [Revised: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
The complicated process of neuronal development is initiated early in life, with the genetic mechanisms governing this process yet to be fully elucidated. Single-cell RNA sequencing (scRNA-seq) is a potent instrument for pinpointing biomarkers that exhibit differential expression across various cell types and developmental stages. By employing scRNA-seq on human embryonic stem cells, we aim to identify differentially expressed genes (DEGs) crucial for early-stage neuronal development. Our focus extends beyond simply identifying DEGs. We strive to investigate the functional roles of these genes through enrichment analysis and construct gene regulatory networks to understand their interactions. Ultimately, this comprehensive approach aspires to illuminate the molecular mechanisms and transcriptional dynamics governing early human brain development. By uncovering potential links between these DEGs and intelligence, mental disorders, and neurodevelopmental disorders, we hope to shed light on human neurological health and disease. In this study, we have used scRNA-seq to identify DEGs involved in early-stage neuronal development in hESCs. The scRNA-seq data, collected on days 26 (D26) and 54 (D54), of the in vitro differentiation of hESCs to neurons were analyzed. Our analysis identified 539 DEGs between D26 and D54. Functional enrichment of those DEG biomarkers indicated that the up-regulated DEGs participated in neurogenesis, while the down-regulated DEGs were linked to synapse regulation. The Reactome pathway analysis revealed that down-regulated DEGs were involved in the interactions between proteins located in synapse pathways. We also discovered interactions between DEGs and miRNA, transcriptional factors (TFs) and DEGs, and between TF and miRNA. Our study identified 20 significant transcription factors, shedding light on early brain development genetics. The identified DEGs and gene regulatory networks are valuable resources for future research into human brain development and neurodevelopmental disorders.
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Affiliation(s)
- Md Alamin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | | | - Isaac Adeyemi Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Muhammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Cyber Futures Institute, Charles Sturt University, Bathurst, NSW 2795, Australia
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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Vingan I, Phatarpekar S, Tung VSK, Hernández AI, Evgrafov OV, Alarcon JM. Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573225. [PMID: 38260257 PMCID: PMC10802250 DOI: 10.1101/2023.12.30.573225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following the recall of active place avoidance (APA) memory. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that recall induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall across an array of spots encompassing putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were transcriptomically and spatially distinct from one another. DEGs detected between Arc+ and Arc- spots exclusively in the trained mouse were enriched in several memory-related gene ontology terms, including "regulation of synaptic plasticity" and "memory." Our results suggest that APA memory recall is supported by regionalized transcriptomic profiles separating the CA1 and CA3 from the DG, transcriptionally and spatially distinct IEG expressing spatial transcriptomic spots, and biological processes related to synaptic plasticity as a defining the difference between Arc+ and Arc- spatial transcriptomic spots.
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Affiliation(s)
- Isaac Vingan
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Shwetha Phatarpekar
- Institute of Genomics in Health, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Victoria Sook Keng Tung
- School of Graduates Studies, Program in Molecular and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - A Iván Hernández
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Pathology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- The Robert F. Furchgott Center for Neural & Behavioral Science, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
| | - Oleg V Evgrafov
- Institute of Genomics in Health, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- School of Graduates Studies, Program in Molecular and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Juan Marcos Alarcon
- School of Graduates Studies, Program in Neural and Behavioral Sciences, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- Department of Pathology, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
- The Robert F. Furchgott Center for Neural & Behavioral Science, State University of New York, Downstate Health Sciences University, Brooklyn, NY, USA
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12
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Zhang Y, Lu Y, Xu F, Zhang X, Wu Y, Zhao J, Luo Q, Liu H, Chen K, Fei S, Cui X, Sun Y, Ou M. Molecular Characterization, Expression Pattern, DNA Methylation and Gene Disruption of Figla in Blotched Snakehead ( Channa maculata). Animals (Basel) 2024; 14:491. [PMID: 38338134 PMCID: PMC10854511 DOI: 10.3390/ani14030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Figla is one of the earliest expressed genes in the oocyte during ovarian development. In this study, Figla was characterized in C. maculata, one of the main aquaculture species in China, and designated as CmFigla. The length of CmFigla cDNA was 1303 bp, encoding 197 amino acids that contained a conserved bHLH domain. CmFigla revealed a female-biased expression patterns in the gonads of adult fish, and CmFigla expression was far higher in ovaries than that in testes at all gonadal development stages, especially at 60~180 days post-fertilization (dpf). Furthermore, a noteworthy inverse relationship was observed between CmFigla expression and the methylation of its promoter in the adult gonads. Gonads at 90 dpf were used for in situ hybridization (ISH), and CmFigla transcripts were mainly concentrated in oogonia and the primary oocytes in ovaries, but undetectable in the testes. These results indicated that Figla would play vital roles in the ovarian development in C. maculata. Additionally, the frame-shift mutations of CmFigla were successfully constructed through the CRISPR/Cas9 system, which established a positive foundation for further investigation on the role of Figla in the ovarian development of C. maculata. Our study provides valuable clues for exploring the regulatory mechanism of Figla in the fish ovarian development and maintenance, which would be useful for the sex control and reproduction of fish in aquaculture.
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Affiliation(s)
- Yang Zhang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Yuntao Lu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Feng Xu
- Chongqing Fisheries Technical Extension Center, Chongqing 404100, China;
| | - Xiaotian Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Yuxia Wu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Jian Zhao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Qing Luo
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Kunci Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Shuzhan Fei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Xiaojuan Cui
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
| | - Mi Ou
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
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13
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Neyazi S, Yamazawa E, Hack K, Tanaka S, Nagae G, Kresbach C, Umeda T, Eckhardt A, Tatsuno K, Pohl L, Hana T, Bockmayr M, Kim P, Dorostkar MM, Takami T, Obrecht D, Takai K, Suwala AK, Komori T, Godbole S, Wefers AK, Otani R, Neumann JE, Higuchi F, Schweizer L, Nakanishi Y, Monoranu CM, Takami H, Engertsberger L, Yamada K, Ruf V, Nomura M, Mohme T, Mukasa A, Herms J, Takayanagi S, Mynarek M, Matsuura R, Lamszus K, Ishii K, Kluwe L, Imai H, von Deimling A, Koike T, Benesch M, Kushihara Y, Snuderl M, Nambu S, Frank S, Omura T, Hagel C, Kugasawa K, Mautner VF, Ichimura K, Rutkowski S, Aburatani H, Saito N, Schüller U. Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation. Acta Neuropathol 2024; 147:22. [PMID: 38265489 PMCID: PMC10808175 DOI: 10.1007/s00401-023-02668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.
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Affiliation(s)
- Sina Neyazi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Karoline Hack
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Takayoshi Umeda
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Alicia Eckhardt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Radiotherapy and Radiation Oncology, Hubertus Wald Tumor Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kenji Tatsuno
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Lara Pohl
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Taijun Hana
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Phyo Kim
- Utsunomiya Neurospine Center, Symphony Clinic, Utsunomiya, Japan
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Toshihiro Takami
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Keisuke Takai
- Department of Neurosurgery, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Shweta Godbole
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ryohei Otani
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fumi Higuchi
- Department of Neurosurgery, University of Teikyo Hospital, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt Am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Yuta Nakanishi
- Department of Neurosurgery, Osaka Metropolitan City University Graduate School of Medicine, Osaka, Japan
| | - Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lara Engertsberger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Keisuke Yamada
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktoria Ruf
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Theresa Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiko Matsuura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuhiko Ishii
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lan Kluwe
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hideaki Imai
- Department of Neurosurgery, Japan Community Health Care Organization Tokyo Shinjuku Medical Center, Tokyo, Japan
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Benesch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York City, USA
| | - Shohei Nambu
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Takaki Omura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuha Kugasawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktor F Mautner
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo, Japan
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hiroyuki Aburatani
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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14
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Wang Y, Tang Y, Liu TH, Shao L, Li C, Wang Y, Tan P. Integrative Multi-omics Analysis to Characterize Herpes Virus Infection Increases the Risk of Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03903-w. [PMID: 38191694 DOI: 10.1007/s12035-023-03903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
Evidence suggests that herpes virus infection is associated with an increased risk of Alzheimer's disease (AD), and innate and adaptive immunity plays an important role in the association. Although there have been many studies, the mechanism of the association is still unclear. This study aims to reveal the underlying molecular and immune regulatory network through multi-omics data and provide support for the study of the mechanism of infection and AD in the future. Here, we found that the herpes virus infection significantly increased the risk of AD. Genes associated with the occurrence and development of AD and genetically regulated by herpes virus infection are mainly enrichment in immune-related pathways. The 22 key regulatory genes identified by machine learning are mainly immune genes. They are also significantly related to the infiltration changes of 3 immune cell in AD. Furthermore, many of these genes have previously been reported to be linked, or potentially linked, to the pathological mechanisms of both herpes virus infection and AD. In conclusion, this study contributes to the study of the mechanisms related to herpes virus infection and AD, and indicates that the regulation of innate and adaptive immunity may be an effective strategy for preventing and treating herpes virus infection and AD. Additionally, the identified key regulatory genes, whether previously studied or newly discovered, may serve as valuable targets for prevention and treatment strategies.
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Affiliation(s)
- Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Lizhen Shao
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chunying Li
- Chongqing Vocational College of Resources and Environmental Protection, Chongqing, China.
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Pengcheng Tan
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
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15
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Elhadi K, Daiwile AP, Cadet JL. Modeling methamphetamine use disorder and relapse in animals: short- and long-term epigenetic, transcriptional., and biochemical consequences in the rat brain. Neurosci Biobehav Rev 2023; 155:105440. [PMID: 38707245 PMCID: PMC11068368 DOI: 10.1016/j.neubiorev.2023.105440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Methamphetamine use disorder (MUD) is a neuropsychiatric disorder characterized by binge drug taking episodes, intervals of abstinence, and relapses to drug use even during treatment. MUD has been modeled in rodents and investigators are attempting to identify its molecular bases. Preclinical experiments have shown that different schedules of methamphetamine self-administration can cause diverse transcriptional changes in the dorsal striatum of Sprague-Dawley rats. In the present review, we present data on differentially expressed genes (DEGs) identified in the rat striatum following methamphetamine intake. These include genes involved in transcription regulation, potassium channel function, and neuroinflammation. We then use the striatal data to discuss the potential significance of the molecular changes induced by methamphetamine by reviewing concordant or discordant data from the literature. This review identified potential molecular targets for pharmacological interventions. Nevertheless, there is a need for more research on methamphetamine-induced transcriptional consequences in various brain regions. These data should provide a more detailed neuroanatomical map of methamphetamine-induced changes and should better inform therapeutic interventions against MUD.
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Affiliation(s)
- Khalid Elhadi
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
| | - Atul P. Daiwile
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
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16
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López-Tobón A, Shyti R, Villa CE, Cheroni C, Fuentes-Bravo P, Trattaro S, Caporale N, Troglio F, Tenderini E, Mihailovich M, Skaros A, Gibson WT, Cuomo A, Bonaldi T, Mercurio C, Varasi M, Osborne L, Testa G. GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders. SCIENCE ADVANCES 2023; 9:eadh2726. [PMID: 38019906 PMCID: PMC10686562 DOI: 10.1126/sciadv.adh2726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates GTF2I as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage-dependent and GTF2I-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological GTF2I levels. Transgenic mice with Gtf2i duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a GTF2I effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing GTF2I-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
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Affiliation(s)
- Alejandro López-Tobón
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Carlo Emanuele Villa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Patricio Fuentes-Bravo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Flavia Troglio
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Adrianos Skaros
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - William T. Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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17
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Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 2023; 624:390-402. [PMID: 38092918 PMCID: PMC10719095 DOI: 10.1038/s41586-023-06819-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.
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Affiliation(s)
- Nathan R Zemke
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ethan J Armand
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Seoyeon Lee
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jingtian Zhou
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Xu
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Keyi Dong
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hannah S Indralingam
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jonathan A Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Miller
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Qiangge Zhang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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18
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Wang NB, Lende-Dorn BA, Adewumi HO, Beitz AM, Han P, O'Shea TM, Galloway KE. Proliferation history and transcription factor levels drive direct conversion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568736. [PMID: 38077004 PMCID: PMC10705288 DOI: 10.1101/2023.11.26.568736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The sparse and stochastic nature of reprogramming has obscured our understanding of how transcription factors drive cells to new identities. To overcome this limit, we developed a compact, portable reprogramming system that increases direct conversion of fibroblasts to motor neurons by two orders of magnitude. We show that subpopulations with different reprogramming potentials are distinguishable by proliferation history. By controlling for proliferation history and titrating each transcription factor, we find that conversion correlates with levels of the pioneer transcription factor Ngn2, whereas conversion shows a biphasic response to Lhx3. Increasing the proliferation rate of adult human fibroblasts generates morphologically mature, induced motor neurons at high rates. Using compact, optimized, polycistronic cassettes, we generate motor neurons that graft with the murine central nervous system, demonstrating the potential for in vivo therapies.
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Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Honour O Adewumi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Adam M Beitz
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Patrick Han
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Timothy M O'Shea
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
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19
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Sato Y, Asahi T, Kataoka K. Integrative single-cell RNA-seq analysis of vascularized cerebral organoids. BMC Biol 2023; 21:245. [PMID: 37940920 PMCID: PMC10634128 DOI: 10.1186/s12915-023-01711-1] [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: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Cerebral organoids are three-dimensional in vitro cultured brains that mimic the function and structure of the human brain. One of the major challenges for cerebral organoids is the lack of functional vasculature. Without perfusable vessels, oxygen and nutrient supplies may be insufficient for long-term culture, hindering the investigation of the neurovascular interactions. Recently, several strategies for the vascularization of human cerebral organoids have been reported. However, the generalizable trends and variability among different strategies are unclear due to the lack of a comprehensive characterization and comparison of these vascularization strategies. In this study, we aimed to explore the effect of different vascularization strategies on the nervous system and vasculature in human cerebral organoids. RESULTS We integrated single-cell RNA sequencing data of multiple vascularized and vascular organoids and fetal brains from publicly available datasets and assessed the protocol-dependent and culture-day-dependent effects on the cell composition and transcriptomic profiles in neuronal and vascular cells. We revealed the similarities and uniqueness of multiple vascularization strategies and demonstrated the transcriptomic effects of vascular induction on neuronal and mesodermal-like cell populations. Moreover, our data suggested that the interaction between neurons and mesodermal-like cell populations is important for the cerebrovascular-specific profile of endothelial-like cells. CONCLUSIONS This study highlights the current challenges to vascularization strategies in human cerebral organoids and offers a benchmark for the future fabrication of vascularized organoids.
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Affiliation(s)
- Yuya Sato
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
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20
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Zhou Z, Pan Y, Zhou S, Wang S, Zhang D, Cao Y, Jiang X, Li J, Zhu L, Zhao L, Gu S, Lin G, Dong Z, Sun HX. Single-cell analysis reveals specific neuronal transition during mouse corticogenesis. Front Cell Dev Biol 2023; 11:1209320. [PMID: 38020907 PMCID: PMC10657809 DOI: 10.3389/fcell.2023.1209320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Currently, the mechanism(s) underlying corticogenesis is still under characterization. Methods: We curated the most comprehensive single-cell RNA-seq (scRNA-seq) datasets from mouse and human fetal cortexes for data analysis and confirmed the findings with co-immunostaining experiments. Results: By analyzing the developmental trajectories with scRNA-seq datasets in mice, we identified a specific developmental sub-path contributed by a cell-population expressing both deep- and upper-layer neurons (DLNs and ULNs) specific markers, which occurred on E13.5 but was absent in adults. In this cell-population, the percentages of cells expressing DLN and ULN markers decreased and increased, respectively, during the development suggesting direct neuronal transition (namely D-T-U). Whilst genes significantly highly/uniquely expressed in D-T-U cell population were significantly enriched in PTN/MDK signaling pathways related to cell migration. Both findings were further confirmed by co-immunostaining with DLNs, ULNs and D-T-U specific markers across different timepoints. Furthermore, six genes (co-expressed with D-T-U specific markers in mice) showing a potential opposite temporal expression between human and mouse during fetal cortical development were associated with neuronal migration and cognitive functions. In adult prefrontal cortexes (PFC), D-T-U specific genes were expressed in neurons from different layers between humans and mice. Conclusion: Our study characterizes a specific cell population D-T-U showing direct DLNs to ULNs neuronal transition and migration during fetal cortical development in mice. It is potentially associated with the difference of cortical development in humans and mice.
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Affiliation(s)
- Ziheng Zhou
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yueyang Pan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Si Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuguang Wang
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dengwei Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaosen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linnan Zhu
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, China
| | - Lijian Zhao
- Medical Technology College, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shen Gu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ge Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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21
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Cota P, Saber L, Taskin D, Jing C, Bastidas-Ponce A, Vanheusden M, Shahryari A, Sterr M, Burtscher I, Bakhti M, Lickert H. NEUROD2 function is dispensable for human pancreatic β cell specification. Front Endocrinol (Lausanne) 2023; 14:1286590. [PMID: 37955006 PMCID: PMC10634430 DOI: 10.3389/fendo.2023.1286590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction The molecular programs regulating human pancreatic endocrine cell induction and fate allocation are not well deciphered. Here, we investigated the spatiotemporal expression pattern and the function of the neurogenic differentiation factor 2 (NEUROD2) during human endocrinogenesis. Methods Using Crispr-Cas9 gene editing, we generated a reporter knock-in transcription factor (TF) knock-out human inducible pluripotent stem cell (iPSC) line in which the open reading frame of both NEUROD2 alleles are replaced by a nuclear histone 2B-Venus reporter (NEUROD2nVenus/nVenus). Results We identified a transient expression of NEUROD2 mRNA and its nuclear Venus reporter activity at the stage of human endocrine progenitor formation in an iPSC differentiation model. This expression profile is similar to what was previously reported in mice, uncovering an evolutionarily conserved gene expression pattern of NEUROD2 during endocrinogenesis. In vitro differentiation of the generated homozygous NEUROD2nVenus/nVenus iPSC line towards human endocrine lineages uncovered no significant impact upon the loss of NEUROD2 on endocrine cell induction. Moreover, analysis of endocrine cell specification revealed no striking changes in the generation of insulin-producing b cells and glucagon-secreting a cells upon lack of NEUROD2. Discussion Overall, our results suggest that NEUROD2 is expendable for human b cell formation in vitro.
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Affiliation(s)
- Perla Cota
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Lama Saber
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Damla Taskin
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Changying Jing
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Munich Medical Research School (MMRS), Ludwig Maximilian University (LMU), Munich, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthew Vanheusden
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Alireza Shahryari
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich (TUM), Munich, Germany
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22
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Montagne J, Preza M, Koziol U. Stem cell proliferation and differentiation during larval metamorphosis of the model tapeworm Hymenolepis microstoma. Front Cell Infect Microbiol 2023; 13:1286190. [PMID: 37908761 PMCID: PMC10614006 DOI: 10.3389/fcimb.2023.1286190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Background Tapeworm larvae cause important diseases in humans and domestic animals. During infection, the first larval stage undergoes a metamorphosis where tissues are formed de novo from a population of stem cells called germinative cells. This process is difficult to study for human pathogens, as these larvae are infectious and difficult to obtain in the laboratory. Methods In this work, we analyzed cell proliferation and differentiation during larval metamorphosis in the model tapeworm Hymenolepis microstoma, by in vivo labelling of proliferating cells with the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU), tracing their differentiation with a suite of specific molecular markers for different cell types. Results Proliferating cells are very abundant and fast-cycling during early metamorphosis: the total number of cells duplicates every ten hours, and the length of G2 is only 75 minutes. New tegumental, muscle and nerve cells differentiate from this pool of proliferating germinative cells, and these processes are very fast, as differentiation markers for neurons and muscle cells appear within 24 hours after exiting the cell cycle, and fusion of new cells to the tegumental syncytium can be detected after only 4 hours. Tegumental and muscle cells appear from early stages of metamorphosis (24 to 48 hours post-infection); in contrast, most markers for differentiating neurons appear later, and the detection of synapsin and neuropeptides correlates with scolex retraction. Finally, we identified populations of proliferating cells that express conserved genes associated with neuronal progenitors and precursors, suggesting the existence of tissue-specific lineages among germinative cells. Discussion These results provide for the first time a comprehensive view of the development of new tissues during tapeworm larval metamorphosis, providing a framework for similar studies in human and veterinary pathogens.
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Affiliation(s)
| | | | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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23
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Feng W, Liu S, Deng Q, Fu S, Yang Y, Dai X, Wang S, Wang Y, Liu Y, Lin X, Pan X, Hao S, Yuan Y, Gu Y, Zhang X, Li H, Liu L, Liu C, Fei JF, Wei X. A scATAC-seq atlas of chromatin accessibility in axolotl brain regions. Sci Data 2023; 10:627. [PMID: 37709774 PMCID: PMC10502032 DOI: 10.1038/s41597-023-02533-0] [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: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is an excellent model for investigating regeneration, the interaction between regenerative and developmental processes, comparative genomics, and evolution. The brain, which serves as the material basis of consciousness, learning, memory, and behavior, is the most complex and advanced organ in axolotl. The modulation of transcription factors is a crucial aspect in determining the function of diverse regions within the brain. There is, however, no comprehensive understanding of the gene regulatory network of axolotl brain regions. Here, we utilized single-cell ATAC sequencing to generate the chromatin accessibility landscapes of 81,199 cells from the olfactory bulb, telencephalon, diencephalon and mesencephalon, hypothalamus and pituitary, and the rhombencephalon. Based on these data, we identified key transcription factors specific to distinct cell types and compared cell type functions across brain regions. Our results provide a foundation for comprehensive analysis of gene regulatory programs, which are valuable for future studies of axolotl brain development, regeneration, and evolution, as well as on the mechanisms underlying cell-type diversity in vertebrate brains.
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Affiliation(s)
- Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Sulei Fu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Yunzhi Yang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Dai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yijin Wang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiangyu Pan
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- Guangdong Cardiovsacular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yue Yuan
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Hanbo Li
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI-Qingdao, Qingdao, 266555, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Xiaoyu Wei
- BGI-Hangzhou, Hangzhou, 310012, China.
- BGI-Shenzhen, Shenzhen, 518103, China.
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Le Ciclé C, Pacini V, Rama N, Tauszig-Delamasure S, Airaud E, Petit F, de Beco S, Cohen-Tannoudji J, L'hôte D. The Neurod1/4-Ntrk3-Src pathway regulates gonadotrope cell adhesion and motility. Cell Death Discov 2023; 9:327. [PMID: 37658038 PMCID: PMC10474047 DOI: 10.1038/s41420-023-01615-7] [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: 03/20/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
Pituitary gonadotrope cells are essential for the endocrine regulation of reproduction in vertebrates. These cells emerge early during embryogenesis, colonize the pituitary glands and organize in tridimensional networks, which are believed to be crucial to ensure proper regulation of fertility. However, the molecular mechanisms regulating the organization of gonadotrope cell population during embryogenesis remain poorly understood. In this work, we characterized the target genes of NEUROD1 and NEUROD4 transcription factors in the immature gonadotrope αT3-1 cell model by in silico functional genomic analyses. We demonstrated that NEUROD1/4 regulate genes belonging to the focal adhesion pathway. Using CRISPR/Cas9 knock-out approaches, we established a double NEUROD1/4 knock-out αT3-1 cell model and demonstrated that NEUROD1/4 regulate cell adhesion and cell motility. We then characterized, by immuno-fluorescence, focal adhesion number and signaling in the context of NEUROD1/4 insufficiency. We demonstrated that NEUROD1/4 knock-out leads to an increase in the number of focal adhesions associated with signaling abnormalities implicating the c-Src kinase. We further showed that the neurotrophin tyrosine kinase receptor 3 NTRK3, a target of NEUROD1/4, interacts physically with c-Src. Furthermore, using motility rescue experiments and time-lapse video microscopy, we demonstrated that NTRK3 is a major regulator of gonadotrope cell motility. Finally, using a Ntrk3 knock-out mouse model, we showed that NTRK3 regulates gonadotrope cells positioning in the developing pituitary, in vivo. Altogether our study demonstrates that the Neurod1/4-Ntrk3-cSrc pathway is a major actor of gonadotrope cell mobility, and thus provides new insights in the regulation of gonadotrope cell organization within the pituitary gland.
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Affiliation(s)
- Charles Le Ciclé
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France
| | - Vincent Pacini
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Nicolas Rama
- Centre de Recherche en Cancérologie de Lyon, Inserm U1052, CNRS UMR 5286, Centre Léon Bérard, Université Lyon1, 69008, Lyon, France
| | - Servane Tauszig-Delamasure
- Institut NeuroMyoGène - CNRS UMR 5310 - Inserm U1217 de Lyon - UCBL Lyon 1, Faculté de Médecine et de Pharmacie, Lyon, France
| | - Eloïse Airaud
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France
| | - Florence Petit
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France
- Faculty of Pharmacy, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Simon de Beco
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Joëlle Cohen-Tannoudji
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France
| | - David L'hôte
- Université Paris Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative, F-75013, Paris, France.
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25
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Vincent E, Chatterjee S, Cannon GH, Auer D, Ross H, Chakravarti A, Goff LA. Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development. Proc Natl Acad Sci U S A 2023; 120:e2211986120. [PMID: 37585461 PMCID: PMC10451519 DOI: 10.1073/pnas.2211986120] [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: 07/14/2022] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
The receptor tyrosine kinase RET plays a critical role in the fate specification of enteric neural crest-derived cells (ENCDCs) during enteric nervous system (ENS) development. RET loss of function (LoF) is associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. Although the major phenotypic consequences and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, cell type- and state-specific effects are unknown. We performed single-cell RNA sequencing on an enriched population of ENCDCs from the developing GI tract of Ret null heterozygous and homozygous mice at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: 1) Ret-expressing ENCDCs are a heterogeneous population comprising ENS progenitors as well as glial- and neuronal-committed cells; 2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; 3) expression patterns of HSCR-associated and Ret gene regulatory network genes are impacted by Ret LoF; and 4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes during development of the ENS, including the specification of inhibitory neuron subtypes, cell cycle dynamics of ENS progenitors, and the developmental timing of neuronal and glial commitment.
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Affiliation(s)
- Elizabeth Vincent
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Gabrielle H. Cannon
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Dallas Auer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Holly Ross
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Loyal A. Goff
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD21205
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26
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Khan MSH, Hefner M, Reddy A, Dhurandhar NV, Hegde V. E4orf1 improves adipose tissue-specific metabolic risk factors and indicators of cognition function in a mouse model of Alzheimer's disease. Nutr Diabetes 2023; 13:13. [PMID: 37573386 PMCID: PMC10423203 DOI: 10.1038/s41387-023-00242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/20/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023] Open
Abstract
OBJECTIVE Obesity, impaired glycemic control, and hepatic steatosis often coexist and are risk factors for developing dementia, and Alzheimer's disease (AD). We hypothesized that a therapeutic agent that improves glycemic control and steatosis may attenuate obesity-associated progression of dementia. We previously identified that adenoviral protein E4orf1 improves glycemic control and reduces hepatic steatosis despite obesity in mice. Here, we determined if this metabolic improvement by E4orf1 will ameliorate cognitive decline in a transgenic mouse model of AD. METHODS Fourteen- to twenty-month-old APP/PS1/E4orf1 and APP/PS1 (control) mice were fed a high-fat diet. Cognition was determined by Morris Water Maze (MWM). Systemic glycemic control and metabolic signaling changes in adipose tissue, liver, and brain were determined. RESULTS Compared to control, E4orf1 expression significantly improved glucose clearance, reduced endogenous insulin requirement and lowered body-fat, enhanced glucose and lipid metabolism in adipose tissue, and reduced de novo lipogenesis in the liver. In the brain, E4orf1 mice displayed significantly greater expression of genes involved in neurogenesis and amyloid-beta degradation and performed better in MWM testing. CONCLUSION This study opens-up the possibility of addressing glycemic control and steatosis for attenuating obesity-related cognitive decline. It also underscores the potential of E4orf1 for the purpose, which needs further investigations.
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Affiliation(s)
- Md Shahjalal Hossain Khan
- Obesity and Metabolic Health Laboratory, Department of Nutritional Sciences, Texas Tech University, Lubbock, TX, 79409, USA
- Neurosignaling Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Marleigh Hefner
- Obesity and Metabolic Health Laboratory, Department of Nutritional Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Arubala Reddy
- Obesity and Metabolic Health Laboratory, Department of Nutritional Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Nikhil V Dhurandhar
- Obesity and Metabolic Health Laboratory, Department of Nutritional Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Vijay Hegde
- Obesity and Metabolic Health Laboratory, Department of Nutritional Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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27
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Yoon M, Kim H, Shin H, Lee H, Kang MJ, Park SH, Han G, Kim Y, Choi KY. Inhibition of CXXC5 function rescues Alzheimer's disease phenotypes by restoring Wnt/β-catenin signaling pathway. Pharmacol Res 2023; 194:106836. [PMID: 37355147 DOI: 10.1016/j.phrs.2023.106836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia and is characterized by cognitive deficits and accumulation of pathological plaques. Owing to the complexity of AD development, paradigms for AD research and drug discovery have shifted to target factors that mediate multiple pathogenesis in AD. Increasing evidence suggests that the suppression of the Wnt/β-catenin signaling pathway plays substantial roles in AD progression. However, the underlying mechanism for the suppression of Wnt/β-catenin pathway associated with AD pathogenesis remains unexplored. In this study, we identified that CXXC5, a negative feedback regulator of the Wnt/β-catenin pathway, was overexpressed in the tissues of AD patients and 5xFAD transgenic mice paired with the suppression of Wnt/β-catenin pathway and its target genes related to AD. The level of CXXC5 was upregulated, upon aging of 5xFAD mice. AD characteristics including cognitive deficits, amyloid-β (Aβ) plaques, neuronal inflammation, and age-dependent increment of AD-related markers were rescued in Cxxc5-/-/5xFAD mice. 5-methoxyindirubin-3'-oxime (KY19334), a small molecule that restores the suppressed Wnt/β-catenin pathway via interference of the CXXC5-Dvl interaction, significantly improved the overall pathogenic phenotypes of 5xFAD mice. Collectively, our findings revealed that CXXC5 plays a key role in AD pathogenesis and suggest inhibition of CXXC5-Dvl interaction as a new therapeutic approach for AD.
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Affiliation(s)
- Minguen Yoon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Heejene Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Heewon Shin
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - HeeYang Lee
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | | | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Gyoonhee Han
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - YoungSoo Kim
- Department of Pharmacy and Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.
| | - Kang-Yell Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; CK Regeon Inc, Seoul 03722, Republic of Korea.
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28
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Raj S, Sifuentes CJ, Kyono Y, Denver RJ. Metamorphic gene regulation programs in Xenopus tropicalis tadpole brain. PLoS One 2023; 18:e0287858. [PMID: 37384728 PMCID: PMC10310023 DOI: 10.1371/journal.pone.0287858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
Amphibian metamorphosis is controlled by thyroid hormone (TH), which binds TH receptors (TRs) to regulate gene expression programs that underlie morphogenesis. Gene expression screens using tissues from premetamorphic tadpoles treated with TH identified some TH target genes, but few studies have analyzed genome-wide changes in gene regulation during spontaneous metamorphosis. We analyzed RNA sequencing data at four developmental stages from the beginning to the end of spontaneous metamorphosis, conducted on the neuroendocrine centers of Xenopus tropicalis tadpole brain. We also conducted chromatin immunoprecipitation sequencing (ChIP-seq) for TRs, and we compared gene expression changes during metamorphosis with those induced by exogenous TH. The mRNA levels of 26% of protein coding genes changed during metamorphosis; about half were upregulated and half downregulated. Twenty four percent of genes whose mRNA levels changed during metamorphosis had TR ChIP-seq peaks. Genes involved with neural cell differentiation, cell physiology, synaptogenesis and cell-cell signaling were upregulated, while genes involved with cell cycle, protein synthesis, and neural stem/progenitor cell homeostasis were downregulated. There is a shift from building neural structures early in the metamorphic process, to the differentiation and maturation of neural cells and neural signaling pathways characteristic of the adult frog brain. Only half of the genes modulated by treatment of premetamorphic tadpoles with TH for 16 h changed expression during metamorphosis; these represented 33% of the genes whose mRNA levels changed during metamorphosis. Taken together, our results provide a foundation for understanding the molecular basis for metamorphosis of tadpole brain, and they highlight potential caveats for interpreting gene regulation changes in premetamorphic tadpoles induced by exogenous TH.
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Affiliation(s)
- Samhitha Raj
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher J. Sifuentes
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yasuhiro Kyono
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert J. Denver
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan, United States of America
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29
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Zhang C, Ye W, Zhao M, Long L, Xia D, Fan Z. KDM6B Negatively Regulates the Neurogenesis Potential of Apical Papilla Stem Cells via HES1. Int J Mol Sci 2023; 24:10608. [PMID: 37445785 PMCID: PMC10341966 DOI: 10.3390/ijms241310608] [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: 05/17/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Stem cells from the apical papilla (SCAPs) are used to regulate the microenvironment of nerve defects. KDM6B, which functions as an H3K27me3 demethylase, is known to play a crucial role in neurogenesis. However, the mechanism by which KDM6B influences the neurogenesis potential of SCAPs remains unclear. We evaluated the expression of neural markers in SCAPs by using real-time RT-PCR and immunofluorescence staining. To assess the effectiveness of SCAP transplantation in the SCI model, we used the BBB scale to evaluate motor function. Additionally, toluidine blue staining and Immunofluorescence staining of NCAM, NEFM, β-III-tubulin, and Nestin were used to assess nerve tissue remodeling. Further analysis was conducted through Microarray analysis and ChIP assay to study the molecular mechanisms. Our results show that KDM6B inhibits the expression of NeuroD, TH, β-III tubulin, and Nestin. In vivo studies indicate that the SCAP-KDM6Bsh group is highly effective in restoring spinal cord structure and motor function in rats suffering from SCI. Our findings suggest that KDM6B directly binds to the HES1 promoter via regulating H3K27me3 and HES1 expression. In conclusion, our study can help understand the regulatory role of KDM6B in neurogenesis and provide more effective treatments for nerve injury.
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Affiliation(s)
- Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China; (C.Z.); (W.Y.); (M.Z.); (L.L.)
- Department of Dental Emergency, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China;
| | - Weilong Ye
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China; (C.Z.); (W.Y.); (M.Z.); (L.L.)
| | - Mengyao Zhao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China; (C.Z.); (W.Y.); (M.Z.); (L.L.)
| | - Lujue Long
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China; (C.Z.); (W.Y.); (M.Z.); (L.L.)
| | - Dengsheng Xia
- Department of Dental Emergency, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China;
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing 100050, China; (C.Z.); (W.Y.); (M.Z.); (L.L.)
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing 100069, China
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing 100069, China
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30
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Hong H, Yoon SB, Park JE, Lee JI, Kim HY, Nam HJ, Cho H. MeCP2 dysfunction prevents proper BMP signaling and neural progenitor expansion in brain organoid. Ann Clin Transl Neurol 2023. [PMID: 37302988 DOI: 10.1002/acn3.51799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVES Sporadic mutations in MeCP2 are a hallmark of Rett syndrome (RTT). Many RTT brain organoid models have exhibited pathogenic phenotypes such as decreased spine density and small size of soma with altered electrophysiological signals. However, previous models are mainly focused on the phenotypes observed in the late phase and rarely provide clues for the defect of neural progenitors which generate different types of neurons and glial cells. METHODS We newly established the RTT brain organoid model derived from MeCP2-truncated iPS cells which were genetically engineered by CRISPR/Cas9 technology. By immunofluorescence imaging, we studied the development of NPC pool and its fate specification into glutamatergic neurons or astrocytes in RTT organoids. By total RNA sequencing, we investigated which signaling pathways were altered during the early brain development in RTT organoids. RESULTS Dysfunction of MeCP2 caused the defect of neural rosette formation in the early phase of cortical development. In total transcriptome analysis, BMP pathway-related genes are highly associated with MeCP2 depletion. Moreover, levels of pSMAD1/5 and BMP target genes are excessively increased, and treatment of BMP inhibitors partially rescues the cell cycle progression of neural progenitors. Subsequently, MeCP2 dysfunction reduced the glutamatergic neurogenesis and induced overproduction of astrocytes. Nevertheless, early inhibition of BMP pathway rescued VGLUT1 expression and suppressed astrocyte maturation. INTERPRETATION Our results demonstrate that MeCP2 is required for the expansion of neural progenitor cells by modulating BMP pathway at early stages of development, and this influence persists during neurogenesis and gliogenesis at later stages of brain organoid development.
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Affiliation(s)
- Hyowon Hong
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sae-Bom Yoon
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung Eun Park
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung In Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun Young Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hye Jin Nam
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Heeyeong Cho
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
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31
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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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32
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Zaghi M, Banfi F, Massimino L, Volpin M, Bellini E, Brusco S, Merelli I, Barone C, Bruni M, Bossini L, Lamparelli LA, Pintado L, D'Aliberti D, Spinelli S, Mologni L, Colasante G, Ungaro F, Cioni JM, Azzoni E, Piazza R, Montini E, Broccoli V, Sessa A. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition. Nat Commun 2023; 14:3212. [PMID: 37270547 DOI: 10.1038/s41467-023-39043-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Luca Massimino
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Monica Volpin
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Simone Brusco
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Ivan Merelli
- CNR Institute of Biomedical Technologies, 20090, Segrate, Italy
| | - Cristiana Barone
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Michela Bruni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Linda Bossini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luigi Antonio Lamparelli
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Laura Pintado
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Deborah D'Aliberti
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Silvia Spinelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Luca Mologni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Gaia Colasante
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Ungaro
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Jean-Michel Cioni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Emanuele Azzoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Rocco Piazza
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy.
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Jiang F, Zhou X, Qian Y, Zhu M, Wang L, Li Z, Shen Q, Wang M, Qu F, Cui G, Chen K, Peng G. Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development. Nat Methods 2023:10.1038/s41592-023-01884-1. [PMID: 37231265 DOI: 10.1038/s41592-023-01884-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/19/2023] [Indexed: 05/27/2023]
Abstract
The brain is a complex tissue whose function relies on coordinated anatomical and molecular features. However, the molecular annotation of the spatial organization of the brain is currently insufficient. Here, we describe microfluidic indexing-based spatial assay for transposase-accessible chromatin and RNA-sequencing (MISAR-seq), a method for spatially resolved joint profiling of chromatin accessibility and gene expression. By applying MISAR-seq to the developing mouse brain, we study tissue organization and spatiotemporal regulatory logics during mouse brain development.
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Affiliation(s)
- Fuqing Jiang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Xin Zhou
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China
| | - Yingying Qian
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Miao Zhu
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Li Wang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhuxia Li
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qingmei Shen
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China
| | - Minhan Wang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fangfang Qu
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Guizhong Cui
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China
- Guangzhou Laboratory, Guangzhou, China
| | - Kai Chen
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, University of Chinese Academy of Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Center for Cell Lineage and Atlas, Bioland Laboratory, Guangzhou, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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Shin U, Choi Y, Ko HS, Myung K, Lee S, Cheon CK, Lee Y. A heterozygous mutation in UBE2H in a patient with developmental delay leads to an aberrant brain development in zebrafish. Hum Genomics 2023; 17:44. [PMID: 37208785 DOI: 10.1186/s40246-023-00491-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Ubiquitin-related rare diseases are generally characterized by developmental delays and mental retardation, but the exact incidence or prevalence is not yet fully understood. The clinical application of next-generation sequencing for pediatric seizures and developmental delay of unknown causes has become common in studies aimed at identification of a causal gene in patients with ubiquitin-related rare diseases that cannot be diagnosed using conventional fluorescence in situ hybridization or chromosome microarray tests. Our study aimed to investigate the effects of ubiquitin-proteasome system on ultra-rare neurodevelopmental diseases, through functional identification of candidate genes and variants. METHODS In our present work, we carried out genome analysis of a patient with clinical phenotypes of developmental delay and intractable convulsion, to identify causal mutations. Further characterization of the candidate gene was performed using zebrafish, through gene knockdown approaches. Transcriptomic analysis using whole embryos of zebrafish knockdown morphants and additional functional studies identified downstream pathways of the candidate gene affecting neurogenesis. RESULTS Through trio-based whole-genome sequencing analysis, we identified a de novo missense variant of the ubiquitin system-related gene UBE2H (c.449C>T; p.Thr150Met) in the proband. Using zebrafish, we found that Ube2h is required for normal brain development. Differential gene expression analysis revealed activation of the ATM-p53 signaling pathway in the absence of Ube2h. Moreover, depletion of ube2h led to induction of apoptosis, specifically in the differentiated neural cells. Finally, we found that a missense mutation in zebrafish, ube2h (c.449C>T; p.Thr150Met), which mimics a variant identified in a patient with neurodevelopmental defects, causes aberrant Ube2h function in zebrafish embryos. CONCLUSION A de novo heterozygous variant in the UBE2H c.449C>T (p.Thr150Met) has been identified in a pediatric patient with global developmental delay and UBE2H is essential for normal neurogenesis in the brain.
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Affiliation(s)
- Unbeom Shin
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yeonsong Choi
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, 44919, Republic of Korea
| | - Hwa Soo Ko
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
- Korean Genomics Center, UNIST, Ulsan, 44919, Republic of Korea.
| | - Chong Kun Cheon
- Division of Medical Genetics and Metabolism Department of Paediatrics, Pusan National University School of Medicine, Pusan National University Children's Hospital, Yangsan, 50612, Republic of Korea.
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, 50612, Republic of Korea.
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, 05278, Republic of Korea.
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Lalonde C, Sreetharan S, Murray A, Stoa L, Cybulski ME, Kennedy A, Landry N, Stillar A, Khurana S, Tharmalingam S, Wilson J, Khaper N, Lees SJ, Boreham D, Tai TC. Absence of Depressive and Anxious Behavior with Genetic Dysregulation in Adult C57Bl/6J Mice after Prenatal Exposure to Ionizing Radiation. Int J Mol Sci 2023; 24:ijms24108466. [PMID: 37239811 DOI: 10.3390/ijms24108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The exposure of ionizing radiation during early gestation often leads to deleterious and even lethal effects; however, few extensive studies have been conducted on late gestational exposures. This research examined the behavior al effects of C57Bl/6J mouse offspring exposed to low dose ionizing gamma irradiation during the equivalent third trimester. Pregnant dams were randomly assigned to sham or exposed groups to either low dose or sublethal dose radiation (50, 300, or 1000 mGy) at gestational day 15. Adult offspring underwent a behavioral and genetic analysis after being raised under normal murine housing conditions. Our results indicate very little change in the behavioral tasks measuring general anxiety, social anxiety, and stress-management in animals exposed prenatally across the low dose radiation conditions. Quantitative real-time polymerase chain reactions were conducted on the cerebral cortex, hippocampus, and cerebellum of each animal; results indicate some dysregulation in markers of DNA damage, synaptic activity, reactive oxygen species (ROS) regulation, and methylation pathways in the offspring. Together, our results provide evidence in the C57Bl/6J strain, that exposure to sublethal dose radiation (<1000 mGy) during the last period of gestation leads to no observable changes in behaviour when assessed as adults, although some changes in gene expression were observed for specific brain regions. These results indicate that the level of oxidative stress occurring during late gestation for this mouse strain is not sufficient for a change in the assessed behavioral phenotype, but results in some modest dysregulation of the genetic profile of the brain.
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Affiliation(s)
- Christine Lalonde
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Shayenthiran Sreetharan
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Alyssa Murray
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Lisa Stoa
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | | | - Allison Kennedy
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Nicholas Landry
- Department of Psychology, Nipissing University, North Bay, ON P1B8L7, Canada
| | - Amy Stillar
- Department of Psychology, Nipissing University, North Bay, ON P1B8L7, Canada
| | - Sandhya Khurana
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Sujeenthar Tharmalingam
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Joanna Wilson
- Department of Biology, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Neelam Khaper
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Simon J Lees
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - Douglas Boreham
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
| | - T C Tai
- Biomolecular Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E2C6, Canada
- Medical Sciences Division, NOSM University, Sudbury, ON P3E2C6, Canada
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Dorsey SG, Mocci E, Lane MV, Krueger BK. Rapid effects of valproic acid on the fetal brain transcriptome: Implications for brain development and autism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538959. [PMID: 37205520 PMCID: PMC10187231 DOI: 10.1101/2023.05.01.538959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
There is an increased incidence of autism among the children of women who take the anti-epileptic, mood stabilizing drug, valproic acid (VPA) during pregnancy; moreover, exposure to VPA in utero causes autistic-like symptoms in rodents and non-human primates. Analysis of RNAseq data obtained from fetal mouse brains 3 hr after VPA administration revealed that VPA significantly [p(FDR) ≤ 0.025] increased or decreased the expression of approximately 7,300 genes. No significant sex differences in VPA-induced gene expression were observed. Expression of genes associated with neurodevelopmental disorders such as autism as well as neurogenesis, axon growth and synaptogenesis, GABAergic, glutaminergic and dopaminergic synaptic transmission, perineuronal nets, and circadian rhythms was dysregulated by VPA. Moreover, expression of 400 autism risk genes was significantly altered by VPA as was expression of 247 genes that have been reported to play fundamental roles in the development of the nervous system, but are not linked to autism by GWAS. The goal of this study was to identify mouse genes that are: (a) significantly up- or down-regulated by VPA in the fetal brain and (b) known to be associated with autism and/or to play a role in embryonic neurodevelopmental processes, perturbation of which has the potential to alter brain connectivity in the postnatal and adult brain. The set of genes meeting these criteria provides potential targets for future hypothesis-driven approaches to elucidating the proximal underlying causes of defective brain connectivity in neurodevelopmental disorders such as autism.
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Bhatti JS, Khullar N, Mishra J, Kaur S, Sehrawat A, Sharma E, Bhatti GK, Selman A, Reddy PH. Stem cells in the treatment of Alzheimer's disease - Promises and pitfalls. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166712. [PMID: 37030521 DOI: 10.1016/j.bbadis.2023.166712] [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: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Alzheimer's disease (AD) is the most widespread form of neurodegenerative disorder that causes memory loss and multiple cognitive issues. The underlying mechanisms of AD include the build-up of amyloid-β and phosphorylated tau, synaptic damage, elevated levels of microglia and astrocytes, abnormal microRNAs, mitochondrial dysfunction, hormonal imbalance, and age-related neuronal loss. However, the etiology of AD is complex and involves a multitude of environmental and genetic factors. Currently, available AD medications only alleviate symptoms and do not provide a permanent cure. Therefore, there is a need for therapies that can prevent or reverse cognitive decline, brain tissue loss, and neural instability. Stem cell therapy is a promising treatment for AD because stem cells possess the unique ability to differentiate into any type of cell and maintain their self-renewal. This article provides an overview of the pathophysiology of AD and existing pharmacological treatments. This review article focuses on the role of various types of stem cells in neuroregeneration, the potential challenges, and the future of stem cell-based therapies for AD, including nano delivery and gaps in stem cell technology.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Abhishek Sehrawat
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Eva Sharma
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Ashley Selman
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
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38
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Chen J, Fuhler NA, Noguchi KK, Dougherty JD. MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. Genome Res 2023; 33:541-556. [PMID: 37100461 PMCID: PMC10234307 DOI: 10.1101/gr.277413.122] [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: 10/18/2022] [Accepted: 03/09/2023] [Indexed: 04/28/2023]
Abstract
In vitro studies indicate the neurodevelopmental disorder gene myelin transcription factor 1-like (MYT1L) suppresses non-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio of DL/UL neurons in the adult mouse cortex. To define potential mechanisms, we conducted Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to map MYT1L binding targets and epigenetic changes following MYT1L loss in mouse developing cortex and adult prefrontal cortex (PFC). We found MYT1L mainly binds to open chromatin, but with different transcription factor co-occupancies between promoters and enhancers. Likewise, multiomic data set integration revealed that, at promoters, MYT1L loss does not change chromatin accessibility but increases H3K4me3 and H3K27ac, activating both a subset of earlier neuronal development genes as well as Bcl11b, a key regulator for DL neuron development. Meanwhile, we discovered that MYT1L normally represses the activity of neurogenic enhancers associated with neuronal migration and neuronal projection development by closing chromatin structures and promoting removal of active histone marks. Further, we showed that MYT1L interacts with HDAC2 and transcriptional repressor SIN3B in vivo, providing potential mechanisms underlying repressive effects on histone acetylation and gene expression. Overall, our findings provide a comprehensive map of MYT1L binding in vivo and mechanistic insights into how MYT1L loss leads to aberrant activation of earlier neuronal development programs in the adult mouse brain.
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Affiliation(s)
- Jiayang Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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Zoabi S, Andreyanov M, Heinrich R, Ron S, Carmi I, Gutfreund Y, Berlin S. A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo. Commun Biol 2023; 6:337. [PMID: 36977781 PMCID: PMC10050006 DOI: 10.1038/s42003-023-04712-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The widespread use of rodents in neuroscience has prompted the development of optimized viral variants for transduction of brain cells, in vivo. However, many of the viruses developed are less efficient in other model organisms, with birds being among the most resistant to transduction by current viral tools. Resultantly, the use of genetically-encoded tools and methods in avian species is markedly lower than in rodents; likely holding the field back. We sought to bridge this gap by developing custom viruses towards the transduction of brain cells of the Japanese quail. We first develop a protocol for culturing primary neurons and glia from quail embryos, followed by characterization of cultures via immunostaining, single cell mRNA sequencing, patch clamp electrophysiology and calcium imaging. We then leveraged the cultures for the rapid screening of various viruses, only to find that all yielded poor to no infection of cells in vitro. However, few infected neurons were obtained by AAV1 and AAV2. Scrutiny of the sequence of the AAV receptor found in quails led us to rationally design a custom-made AAV variant (AAV1-T593K; AAV1*) that exhibits improved transduction efficiencies in vitro and in vivo (14- and five-fold, respectively). Together, we present unique culturing method, transcriptomic profiles of quail's brain cells and a custom-tailored AAV1 for transduction of quail neurons in vitro and in vivo.
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Affiliation(s)
- Shaden Zoabi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Michael Andreyanov
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ronit Heinrich
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shaked Ron
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Yoram Gutfreund
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel.
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40
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Politano D, Gana S, Pezzotti E, Berardinelli A, Pasca L, Carmen Barbero V, Pichiecchio A, Maria Valente E, Errichiello E. A novel variant in NEUROD2 in a patient with Rett-like phenotype points to Glu130 codon as a mutational hotspot. Brain Dev 2023; 45:179-184. [PMID: 36446697 DOI: 10.1016/j.braindev.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND NEUROD2, encoding the neurogenic differentiation factor 2, is essential for neurodevelopment. To date, heterozygous missense variants in this gene have been identified in eight patients (from six unrelated families) with epileptic encephalopathy and developmental delay. CASE REPORT We describe a child with initial clinical suspicion of Rett/Rett-like syndrome, in whom exome sequencing detected a novel de novo variant (c.388G > A, p.Glu130Lys) in NEUROD2. Interestingly, a missense change affecting the same codon, c.388G > C (p.Glu130Gln), was previously identified in other two patients. CONCLUSIONS Our results suggest that Glu130 might represent a potential mutational hotspot of NEUROD2. Furthermore, the clinical findings (especially the absence of clinically overt seizures) strengthen the NEUROD2-phenotypic spectrum, implying that developmental delay may also manifest isolatedly. We suggest inclusion of NEUROD2-associated developmental and epileptic encephalopathies (DEEs) in the differential diagnosis of atypical Rett syndrome as well as gene panels related to autism spectrum disorder.
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Affiliation(s)
- Davide Politano
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Simone Gana
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Elena Pezzotti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Angela Berardinelli
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | - Ludovica Pasca
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Anna Pichiecchio
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Neuroradiology, Advanced Imaging and Radiomics Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Enza Maria Valente
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Edoardo Errichiello
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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Yan K, Bormuth I, Bormuth O, Tutukova S, Renner A, Bessa P, Schaub T, Rosário M, Tarabykin V. TrkB-dependent EphrinA reverse signaling regulates callosal axon fasciculate growth downstream of Neurod2/6. Cereb Cortex 2023; 33:1752-1767. [PMID: 35462405 DOI: 10.1093/cercor/bhac170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
Abnormal development of corpus callosum is relatively common and causes a broad spectrum of cognitive impairments in humans. We use acallosal Neurod2/6-deficient mice to study callosal axon guidance within the ipsilateral cerebral cortex. Initial callosal tracts form but fail to traverse the ipsilateral cingulum and are not attracted towards the midline in the absence of Neurod2/6. We show that the restoration of Ephrin-A4 (EfnA4) expression in the embryonic neocortex of Neurod2/6-deficient embryos is sufficient to partially rescue targeted callosal axon growth towards the midline. EfnA4 cannot directly mediate reverse signaling within outgrowing axons, but it forms co-receptor complexes with TrkB (Ntrk2). The ability of EfnA4 to rescue the guided growth of a subset of callosal axons in Neurod2/6-deficient mice is abolished by the co-expression of dominant negative TrkBK571N (kinase-dead) or TrkBY515F (SHC-binding deficient) variants, but not by TrkBY816F (PLCγ1-binding deficient). Additionally, EphA4 is repulsive to EfnA4-positive medially projecting axons in organotypic brain slice culture. Collectively, we suggest that EfnA4-mediated reverse signaling acts via TrkB-SHC and is required for ipsilateral callosal axon growth accuracy towards the midline downstream of Neurod family factors.
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Affiliation(s)
- Kuo Yan
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Ingo Bormuth
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Olga Bormuth
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany.,Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
| | - Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia.,Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ana Renner
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Paraskevi Bessa
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Theres Schaub
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Marta Rosário
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany.,Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia.,Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
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42
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Arcuschin CD, Pinkasz M, Schor IE. Mechanisms of robustness in gene regulatory networks involved in neural development. Front Mol Neurosci 2023; 16:1114015. [PMID: 36814969 PMCID: PMC9940843 DOI: 10.3389/fnmol.2023.1114015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
The functions of living organisms are affected by different kinds of perturbation, both internal and external, which in many cases have functional effects and phenotypic impact. The effects of these perturbations become particularly relevant for multicellular organisms with complex body patterns and cell type heterogeneity, where transcriptional programs controlled by gene regulatory networks determine, for example, the cell fate during embryonic development. Therefore, an essential aspect of development in these organisms is the ability to maintain the functionality of their genetic developmental programs even in the presence of genetic variation, changing environmental conditions and biochemical noise, a property commonly termed robustness. We discuss the implication of different molecular mechanisms of robustness involved in neurodevelopment, which is characterized by the interplay of many developmental programs at a molecular, cellular and systemic level. We specifically focus on processes affecting the function of gene regulatory networks, encompassing transcriptional regulatory elements and post-transcriptional processes such as miRNA-based regulation, but also higher order regulatory organization, such as gene network topology. We also present cases where impairment of robustness mechanisms can be associated with neurodevelopmental disorders, as well as reasons why understanding these mechanisms should represent an important part of the study of gene regulatory networks driving neural development.
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Affiliation(s)
- Camila D. Arcuschin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marina Pinkasz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ignacio E. Schor
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Ignacio E. Schor ✉
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43
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Dixon SC, Calder BJ, Lilya SM, Davies BM, Martin A, Peterson M, Hansen JM, Suli A. Valproic acid affects neurogenesis during early optic tectum development in zebrafish. Biol Open 2023; 12:286129. [PMID: 36537579 PMCID: PMC9916031 DOI: 10.1242/bio.059567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/09/2022] [Indexed: 02/01/2023] Open
Abstract
The mammalian superior colliculus and its non-mammalian homolog, the optic tectum (OT), are midbrain structures that integrate multimodal sensory inputs and guide non-voluntary movements in response to prevalent stimuli. Recent studies have implicated this structure as a possible site affected in autism spectrum disorder (ASD). Interestingly, fetal exposure to valproic acid (VPA) has also been associated with an increased risk of ASD in humans and animal models. Therefore, we took the approach of determining the effects of VPA treatment on zebrafish OT development as a first step in identifying the mechanisms that allow its formation. We describe normal OT development during the first 5 days of development and show that in VPA-treated embryos, neuronal specification and neuropil formation was delayed. VPA treatment was most detrimental during the first 3 days of development and did not appear to be linked to oxidative stress. In conclusion, our work provides a foundation for research into mechanisms driving OT development, as well as the relationship between the OT, VPA, and ASD. This article has an associated First Person interview with one of the co-first authors of the paper.
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Affiliation(s)
- Sierra C. Dixon
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Bailey J. Calder
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Shane M. Lilya
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Brandon M. Davies
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Annalie Martin
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Maggie Peterson
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Jason M. Hansen
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Arminda Suli
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA,Author for correspondence ()
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Protective Effects of Early Caffeine Administration in Hyperoxia-Induced Neurotoxicity in the Juvenile Rat. Antioxidants (Basel) 2023; 12:antiox12020295. [PMID: 36829854 PMCID: PMC9952771 DOI: 10.3390/antiox12020295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
High-risk preterm infants are affected by a higher incidence of cognitive developmental deficits due to the unavoidable risk factor of oxygen toxicity. Caffeine is known to have a protective effect in preventing bronchopulmonary dysplasia associated with improved neurologic outcomes, although very early initiation of therapy is controversial. In this study, we used newborn rats in an oxygen injury model to test the hypothesis that near-birth caffeine administration modulates neuronal maturation and differentiation in the hippocampus of the developing brain. For this purpose, newborn Wistar rats were exposed to 21% or 80% oxygen on the day of birth for 3 or 5 days and treated with vehicle or caffeine (10 mg/kg/48 h). Postnatal exposure to 80% oxygen resulted in a drastic reduction of associated neuronal mediators for radial glia, mitotic/postmitotic neurons, and impaired cell-cycle regulation, predominantly persistent even after recovery to room air until postnatal day 15. Systemic caffeine administration significantly counteracted the effects of oxygen insult on neuronal maturation in the hippocampus. Interestingly, under normoxia, caffeine inhibited the transcription of neuronal mediators of maturing and mature neurons. The early administration of caffeine modulated hyperoxia-induced decreased neurogenesis in the hippocampus and showed neuroprotective properties in the neonatal rat oxygen toxicity model.
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45
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Zheng A, Shen Z, Glass CK, Gymrek M. Deep learning predicts the impact of regulatory variants on cell-type-specific enhancers in the brain. BIOINFORMATICS ADVANCES 2023; 3:vbad002. [PMID: 36726730 PMCID: PMC9887460 DOI: 10.1093/bioadv/vbad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Motivation Previous studies have shown that the heritability of multiple brain-related traits and disorders is highly enriched in transcriptional enhancer regions. However, these regions often contain many individual variants, while only a subset of them are likely to causally contribute to a trait. Statistical fine-mapping techniques can identify putative causal variants, but their resolution is often limited, especially in regions with multiple variants in high linkage disequilibrium. In these cases, alternative computational methods to estimate the impact of individual variants can aid in variant prioritization. Results Here, we develop a deep learning pipeline to predict cell-type-specific enhancer activity directly from genomic sequences and quantify the impact of individual genetic variants in these regions. We show that the variants highlighted by our deep learning models are targeted by purifying selection in the human population, likely indicating a functional role. We integrate our deep learning predictions with statistical fine-mapping results for 8 brain-related traits, identifying 63 distinct candidate causal variants predicted to contribute to these traits by modulating enhancer activity, representing 6% of all genome-wide association study signals analyzed. Overall, our study provides a valuable computational method that can prioritize individual variants based on their estimated regulatory impact, but also highlights the limitations of existing methods for variant prioritization and fine-mapping. Availability and implementation The data underlying this article, nucleotide-level importance scores, and code for running the deep learning pipeline are available at https://github.com/Pandaman-Ryan/AgentBind-brain. Contact mgymrek@ucsd.edu. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA,Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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46
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Konrad KD, Song JL. microRNA-124 regulates Notch and NeuroD1 to mediate transition states of neuronal development. Dev Neurobiol 2023; 83:3-27. [PMID: 36336988 PMCID: PMC10440801 DOI: 10.1002/dneu.22902] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 09/12/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
MicroRNAs regulate gene expression by destabilizing target mRNA and/or inhibiting translation in animal cells. The ability to mechanistically dissect miR-124's function during specification, differentiation, and maturation of neurons during development within a single system has not been accomplished. Using the sea urchin embryo, we take advantage of the manipulability of the embryo and its well-documented gene regulatory networks (GRNs). We incorporated NeuroD1 as part of the sea urchin neuronal GRN and determined that miR-124 inhibition resulted in aberrant gut contractions, swimming velocity, and neuronal development. Inhibition of miR-124 resulted in an increased number of cells expressing transcription factors (TFs) associated with progenitor neurons and a concurrent decrease of mature and functional neurons. Results revealed that in the early blastula/gastrula stages, miR-124 regulates undefined factors during neuronal specification and differentiation. In the late gastrula/larval stages, miR-124 regulates Notch and NeuroD1 during the transition between neuronal differentiation and maturation. Overall, we have improved the neuronal GRN and identified miR-124 to play a prolific role in regulating various transitions of neuronal development.
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Affiliation(s)
- Kalin D Konrad
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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47
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Mukhtar T, Breda J, Adam MA, Boareto M, Grobecker P, Karimaddini Z, Grison A, Eschbach K, Chandrasekhar R, Vermeul S, Okoniewski M, Pachkov M, Harwell CC, Atanasoski S, Beisel C, Iber D, van Nimwegen E, Taylor V. Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis. EMBO J 2022; 41:e111132. [PMID: 36345783 PMCID: PMC9753470 DOI: 10.15252/embj.2022111132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/09/2022] [Accepted: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
The cerebral cortex contains billions of neurons, and their disorganization or misspecification leads to neurodevelopmental disorders. Understanding how the plethora of projection neuron subtypes are generated by cortical neural stem cells (NSCs) is a major challenge. Here, we focused on elucidating the transcriptional landscape of murine embryonic NSCs, basal progenitors (BPs), and newborn neurons (NBNs) throughout cortical development. We uncover dynamic shifts in transcriptional space over time and heterogeneity within each progenitor population. We identified signature hallmarks of NSC, BP, and NBN clusters and predict active transcriptional nodes and networks that contribute to neural fate specification. We find that the expression of receptors, ligands, and downstream pathway components is highly dynamic over time and throughout the lineage implying differential responsiveness to signals. Thus, we provide an expansive compendium of gene expression during cortical development that will be an invaluable resource for studying neural developmental processes and neurodevelopmental disorders.
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Affiliation(s)
- Tanzila Mukhtar
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Jeremie Breda
- BiozentrumUniversity of BaselBaselSwitzerland
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
| | - Manal A Adam
- Eli and Edythe Broad Center of Regeneration Medicine and Stem cell ResearchUniversity of California, San FranciscoSan FranciscoCAUSA
- Weill Institute for NeuroscienceSan FranciscoCAUSA
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Marcelo Boareto
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
- Computational Biology Group, D‐BSSEETH ZürichBaselSwitzerland
| | - Pascal Grobecker
- BiozentrumUniversity of BaselBaselSwitzerland
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
| | - Zahra Karimaddini
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
- Computational Biology Group, D‐BSSEETH ZürichBaselSwitzerland
| | - Alice Grison
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Katja Eschbach
- Department of Biosystems Science and EngineeringETH ZürichBaselSwitzerland
| | | | - Swen Vermeul
- Scientific IT ServicesETH ZürichZürichSwitzerland
| | | | - Mikhail Pachkov
- BiozentrumUniversity of BaselBaselSwitzerland
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
| | - Corey C Harwell
- Eli and Edythe Broad Center of Regeneration Medicine and Stem cell ResearchUniversity of California, San FranciscoSan FranciscoCAUSA
- Weill Institute for NeuroscienceSan FranciscoCAUSA
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Suzana Atanasoski
- Department of BiomedicineUniversity of BaselBaselSwitzerland
- Faculty of MedicineUniversity of ZürichZürichSwitzerland
| | - Christian Beisel
- Department of Biosystems Science and EngineeringETH ZürichBaselSwitzerland
| | - Dagmar Iber
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
- Weill Institute for NeuroscienceSan FranciscoCAUSA
| | - Erik van Nimwegen
- BiozentrumUniversity of BaselBaselSwitzerland
- Swiss Institute of Bioinformatics (SIB)BaselSwitzerland
| | - Verdon Taylor
- Department of BiomedicineUniversity of BaselBaselSwitzerland
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48
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Faure L, Techameena P, Hadjab S. Emergence of neuron types. Curr Opin Cell Biol 2022; 79:102133. [PMID: 36347131 DOI: 10.1016/j.ceb.2022.102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/31/2023]
Abstract
Neuron types are the building blocks of the nervous system, and therefore, of functional circuits. Understanding the origin of neuronal diversity has always been an essential question in neuroscience and developmental biology. While knowledge on the molecular control of their diversification has largely increased during the last decades, it is now possible to reveal the dynamic mechanisms and the actual stepwise molecular changes occurring at single-cell level with the advent of single-cell omics technologies and analysis with high temporal resolution. Here, we focus on recent advances in the field and in technical and analytical tools that enable detailed insights into the emergence of neuron types in the central and peripheral nervous systems.
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Affiliation(s)
- Louis Faure
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, 1090, Vienna, Austria
| | - Prach Techameena
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Saida Hadjab
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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49
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Konrad KD, Song JL. NeuroD1 localizes to the presumptive ganglia and gut of the sea urchin larvae. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000682. [PMID: 36468156 PMCID: PMC9709636 DOI: 10.17912/micropub.biology.000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 01/25/2023]
Abstract
NeuroD is a transcription factor (TF) that plays a dual role in vertebrate neurogenesis and glucose homeostasis in the pancreas. We identified a NeuroD antibody developed against human that cross-reacts with the sea urchin NeuroD1. NeuroD1 protein localizes to the presumptive ganglia and neurofilament structures in the ciliary band of the sea urchin larvae. In addition, we also observed NeuroD1 in the perinuclear region in the sea urchin gut which is analogous to the mammalian pancreas. These results suggest that NeuroD1 may play an evolutionarily conserved role in the invertebrate sea urchin.
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Affiliation(s)
| | - Jia L. Song
- University of Delaware
,
Correspondence to: Jia L. Song (
)
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50
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Lee DG, Kim YK, Baek KH. The bHLH Transcription Factors in Neural Development and Therapeutic Applications for Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms232213936. [PMID: 36430421 PMCID: PMC9696289 DOI: 10.3390/ijms232213936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The development of functional neural circuits in the central nervous system (CNS) requires the production of sufficient numbers of various types of neurons and glial cells, such as astrocytes and oligodendrocytes, at the appropriate periods and regions. Hence, severe neuronal loss of the circuits can cause neurodegenerative diseases such as Huntington's disease (HD), Parkinson's disease (PD), Alzheimer's disease (AD), and Amyotrophic Lateral Sclerosis (ALS). Treatment of such neurodegenerative diseases caused by neuronal loss includes some strategies of cell therapy employing stem cells (such as neural progenitor cells (NPCs)) and gene therapy through cell fate conversion. In this report, we review how bHLH acts as a regulator in neuronal differentiation, reprogramming, and cell fate determination. Moreover, several different researchers are conducting studies to determine the importance of bHLH factors to direct neuronal and glial cell fate specification and differentiation. Therefore, we also investigated the limitations and future directions of conversion or transdifferentiation using bHLH factors.
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Affiliation(s)
- Dong Gi Lee
- Joint Section of Science in Environmental Technology, Food Technology, and Molecular Biotechnology, Ghent University, Incheon 21569, Korea
| | - Young-Kwang Kim
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam 13488, Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA Stem Cell Institute, CHA University, Seongnam 13488, Korea
- Correspondence: ; Tel.: +82-31-881-7134
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